ljl-covid / links

Collection of links and information about COVID-19

For less commented but more extensive, and categorizes, scientific resources (mainly papers, but also scientific article and press releases from relevant bodies and companies), see also our Zotero group (Zotero is open source software for bibliography management, available both online and as a standalone application).

• Questions
  • Do I have it?
  • Why is WHO information confusing?
• Basics
• Trackers
  • Asia
  • Europe
  • North America
• Info
  • Tracing
  • Public deployments
• Science
  • Genetics
  • Medicine
    • Therapeutics
    • Vaccines
    • Diagnostics
  • Epidemiology
  • Follow-up
  • Models
  • Masks
  • Syndrome in children
  • Prior research
• News
  • API and feeds
• Italy

Questions

First and foremost: Please read this article and understand what is happening, and about to happen again. This virus is not a joke, and let's get one thing straight: it's definitely NOT a flu. It is not even very bad flu:

• it is a completely different type of virus (the coronavirus dubbed SARS-CoV-2, while influenza is caused by an influenzavirus)
• it has a much longer incubation time, during which evidence is starting to accumulate that it can very well be transmissible
• it may be more easily transmissible than even some of the very bad flus
• mortality rates are higher than regular seasonal flus and if they are allowed to spike, they may dwarf death figures from all causes (graphs from The New Atlantis)
• the mortality profile is quite different from seasonal flu, with the sick and elderly being disproportionately at risk, and some similarities only arise with the hugely lethal "Spanish" flu pandemic
• many people (roughly 15% to 30%) require hospitalization, putting strain on resources that risks driving up COVID-19 and all-cause mortality during critical shortages
• about 5% to 10% develop a very serious viral pneumonia, while people developing pneumonia from influenza usually develop a more treatable bacterial pneumonia
• while there are now some vaccines available, the effort to scale them to cover the entire population is enormous, and for now the majority of people don't have access to them
• we have no immune defenses against it currently, while we have varying degree of immune response to influenza, depending on the strain we're seeing

But it does tend to present with fever, joint aches and a dry cough. Right, those are similar symptoms to flu. They are also symptoms of a myriad other diseases too, so there is no reason in particular to compare it with flu. Bottom line: it has nothing to do with the flu except for having some similar symptoms just like most other viral diseases.

Do I have it ?

Short answer: we don't know.

A very important thing about this disease is having tests, because this disease cannot be diagnosed clinically, meaning that even a doctor won't be able to tell you whether or not you have it just based on looking at you and checking out your symptoms.

This is because COVID-19 can be considered a flu-like illness: this doesn't mean it has actually anything to do with flu (see the relevant section!), but merely that it causes symptoms that are extremely generic and common to many illnesses, such as fever and cough.

So if you have some symptoms, unfortunately, it needs to be clear that you cannot determine wether or not it's COVID-19 on your own, or even with others' help, or even with a doctor's help, without a test. On the other hand, there are signs and symptoms that indicate you should probably call a doctor (don't go to one, call them first!) on the suspicion you may have COVID-19, or simply because they are concerning enough.

You can read and follow this self-triage tool to determine whether your symptoms warrant consulting medical services.

ProPublica requests information sharing from people who have been affected by the virus (as patients, caregivers or health workers). If you are or have been a patient, please feel free to write there.

Why is WHO information confusing?

The WHO is more of a political body than a scientific information body. They will say what their member states and their committees think will make people behave in desired ways, not necessarily state the exact scientific truth, or that we don't know it yet. This can explain why they seemed to be against wearing masks while there was a shortage of them for healthcare workers.

When the WHO says "there is no evidence" for something, that's exactly what they are saying: "there is no [sufficient] evidence for it", not "it isn't true"; often their information seems to imply something isn't true when there merely hasn't been extremely solid evidence accumulated yet to corroborate it.

Note that the WHO will generally be unable to make statements that their more prominent member states do not want them to make, even if those statements would be scientifically valid, which has been admitted by WHO representatives themselves.

Basics

• Flatten the curve: what you can and should do even before your government mandates it
• WHO's COVID-19 technical guidance
• ArsTechnica's "comprehensive guide" to COVID-19
• Our World In Data's comprehensive introductions to COVID-19 both as the disease and its epidemiology
• CDC's "When and How" to use hand sanitizers
• WHO instructions for making hand sanitizer (liquid version)
• Folding@Home is devoting all resources to COVID-19 project (see this Reddit post), and anyone with a computer can contribute

Trackers

• Covidly, likely the most comprehensive tracker including many subnational units, graphs and derived data
• Coronalevel, a fast no-frills tracker with linear and log graphs for countries and sub-national units
• Reddit user map: may not be the most up to date, but it has details others don't
• Coronatracker: see this description
• Offloop.net's COVID19 has comparison charts for countries (take note of all the buttons)
• Google News tracker with data sourced from Wikipedia, The New York Times, and John Hopkins University
• Bing COVID-19 Tracker to comply with antitrust laws given Google above
• Covid19.health probably has the most comprehensive maps and graphs, although the data aren't always current
• Visualizing COVID-19's Effective Reproduction Number (Rt), focusing on this important parameter worldwide, calculated using the EpiEstim method
• Flatten The Curve, with graphs that compare the epidemic progression in different countries
• nCoV Tracker has a map with an (animated) timeline
• Global Kaggle Data's dashboard, another animated dashboard
• Healthmap, a third animated dashboard
• SCMP published a semi-regularly updated article with many infographics
• WHO's Coronavirus tracker, with a world map and data by country (no sub-national entities)
• The John Hopkin's University map is probably the best-known COVID-19 tracker worldwide. See their introduction
• Worldometers Coronavirus
• Covid Trends is an animated chart with total cases on an axis and new cases on the other, for an unusual type of trajectory comparison
• BNONews' page is likely not the best tracking page, but the more the merrier
• Coronawiki, a somewhat up-to-date tracker with usable comparison charts between countries, combined with information on COVID-19 provided by medical doctors
• COVID19INFO, a tracker with a black background, comparison with other diseases, and a news section
• outbreak.info is not primarily a case tracker, but it does offer various case visualizations including for some sub-national regions (United States, Brazil, India...)
• Our World In Data Coronavirus (COVID-19) Vaccinations tracks vaccination shots given per country with a number of different graphs

Asia

• DXY is the most used site by Chinese medical researchers, and has many graphs and maps in Chinese
• Sina, also in Chinese
• COVID19 India, with maps and graphs by state and district
• Japan COVID-19 Coronavirus Tracker with data by prefecture
• Coronavirus Disease (COVID-19) Situation Report in Japan by Tokyo Keizai, including nationwide graphs and data by prefecture, PCR tests, critically ill cases, and age breakdown

Europe

• The ECDC's case distribution map and their COVID-19 dashboard probably deserve a mention
• Fraunhofer's Tracking Map Europe - SARS-CoV-2 Coronavirus (2019-nCoV) including sub-national units for most European countries
• WHO European Region COVID19 Subnational Explorer has total cases as well as 7-day and 14-day cases and incidence, collated for subnational regions from various European sources
• COVID-19 outbreak in Italy with a map and data for Italy by provinces
• Il Sole 24 Ore's Italy-specific tracker with cases by region and province as well as hospitalization/ICU rates and other detailed graphs (in Italian)
• Covid-19 Situación en España, a map of contagion in Spain by autonomous regions
• El Pais Coronavirus tracker with maps and data for Spain and the world, in Spanish
• El Comercio's tracker with a map for Spain and several graphs for Spain and other countries
• DGS's COVID-19 em Portugal map for Portugal
• Coronavirus (COVID-19) in the UK, official data and map for the United Kingdom
• Coronavirus (COVID-19) positive cases by Middle Super Output Area (MSOA) in England covering only England in a very granular way by MSOA
• Robert Koch-Institut's COVID-19-Dashboard for Germany
• SARS-CoV2 infection cases as heatmaps for Germany, also from RKI data (see API and feeds section for details)
• COVID-19 - France is the government's dashboard for France, including subnational units and indicators such as ICU occupation
• Epidémie COVID-19, a map by department for France with data on hospitalizations, fatalities and ICU cases
• Suivi des patients Covid-19 en France with maps, graphs and numbers for France, including number of hospitalizations and ICU admissions
• Coronavirus France, a case map by region for France
• Current situation in the Netherlands is the official dashboard by the Netherlands government, with case data and maps about local cases and restriction levels, plus information on vaccinations; COVID-19 Dashboard NL has similar information as an ArcGIS dashboard
• Scienceano's Epistat has data for cases, hospitalizations, death and tests in Belgium, as well as data by municipality, and it's accessible both as graphs and JSON and CSV datasets
• Lombardy Region map and data from Italy's hardest-hit region
• NPGEO COVID-19 Dashboard - Schweiz und Fürstentum Liechtenstein for Switzerland and Lichtenstein
• NPGEO COVID-19 Dashboard Österreich Mit öffentlich zugänglichen Informationen des Sozialministeriums for Austria
• COVID‑19: Přehled aktuální situace v ČR with data for Czechia
• COVID-19 Cases in Scotland, map and graphs
• Analysis and spread of COVID-19 in Slovenia drawing from various sources, among witch COVID-19 Sledilnik which also has regional data

North America

• 1Point3Acres COVID-19 in US and Canada with a map by state/province, and then detailed subsections with counties or other divisions and specific case reports
• New Jersey COVID-19 Dashboard
• Virginia's Department of Health tracker for the US state of Virginia
• COVID-19 Canada, with a tracker as well as plenty of useful links both specific to Canada and global
• COVID-19 Canadian Outbreak Tracker based on the data from ViriHealth
• Coronavirus Statistics: Tracking The Epidemic In New York, Gothamist's tracker for the City of New York in particular
• Tracking COVID-19 in California, with data by county, including testing, hospitalizations and ICU availability, as well as data by ethnicity
• The COVID Tracking Project used to independently gather some of the most detailed US data available, but the project has ended as of April 2021

Info

• Google's COVID-19 information page
• CDC's situation summary
• WHO's general information page
• ECDC's general information page
• ECDC guidance for cleaning contaminated surfaces
• microCOVID reviewed published research about COVID, and used it to make rough estimates about the risk level of various activities
• outbreaks.info has a large number of COVID-19 resources, going from case data to a collection of publications, trials and more, as well as detailed informations over mutations and variants, all with sophisticated search features and APIs available
• COVID InfoHub by the Institute for Disease Modeling (IDM)
• COVID-19 Vaccine Spotter is a tool for US residents to track down COVID-19 vaccine appointment openings at state pharmacies, with information on available dates, lack of availability, and types of vaccine employed
• ChannelNewsAsia's page is predictably centered on the impact in Asia
• COVID-19 Travel Regulations Map by the IATA, with information on who qualifies to enter each country
• Re-open EU, with detailed travel information for trips to countries in the European Union
• An overview of "who is getting sick" by various factors
• New Yorker's take on what's gone wrong with testing in the US, as the situation evolves from testing by the CDC only to public-health lab testing
• https://www.straitstimes.com/asia/east-asia/reporters-notebook-life-and-death-in-a-wuhan-coronavirus-icu interview
• Community Mutual Aid Coronavirus Response Mapping shows help networks around the world (but mostly in the US and UK) for people who are most vulnerable
• Covidaire, a network and map for mutual aid in France specifically
• Coronavirus is most contagious before and during the first week of symptoms, states a ScienceNews article based on a German clinical study
• How far away are ‘immunity passports’?, an article explaining the probability theory pitfalls of random-sample antibody tests
• The Risks - Know Them - Avoid Them, a post by a professor of biology explaining the risks you may run during "re-opening" in terms of time and amount of exposure
• Long Covid, lobbying for support and recognition of "large numbers of people report suffering from prolonged, debilitating and sometimes serious symptoms following infection with suspected or confirmed Covid-19"
• Paul Garner, professor of infectious diseases at Liverpool School of Tropical Medicine, discusses his experience of having covid-19 in a BMJ opinion piece describing persistent symptoms after 7 weeks; his and others' experiences are reported in a Huffington Post article about post-COVID fatigue, and this Guardian article about a "long tail" of symptoms also observed by Prof. Tim Spector, who developed a COVID symptom tracker app
• Sadly, COVID-19 Could Just Be The Start Of Your Problems.. is a blog article containing information and resources on "ongoing life-altering symptoms" from COVID-19 from the perspective of chronique fatigue sufferers
• The Lab-Leak Hypothesis from The Intelligencer is a long article on the opinions and studies about the virus being of natural origin versus leaked from a lab after artificial modifications
• Coronavirus variants: What they do and how worried you should be covers "variants of interest" as of January 2021, with accessible language but details for each variant and their mutations, how they influence transmission, disease severity and mortality, and vaccine efficacy

Tracing

• MIT Technology Review Covid Tracing Tracker, trying to keep track of all automated tracing apps, also available on Florish and Google Docs
• Amnesty-hosted Joint civil society statement: States use of digital surveillance technologies to fight pandemic must respect human rights from April 2020
• European Union Guidelines on the use of location data and contact tracing tools in the context of the COVID-19 outbreak as of April 2020, which clarify that while installation would be voluntary, data treatment would occur not under a "consent" basis but on an overriding "public interest" basis, and EU Parliament resolution describing the preferred approach by MEPs
• Coronavirus: An EU approach for efficient contact tracing apps to support gradual lifting of confinement measures, an EU press release covering the main points of an envisioned app tracing system compatible with EU principles
• Official Statement on the processing of personal data in the context of the COVID-19 outbreak in the European Union, adopted as of March 2020
• DP-3T Committee's Decentralized Privacy-Preserving Proximity Tracing white paper on the decentralized approach being backed by some European entities, roughly compatible with Google and Apple's proposal
• Pan-European Privacy-Preserving Proximity Tracing (PEPP-PT) committee's homepage and whitepaper on their architecture
• DP-3T's security and privacy analysis of the PEPP-PT proposal
• Documents about the ROBERT system developed by French and German researchers, which would allow governments more access to data for purposes such as developing "contact graphs"
• TCN (Git repository) is a decentralized protocol that operates as an alternative to the Apple and Google coalition, and is implemented so far by CoEpi (Git repository) and Covid Watch (Git repository)
• Google and Apple cover their common approach to OS-baked contact tracing API, with also a more detailed whitepaper on the protocol
• BlueTrace, a proposed protocol with open-source reference implementation as smartphone apps to enhance contact tracing internationally, developed and currently used in Singapore, and the whitepaper describing its functioning
• TechCrunch articles on how Apple and Google's system works and questions and answers on it
• Wikipedia's COVID-19 apps article contains comparison tables for contact tracing protocols and apps
• Contact-tracing apps: a major test for privacy in Europe, an EUobserver opinion pieces discussing contact tracing app strategies in Europe and internationally
• PEPP-PT vs DP-3T: The coronavirus contact tracing privacy debate kicks up another gear, an article at NewStatesman on the differences and ideological struggles between the two main camp in Europe over contac tracing app deployment ("centralized" vs "decentralized"), also discussing some high-level details of the protocols
• Immuni sarà open source: parola del ministero, Italy's Punto Informatico article, detailing some of the specifics of the Immuni app, which the government contracted and announced will be open-source, and which was changed from a centralized to a decentralized model according to the Sole 24 Ore article L'app Immuni cambia. Seguirà il modello decentralizzato di Apple e Google, a change discussed by PrivacyItalia in I dati di Immuni in ‘sistema decentralizzato’. Ma il Governo non l’aveva scelta per modello centralizzato?
• Extensive "informal hearing" of the Italian Privacy Authority on tracing apps, in Italian
• Source code of Google's exposure notification API internals available on GitHub under the Apache 2 license (though it's an old version not representing the current code, and an issue about that was opened and closed by Google, followed by removal of the issue tracker), and integrated as part of microG for Android users who avoid the proprietary Google services
• Digital contact tracing apps: do they actually work? A review of early evidence covers various studies and articles that look at the efficacy of contact tracing apps in different countries where they have been deployed

Public deployments

• Google COVID-19 Community Mobility Reports, a set pf PDF documents showing changes in frequentation of various types of places as recorded by Android smartphones during the epidemic
• COVID-19 Location Data Toolkit with a "scoreboard" of the degree of respect of social distancing in the US, changes in mobility, and a graph showing impact on retail, based on location data Unacast obtains from a number of smartphone apps with implicit consent
• Corona-Warn-App (CWA): Key performance indicators for the exposure notification and contact tracing app deployed by Germany
• The numbers of immuni for the exposure notification and contact tracing app deployed by Italy
• SwissCovid App Monitoring for the exposure notification and contact tracing app deployed by Switzerland
• Kinsa US Health Weather Map, a mapping of "atypical" temperatures recorded by connected body thermometer in the US
• Übersicht zu aktuellen und früherer Zahlen und Fakten zur Corona-Warn-App has official statistics on the German Corona-Warn-App including people who received a test result through it, amount of positive ones, and of those, how many were actually uploaded to provide notifications for contacts
• The numbers of immuni has a dashboard for the Italian app with similar data, but also including a subset of the total amount of notifications sent (which is not available in Germany due to privacy concerns, while with the Italian app, only phones capable of hardware attestation "phone back home" on the event of an exposure notification)
• India is forcing people to use its covid app, unlike any other democracy, according to Technology Review, although it does on to qualify it's not just compulsory across the country; Not having Aarogya Setu app is a punishable offence, say Noida police, states more specifically the Indian Express, with statements from police officers on the details
• European eHealth network - digital covid certificate coordination and the Official GitHub Organization of the EU Digital COVID Certificates (EUDCC) project, previously known as the EU Digital Green Certificates (DGC) set the standards and provide reference implementations for the EU Digital COVID Certificate

Science

• ZB MED COVID-19 Hub collects a variety of scientific information and tools for SARS-CoV-2, and their preVIEW service is an aggregator and search engine for preprints
• outbreak.info's resources library collects publications, clinical trials, protocols, and various datasets about COVID-19, with a sophisticated search syntax
• Semantic Scholar's COVID-19 Open Research Dataset, a free resource of over 47,000 scholarly articles, including over 36,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community
• Chemical & Engineering News COVID-19 portal
• Retracted coronavirus (COVID-19) papers section maintained by Retraction Watch
• Report from the WHO-China joint mission
• Harvard CCDD's work on COVID-19
• Eurosurveillance early incubation period study
• Lancet early spread study using Tencent data
• Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1, a study published on the NEJM indicating aerosol and fomite transmission is plausible for hours or days
• The influence of temperature, humidity, and simulated sunlight on the infectivity of SARS-CoV-2 in aerosols studies the viability of actual infectious virus in a simulated aerosol scenario, finding that it decreases by 90% in about 5 minutes if exposed to 40°C, 20% humidity and sunlight, as expected outdoors on a summer day at 40°N latitude, but takes longer than two hours in conditions representative of indoors location and night time
• The effect of temperature on persistence of SARS-CoV-2 on common surfaces finds that the virus can stay viable on surfaces for periods of time up to a month, at least in stable, dark conditions, and decreasing sharply above 20°C
• Earlier preliminary study of coronavirus persistence on surfaces for previously-known coronavirus (not SARS-CoV-2 specifically yet)
• BMJ "Rapid responses" to potential treatment suggestions
• Analysis of outcome-influencing factors in serious cases (smoking, etc.)
• Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2
• Study on extent of environmental contamination from COVID-19 patients in China
• SARS-CoV-2 viral load predicts COVID-19 mortality, correspondence to The Lancet, finds that viral load at diagnosis is an independent predictor of mortality in a large hospitalised cohort
• Study about the neuroinvasive potential of SARS-COV-2 (full text not available) and passage from it about the effectiveness of masks
• Brain imaging before and after COVID-19 in UK Biobank uses a large dataset of brain imaging scans performed on healthy people before COVID, and compared them with scans of roughly 400 people who later got COVID against roughly 400 controls who didn't, and finds significant loss of brain matter in various parts of the brain, particularly those closely related with the senses of smell and taste, although it also finds that the thalamus of patients who get COVID-19 tends to already be different beforehand, suggesting an effect on chances of contracting the virus
• Dysregulation of brain and choroid plexus cell types in severe COVID-19, on Nature, looks at brain cells in autopsies of 8 COVID patients and 8 controls, partly using automated clustering methods, and finds consistent differences including an infiltration of T-cells and a distuprion of brain barrier cells
• Self-reported olfactory and taste disorders in SARS-CoV-2 patients, a cross-sectional study
• American Association for Clinical Chemistry, how US labs can prepare
• The variability of critical bed numbers in Europe, a somewhat detailed, if outdated, source of information on ICU and "acute care" beds (both needed to treat serious COVID-19 patients) over the European Union
• A call to honesty in pandemic modelling, a reminder that disease does come back after lockdowns are lifted
• Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region, a preprint showing that nearly all confirmed patients had developed antibodies to the SARS-CoV-2 spike protein
• Human coronavirus reinfection dynamics: lessons for SARS-CoV-2 warns that the duration of immunity after infection from other human coronaviruses is found to be as low as 12 or 6 months
• What reinfections mean for COVID-19 analyzes and discusses available information on early detected cases of re-infection, some of which have had worse manifestation of disease than the original infection
• Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity, finds a Chinese study, which appears confirmed by a German study on SARS‐CoV‐2 asymptomatic and symptomatic patients and risk for transfusion transmission
• Probability of symptoms and critical disease after SARS-CoV-2 infection is shown to vary by age and sex in this Italian study performed on contacts of positive patients in Lombardy, with 36.1% of all infections being asymptomatic
• SARS-Cov-2 RNA found on particulate matter of Bergamo in Northern Italy: First evidence finds viral RNA (not tested for viability) in PM10 samples collected over a 3-week period
• RKI's Fever Monitor is an experiment to create a fever detection algorithm for smart wearable based on heartrate and activity levels, and correlating it with confirmed COVID-19 cases in Germany, with an app for the public to "donate" such data, and the resulting data open the public

Genetics

• Nextstrain genomic epidemiology showing genetic variants of the virus by area and other factors (see also this article about "cryptic" transmission)
• SARS-CoV-2 lineages is "dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology" and the site also contains links to a number of tools including the web application version of PANGOLIN
• CoVariants contains information about mutations and the variants they are found in, with both textual descriptions of their origin, characteristics and relevant concerns, and graphs showing how frequently they were sequenced in various countries, as well as dedicated Nextstrain builds maintained by Emma Hodcroft
• outbreak.info Mutation Reports lists variants of concern and variants of interest while highlighting their main characteristics in a compact format as well as more articulated reports showing their prevalence in time and regions, and location reports where the variants situation in a specified country or region is presented
• Cov2Tree, "interactive SARS-CoV-2 phylogeny", offers access to more than one million public SARS-COV-2 sequences, in the form of a zoomable and seearchable tree, with mutation annotations for each sequence; powered by Taxodium and with source data freely downloadable
• COVIDCG is a genetics browser was designed to empower diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and tracking of interventions.
• Sanger COVID–19 Genomic Surveillance models sequenced variants in England, with an attempt to select them so as to obtain something akin to random sampling
• Official hCoV-19 Reference Sequence and Genomic epidemiology of hCoV-19 at GISAID, which offers many other COVID-19 resources such as its Mutation Surveillance Dashboard
• How the novel coronavirus has evolved, a Reuters article breaking down the evolution and mutations of the virus and the way they affected different areas of the world in a way more understandable to the layman than Nextstrain
• Structural genomics and interactomics of SARS-CoV-2 novel coronavirus by Korkin Lab at the Worcester Polytechnic Institute
• Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility uses Bayesian computational methods published as open source to infer transmissibility advantages given by individual mutations, and forecast growth of new lineages
• Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2, an April 30 preprint highlighting how a mutated form of the virus appears to be circulating much faster and taking over the original strain in Europe and elsewhere, with another preprint finding that Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes although an article on ArsTechnica highlights various issues other researchers have raised with this paper; later research shows SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo and Spike mutation D614G alters SARS-CoV-2 fitness; an analysis published on Cell, Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus, wraps up the situation as it's known as of November 2020
• CoVsurver (CoronaVirus Surveillance Server) can automatically find the closest strain to compare a protein or nucleotide to the ones currently known, and show a 3D view of it with the differences highlighted

Medicine

• Cytel's Global Coronavirus COVID-19 Clinical Trial Tracker
• Treatments and vaccines for COVID-19 as approved or being evaluated by the European Medicine Agency
• COVID-19 therapies and vaccines: Clinical on BioCentury
• COVID-19 vaccines and therapies: preclinical also on BioCentury
• As COVID-19 vaccines progress, science and policy questions become more urgent, published on BioCentury, discusses the agreement between Sanofi and GlaxoSmithKline giving opinions on practicality of trials, scaling up, and manufacturing capacity
• The role of Vitamin D in the prevention of Coronavirus Disease 2019 infection and mortality, a study, finding that low levels of vitamin D in certain areas were "strongly associated" with number of COVID-19 cases and mortality rates, and concluding that they can "can advise Vitamin D supplementation to protect against SARS-CoV2 infection", which is consistent with the preprint claiming Vitamin D Insufficiency is Prevalent in Severe COVID-19
• Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications, a preprint, and Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 try to delineate antibody production in COVID-19 patients
• Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2 concludes that saliva-based sampling may be more sensitive, more consistent in results, and more comfortable for the patient, who can self-administer it
• Physical phenotype of blood cells is altered in COVID-19 finds that the circulatory issues associated with COVID-19 may be related to actual physical change of blood cells, where in particular erythrocytes, lymphocytes, monocytes, neutrophils, and eosinophils are evaluated from 17 patients at varying levels of severity, and significant changes are found, some reversing shortly after the end of the acute phase, but others persisting

Therapeutics

• NCAT COVID-19 OpenData is generating a collection of datasets by screening a panel of SARS-CoV-2-related assays against all approved drugs
• Monoclonal Antibodies for the Coronavirus, probably the most promising potential treatment right now
• A review of current possible treatments discussing clinical trials or lack thereof
• About Remdesivir and About “Game-Changers”, a critical look at Remdesivir trials and the general outlook for practical treatments
• Repurposed antiviral drugs for COVID-19; interim WHO SOLIDARITY trial results finds no benefit from any of the antiviral drugs tested (Remdesivir, Hydroxychloroquine, Lopinavir and Interferon) in 11266 hospitalized adults, although Remdesivir for the Treatment of Covid-19 — Final Report published on the NEJM finds modest benefit from Remdesivir; this "Pipeline" article tries to reconcile the findings
• Covid-19 Biologic Therapies Reviewed, an older article covering both treatments based on antibodies isolated from plasma and vaccine prospects
• Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19), a review analyzing various proposed treatments and concluding there is as of yet no reliable evidence-based treatment
• Merck and Ridgeback’s Investigational Oral Antiviral Molnupiravir Reduced the Risk of Hospitalization or Death by Approximately 50 Percent Compared to Placebo for Patients with Mild or Moderate COVID-19 in Positive Interim Analysis of Phase 3 Study and the phase 3 of the MOVe-OUT trial was stopped early due to effectiveness, of what could be the first oral treatment with substantial effectiveness on non-hospitalized patients with risk factors
• Nafamostat
• New data on Gilead’s remdesivir, released by accident, show no benefit for coronavirus patients. Company still sees reason for hope, claims a CNBC article based on a paper mistakenly published on the WHO website, which responds that the data is incomplete and the study was terminated early, so no conclusions can be made from it
• A human monoclonal antibody blocking SARS-CoV-2 infection has been identified in a paper on Nature (see also Eurekalert article)
• A non-competing pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2
• Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2 might cause most of the SARS-COV-2 virions to attach to "decoy" receptors instead of the actual ACE2 receptors of human cells, likely rendering them harmless, especially with such "decoy" receptors being engineered to bind more tightly than human ACE2, and this study finds that such decoy ACE2 has similar efficacy to neutralizing antibodies in vitro
• Early Safety Indicators of COVID-19 Convalescent Plasma in 5,000 Patients (and a Mayo Clinic article discusses this)
• Effect of Calcifediol Treatment and best Available Therapy versus best Available Therapy on Intensive Care Unit Admission and Mortality Among Patients Hospitalized for COVID-19: A Pilot Randomized Clinical study showing that the role of vitamin D is possibly causative and not simply a correlation, with hospital patients receiving a dose of calcifediol having much lower rates of ICU admission
• Here are the top drugs in development as of May 13 according to the CNBC, which presents vaccines and treatments with their clinical trial phase, and brief descriptions
• Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis, published on The Lancet, reviews use of (hydroxy)chloroquine in many hospitals internationally, and finds that no positive effects could be observed on patients using them, but that both "associated with decreased in-hospital survival and an increased frequency of ventricular arrhythmias"

Vaccines

• CovidVax is an updated list of COVID-19 vaccines, with information on the companies involved, trials and stages (with links to news and other sources used for the data), and a tracker for how many doses have been administered in each country
• COVID19 Vaccine Tracker has another comprehensive list of vaccines with information about vaccine type, and the trials, stage and approvals by country
• UNICEF COVID-19 Vaccine Market Dashboard (or direct link to the full-screen page) with vaccines by approval state and type, countries where approved, current and projected production capacity per type, amounts purchased per country or other buyer, price ranges, and map of delivered doses
• RAPS COVID-19 vaccine tracker
• Precision Vaccinations - COVID-19 Vaccines lists a number of COVID-19 vaccine candidates, divided by clinical stage, with brief description and detail pages for each (the main page is now discontinued, the link being from the Internet Archive, although individual vaccines are still listed with details)
• VIEW-hub Vaccine Characteristics has a list of vaccines with specific details other sites lack, such as the cold chain requirements of each vaccine, and descriptions of how the vaccines are packaged, plus a spot value on efficacy; next to this page there is a list of studies on vaccine effectiveness by country and variant analyzed
• Contagion Live also has descriptions for a few of the vaccines, divided by stage
• Our World In Data Coronavirus (COVID-19) Vaccinations tracks vaccination shots given per country with a number of different graphs
• COVID-19 Vaccine Spotter is a tool for US residents to track down COVID-19 vaccine appointment openings at state pharmacies, with information on available dates, lack of availability, and types of vaccine employed
• COVID-19 vaccine surveillance reports issued regularly by the UK government
• Coronavirus (COVID-19) vaccine adverse reactions detail analyses by the British agency MHRA
• Coronavirus Vaccine Update, July 7 by Derek Lowe nicely covers the "frontrunners" and also some lesser known vaccines, divided by type, with commentary; Coronavirus Vaccine Roundup, Early September follows up on that, and Vaccine Roundup, Late December looks at the situation at the end of 2020
• Vaccine Possibilities also by Derek Lowe, from November 2020, covers length of protection, effectiveness, possible mutations, demographics, safety, distribution and rollout
• The race for coronavirus vaccines: a graphical guide, an introductory article on Nature
• KFF COVID-19 Vaccine Monitor tracks the public's attitudes towards COVID-19 vaccines, with polls on vaccine hesitancy among Americans
• A Close Look at the Frontrunning Coronavirus Vaccines As of April 28, another In The Pipeline article
• Coronavirus Vaccine Prospects, an April 15 In The Pipeline article
• SARS-CoV-2 Vaccines: Status Report, published on Cell on April 14, also covers therapeutics and has a summary table of vaccine types being investigated and their main characteristics on page 386
• The COVID-19 vaccine development landscape, published on Nature on April 9, presenting charts with breakdowns of vaccine types under study and their profit models
• A COVID-19 Vaccine: Big Strides Come with Big Challenges discusses the different phases of vaccine development and the various platforms in use for candidate COVID-19 vaccines, including their progress as to January 2021, with the major characteristics of vaccines in advanced phases summarized in Table 1
• The Vaccine Tightrope by Derek Lowe analyzes the problem of vaccines being deployed before trials for other vaccines are over, as well as of providing placebo arms with the actual vaccine before the full trial length of two years is completed, with ethical and practical repercussions on participants
• mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants reports on immune response of recipients of Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines and notes that activity of their serum against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin
• Effectiveness of First Dose of COVID-19 Vaccines Against Hospital Admissions in Scotland: National Prospective Cohort Study of 5.4 Million People shows that the Pfizer/BioNTech (BNT162b2) vaccine was associated with a vaccine effect of 85% against hospitalization at 28-34 days post-vaccination, while the effect of the Oxford/Astrazeneca (ChAdOx1) vaccine was 94%, although the age cohorts in the two vaccines were different, and the efficacy against hospitalization was similar for the two vaccines, at 81%, when looking at people over 80
• Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 has worse findings, B.1.351 in particular being worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely owing to an E484K mutation, and it is very resistant to neutralization by both convalescent plasma and sera from people who received the Pfeizer and Moderna vaccines, 10 to 12-fold; Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies finds a 14-fold reduction with B.1.351, though again no significant difference with B.1.1.7, on sera from individuals vaccinated with Pfizer/BioNTech
• FDA-authorized COVID-19 vaccines are effective per real-world evidence synthesized across a multi-state health system is a preprint that analyzes more than 60000 individuals at Mayo Clinic, dividing them into a vaccinated cohort (with Pfizer/BioNTech or Moderna) and an unvaccinated one, and retrospectively concluding there was 88.7% efficacy in preventing infection, i.e. a positive RT-PCR test at all, and hence likely also contagiousness, as opposed to just symptomatic cases, which was the benchmark of most of the vaccine trials
• Single-dose Oxford–AstraZeneca COVID-19 vaccine followed by a 12-week booster tries to make sense of the confusing dosing issues with the Oxford/Astrazeneca (ChAdOx1) vaccine, and provides some tentative evidence in favor of the UK choice of delaying the booster shot to 12 weeks after the initial shot
• Meeting highlights from the Pharmacovigilance Risk Assessment Committee (PRAC) 6-9 April 2021 reports the EMA/PRAC investigating on "safety signals" due to blood-related adverse events with the AstraZeneca and the Janssen vaccines
• Impact of vaccination on household transmission of SARS-COV-2 in England was assessed by Publish Health England, which found the likelihood of infecting another person with COVID (infectiousness) if someone has received Pfizer/BNT or Oxford/AstraZeneca is roughly halved even when the vaccinated person does get infected, as reported in this abstract
• Effectiveness of COVID-19 vaccines against the B.1.617.2 variant shows that in the UK, vaccine effectiveness went down from 93.4% to 87.9% (with Pfizer/BNT162b2) and from 66.1% to 59.8% (with Oxford/AstraZenea/ChAdOx1), although the confidence intervals were large, and effectiveness went down further on people who had taken only one dose of the vaccine; this study doesn't cover effectiveness on severe disease, hospitalization or deaths, which the UK surveillance data state are mostly retained
• Assemblies of putative SARS-CoV2-spike-encoding mRNA sequences for vaccines BNT- 162b2 and mRNA-1273 offers a third-party "reverse-engineered" reconstruction of the modified mRNA sequences of the mRNA-1237 (Moderna) and BNT-162b2 (BioNTech/Pfizer) vaccines obtained by sampling discarded portions of the vaccines, with color-coding of the sequences' main portions, and a discussion of the results and how they were obtained

Spikevax by Moderna (mRNA-1273)

• Moderna’s Covid-19 vaccine is strongly effective, early look at data show, with more than 94% efficacy and severe COVID-19 cases only in the control arm, at an interim point of the COVE trial, as covered by an article on StatNews
• Moderna’s COVID-19 Vaccine Candidate Meets its Primary Efficacy Endpoint in the First Interim Analysis of the Phase 3 COVE Study, announces the company in a press release claiming a first interim analysis of 95 COVID cases showed an efficacy of 94.5% for their mRNA-1273 vaccine, and severe cases only in the control arm, during their COVE Phase 3 trial
• Moderna Announces Primary Efficacy Analysis in Phase 3 COVE Study for Its COVID-19 Vaccine Candidate and Filing Today with U.S. FDA for Emergency Use Authorization in a press release where efficacy is put at 94.1%, with 100% efficacy against "severe" cases, after 196 COVID cases have developed within the trial participants, and after more than two months of follow-up
• Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine looks at the results from Moderna's phase 3 COVE study and finds a 94.1% efficacy, with confidence interval from 89.3% to 96.8%, with no severe cases in the vaccine arm, and rare occurrence of serious adverse effects
• EMA recommends COVID-19 Vaccine Moderna for authorisation in the EU and issues an opinion with key facts including documents about risk management and the produt leaflet
• Moderna COVID-19 Vaccine Retains Neutralizing Activity Against Emerging Variants First Identified in the U.K. and the Republic of South Africa as announced in a press release by Moderna, based on a study showing mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants, although titers against the South African B.1.351 strain appear much reduced, and the company is studying a "third booster" to address this and potentially other variants
• Moderna Announces it has Shipped Variant-Specific Vaccine Candidate, mRNA-1273.351, to NIH for Clinical Study in a press release issued in February 2021, to address in particular the South African variant, with three possible booster candidate (a variant-specific one, a multivalent one, and a simple third booster of the original vaccine), and later in March, Moderna Announces First Participants Dosed in Study Evaluating COVID-19 Booster Vaccine Candidates, with 60 participants to its phase 2 trial additionally receiving one of the booster candidates; in May 2021, Moderna Announces Positive Initial Booster Data Against SARS-CoV-2 Variants of Concern, with a dose of either mRNA-1273 (the original vaccine) or mRNA-1273.351 (a modification targeted to the B.1.351, South African, variant) enhancing antibody titers against B.1.351 (half of the participants originally not having detectable antibodies against it) and P.1 (Brazil variant), although efficacy against B.1.351 was predictably higher with the targeted vaccine

Comirnaty by Pfizer-BioNTech (BNT162b2)

• Background document on the mRNA vaccine BNT162b2 (Pfizer-BioNTech) against COVID-19 by the WHO
• Pfizer-BioNTech COVID-19 vaccine and related biological product advisory committee briefing document announces that this vaccine meets the FDA success criteria, with vaccine efficacy after the booster dose at 95.0%, counting 8 COVID-19 cases in the vaccine group compared to 162 COVID-19 cases in the placebo group, with a 95% credible interval of 90.3% to 97.6%
• Pfizer and BioNTech Announce Vaccine Candidate Against COVID-19 Achieved Success in First Interim Analysis from Phase 3 Study in a press release where they state that their BNT162b2 vaccine has more than 90% efficacy, based on 94 participant who got COVID-19 during the trial, without any serious safety concerns; the article Vaccine Efficacy Data! by Derek Lowe provides an early opinion on these results
• Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine is the phase III study paper
• Pfizer and BioNTech Initiate a Study as Part of Broad Development Plan to Evaluate COVID-19 Booster and New Vaccine Variants as announced in a BioNTech press release, where the company reveals it plans to study the effects of a third booster shots of 30µg of the original vaccine, as well as ongoing discussions with regulatory agencies about potential approval of vaccines specific to B.1.351 (South African) or other variants
• Estimating the effectiveness of the Pfizer COVID-19 BNT162b2 vaccine after a single dose. A reanalysis of a study of ‘real-world’ vaccination outcomes from Israel
• Pfizer’s vaccine appears to reduce coronavirus transmission as evidenced by a couple of studies estimating lower viral load in vaccinated people
• BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting in Israel show that in a large number people vaccinated with Pfizer/BioNTech, matched up against unvaccinated individuals, after taking the second shot, efficacy was 94% for symptomatic COVID-19, 92% for "documented infection" (positive RT-PCR, with potentially unclear knowledge of who sought a test), 92% for severe disease, and 87% for hospitalization
• Pfizer and BioNTech Confirm High Efficacy and No Serious Safety Concerns Through Up to Six Months Following Second Dose in Updated Topline Analysis of Landmark COVID-19 Vaccine Study with 91.3% efficacy measured up to six months after vaccination, safety confirmed in 44000 participants 16 and older, and suggested efficacy against the B.1.351 (South African) variant, though with a wide confidence interval of 53% to 100%
• Pfizer and BioNTech Submit Request to Expand Conditional Marketing Authorization of COMIRNATY® in the EU to Adolescents as well as filing for emergency use authorization with the FDA in the US, after a phase 3 trial on children between 12 and 15 years of age, with around 2000 participants who generally tolerated the vaccine well, resulting in a vaccine efficacy of 100%; Canada approves the vaccine for use in ages 12-15 on 5 May 2021
• Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals looks at variants of COVID acquired by individuals vaccinated with Pfizer/BioNTech in Israel, and finds an odds ratio of 8:1 for being infected with B.1.351 (South African variant) compared to unvaccinated individuals, and of 26:10 for B.1.1.7 (UK variant)
• Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants shows that in Qatar, where vaccination with Pfizer/BioNTech is at an advanced state, most cases of COVID since March 2021 have been either B.1.1.7 (UK variant) or B.1.351 (South African variant), and the effectiveness against B.1.1.7 is 89.5%, while against B.1.351 it is 75%, with overall effectiveness against severe or fatal disease being 97.4%
• Pfizer and BioNTech Provide Update on Booster Program in Light of the Delta-Variant, stating that a third shot of the original vaccine (BNT162b2) makes neutralization titers against the original virus and the Beta variant 5 to 10 times higher than after two shots, and they anticipate efficacy against Delta as well, but at the same time they are developing a modified vaccine that targets the full spike protein of the Delta variant, and an initial trial for it should begin in August 2021

Vaxzevria by Oxford-AstraZeneca (AZD 1222 or ChAdOx1)

• Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial, encouraging preliminary results from the Oxford/AstraZeneca adenovirus-vectored vaccine, showing an acceptable safety profile and strong immune response after a booster, while Derek Lowe's "In The Pipeline" blog provides a critical commentary on it; in November 2020 Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial was published showing that older adults develop similar levels of immune response as younger adults, and with fewer side effects, and interim results showed an overall efficacy of 70%, importantly divided into 62% for a group that received two full doses, and 90% for a group receiving a half dose followed by a full-dose booster, a division in two trial arms that appears to have arisen accidentally; later in December 2020, a study partly funded by AstraZeneca looks at Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK and finds that the vaccine had an "acceptable" profile, although the lower-end confidence interval values for efficacy are revealed as 54.8% overall, of which 67.4% in the half-dose group and 41.0% in the full-dose group
• Oxford University and AstraZeneca both issue press releases on interim efficacy assessment of their ChAdOx1 nCoV-2019 vaccine, showing overall 70% efficacy but divided into 62% for a group that received two full doses, and 90% for a group receiving a half dose followed by a full-dose booster, and Derek Lowe discusses these results and the methodological differences compared to Pfizer and Moderna in Oxford/AZ Vaccine Efficacy Data
• AstraZeneca’s COVID-19 vaccine authorised for emergency supply in the UK announces an AstraZeneca press release, claiming effectiveness based on the lack of hospitalizations and severe cases more than 14 days after the second dose, and saying the decision is based on data including the Lancet interim analysis above; MHRA reports data about this vaccine and administration information, saying that two 0.5ml doses will be used, seemingly ignoring the presumed 90% efficacy in the "half-dose" group, at a distance of 4 to 12 weeks (in the trials, "because of logistical constraints, the interval between dose 1 and dose 2 ranged from 4 to 26 weeks"), and for an overall efficacy of around 70%
• Pascal Soriot: "There are a lot of emotions on vaccines in EU. But it's complicated" is an extensive interview with the CEO of AstraZeneca discussing the reduced number of vaccine doses expected to be initially delivered to the EU, with some countries threatening legal action over failure to meet contractual obligation, and the interview also covers many specifics on vaccine production and testing
• Contract between European Commission and AstraZeneca now published, after pressure from the European Commission, albeit with a number of redactions
• Efficacy of ChAdOx1 nCoV-19 (AZD1222) Vaccine Against SARS-CoV-2 VOC 202012/01 (B.1.1.7) finds that while virus neutralization activity is 9-fold lower in the B.1.1.7 variant than in the "common" virus, the vaccine was similarly efficacious in preventing symptomatic COVID-19 in both variants
• Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa concludes that the vaccine did not show protection against the variant in mild to moderate cases, while protection against severe cases remains undetermined due to the study participants who became positive to the virus being small numbers, and young and healthy, with no hospitalizations or deaths necessarily expected in any case; the University of Oxford announces these results, stating that ChAdOx1 nCov-19 provides minimal protection against mild-moderate COVID-19 infection from B.1.351 coronavirus variant in young South African adults, and in response, South Africa suspends use of AstraZeneca’s COVID-19 vaccine after it fails to clearly stop virus variant
• After 10 March 2021, several European countries suspended administration of the AstraZeneca COVID-19 vaccine, following some unusual blood clotting events. Statements in English are available from the Norwegian Medicines Agency and the German Paul Ehrlich Institute. Later on 15 March, Germany suspends use of AstraZeneca vaccine, along with Italy, France, Spain despite the Italian Medicines Agency having stated the previous day Unjustified alarm on safety of AstraZeneca vaccine. In April 2021, the EMA announces AstraZeneca’s COVID-19 vaccine: EMA finds possible link to very rare cases of unusual blood clots with low blood platelets and calls for this issue to be listed as a very rare side effects, but still recommends the vaccine for all adults; however, the UK regulator recommends against using the vaccine in people below 30, and further European countries (Italy, Spain, Belgium) limit it to older ages
• AZD1222 US Phase III trial met primary efficacy endpoint in preventing COVID-19 at interim analysis in an AstraZeneca press release announcing the US trial found overall 79% efficacy including in 65+ people (who constituted 20% of the trial subjects, and 60% of them had comorbidities), and 100% efficacy in preventing severe disease and hospitalization; AstraZeneca also points out that the specifically monitored for thrombosis in general and cerebral venous sinus thrombosis (due to the events in Europe) and found no signs of it; however, this press release was criticized the following night, in an unusual move, by the DSMB, which was quickly picked up by the NIIAD and NIH as well as Anthony Fauci commenting on it; the Washington Post, which has obtained a letter from the DSMB to AstraZeneca, states that AstraZeneca used ‘outdated and potentially misleading data’ that overstated the effectiveness of its vaccine, independent panel says, the criticism mainly being around the fact that the data appeared cherry-picked to claim a higher efficacy than the 69% to 75% inferred when all data are included, and the DSMB having discussed this with AstraZeneca prior to their press release
• Thrombosis and Thrombocytopenia after ChAdOx1 nCoV-19 Vaccination is a study published on the NEJM on 28 patients in Germany and Austria, after the German Society for Thrombosis and Hemostasis Research (GTH) issued a statement on vaccination with the AstraZeneca COVID-19 vaccine which describes their findings that a HIT-like reaction has occurred in examined patients who suffered or died from sinus or cerebral vein thrombosis after being administered the AstraZeneca AZD11222 vaccine in Germany; Thrombosis and Thrombocytopenia after ChAdOx1 nCoV-19 Vaccination reports analogous findings in 5 patients in Norway, and Pathologic Antibodies to Platelet Factor 4 after ChAdOx1 nCoV-19 Vaccination reports on 23 patients in the United Kingdom, with 30% older than 50 and 61% female, of which 7 died
• 14 July 2021 COVID-19 vaccine safety update VAXZEVRIA informs that the EMA is currently investigating adverse reactions related to Guillain-Barré syndrome, Acute Macular Retinopathy, Myocarditis and Pericarditis (also observed with Pfizer/BNT), and two conditions involving Thrombocytopenia, for which the vaccine had already been suspended, in whole or for certain age groups, in various parts of the EU
• First COVID-19 variant vaccine AZD2816 Phase II/III trial participants vaccinated as announced in an August 2021 AstraZeneca press release about its booster vaccine based on the B.1.351 (Beta, South African) variant, undergoing a trial on 2,250 participants across UK, South Africa, Brazil and Poland.

Johnson&Johnson Janssen (aka Ad26.COV2.S, JNJ-78436735, Ad26COVS1, VAC31518)

• Johnson & Johnson Announces Single-Shot Janssen COVID-19 Vaccine Candidate Met Primary Endpoints in Interim Analysis of its Phase 3 ENSEMBLE Trial, with an overall efficacy of 66% using a single-shot scheme, although the efficacy was 72% in the US and 57% in South Africa, possibly owing to the variant there (95% of cases), and 85% effectiveness in preventing severe disease, and the vaccine was well tolerated
• FDA Issues Emergency Use Authorization for Third COVID-19 Vaccine after the document Janssen Ad26.COV2.S Vaccine for the Prevention of COVID-19 briefing document was released by the FDA endorsing the Johnson&Johnson vaccine; Derek Lowe and StatNews discuss the data
• EMA recommends COVID-19 Vaccine Janssen for authorisation in the EU and subsequently the Janssen (Johnson & Johnson) Ad26.COV2.S vaccine is authorized across the EU, with a 67% reduction in the number of symptomatic COVID-19 cases (efficacy) found after 2 weeks from the jab; the EMA also released a Q&A document in "lay language" and a summary of product characteristics for healthcare providers that includes an efficacy table by ages showing higher efficacy in older people
• COVID-19 Vaccine Janssen: EMA finds possible link to very rare cases of unusual blood clots with low blood platelets after eight cases in the US, one of which fatal, were observed, which were "were very similar to the cases that occurred with the COVID-19 vaccine developed by AstraZeneca" (cerebral venous sinus thrombosis, or splanchnic thrombosis, with thrombocytopenia) and occurred mainly in women below 60 years of age; the EMA maintains that the benefits outweigh the risks and as such it still recommends its use as a safe and effective vaccine against COVID, without any specific limitations
• Positive New Data for Johnson & Johnson Single-Shot COVID-19 Vaccine on Activity Against Delta Variant and Long-lasting Durability of Response is announced by J&J and Janssen in press releases announcing studies showing that Ad26.COV2.S elicited neutralizing activity against Delta and other SARS-CoV-2 variants of concern, with stronger activity against the Delta (Indian) variant than it did against the Beta (B.1.351, South African) variant (which was previously shown in Safety and Efficacy of Single-Dose Ad26.COV2.S Vaccine against Covid-19 to retain substantial efficacy), and also that the durability of response lasts at least 8 months

Nuvaxovid by Novavax (NVX-CoV2373)

• Novavax COVID-19 Vaccine Demonstrates 89.3% Efficacy in UK Phase 3 Trial, as announced in a press release by the company about their NVX-CoV2373 protein-based vaccine, based on a trial that included 27% over the age of 65, and on an interim analysis after 62 cases developed, of which 56 were in the placebo group; at the same time, Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant in South Africa was 60% (among HIV-negative individuals), likely due to 90% prevalence of the South African escape variant, which the company says has initiated development of boosters for
• Novavax announcement of UK and South AfricaTrial Results is fairly boasting ("breaking news", seriously?) but contains a lot of nice infographics and variant spread graphs
• Novavax COVID-19 Vaccine Demonstrates 90% Overall Efficacy and 100% Protection Against Moderate and Severe Disease in PREVENT-19 Phase 3 Trial with 29,960 in the United States and Mexico, among which 63 cases of COVID were seen in the placebo group and 14 in the vaccine group, and the efficacy appears to remain high in patients with sequenced variants of concern
• Novavax Announces COVID-19 Vaccine Booster Data Demonstrating Four-Fold Increase in Neutralizing Antibody Levels Versus Peak Responses After Primary Vaccination, joining other vaccine makers in suggesting a third dose may be useful against the Delta variant, with a six-fold increase in functional antibodies against it, in a phase 2 study run in the US and Australia

Others

• Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial, published on The Lancet, concludes after testing an experimental vaccine on about 200 individual that, despite some mild or moderate adverse effect, this vaccine may be safe and at least temporarily immunogenic in all individuals who received it
• Second interim analysis of clinical trial data showed a 91.4% efficacy for the Sputnik V vaccine on day 28 after the first dose; vaccine efficacy is over 95% 42 days after the first dose, as announced by Gamaleya in a press release, where it was also specified that no significant adverse reactions have occurred; the international price for this vaccine was stated as being below $10
• The Sputnik V vaccine’s efficacy is confirmed at 91.4% based on data analysis of the final control point of clinical trials as announced in a subsequent Gamaleya press release, where it is stated that "the research data will be published by the Gamaleya Center team in one of the leading international peer-reviewed medical journals" and that "the Gamaleya Center will create a report that will be used to submit for accelerated registration of the Sputnik V vaccine in various countries"
• Sanofi and GSK announce a delay in their adjuvanted recombinant protein-based COVID-19 vaccine program to improve immune response in the elderly in a press release where they disclose that while the vaccine produces an immune response similar to COVID-19 patients when administered to people between 18 and 49 years, the response in older adult is insufficient
• Novavax COVID-19 Vaccine Demonstrates 89.3% Efficacy in UK Phase 3 Trial, as announced in a press release by the company about their NVX-CoV2373 protein-based vaccine, based on a trial that included 27% over the age of 65, and on an interim analysis after 62 cases developed, of which 56 were in the placebo group; at the same time, Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant in South Africa was 60% (among HIV-negative individuals), likely due to 90% prevalence of the South African escape variant, which the company says has initiated development of boosters for
• Novavax announcement of UK and South AfricaTrial Results is fairly boasting ("breaking news", seriously?) but contains a lot of nice infographics and variant spread graphs
• Novavax COVID-19 Vaccine Demonstrates 90% Overall Efficacy and 100% Protection Against Moderate and Severe Disease in PREVENT-19 Phase 3 Trial with 29,960 in the United States and Mexico, among which 63 cases of COVID were seen in the placebo group and 14 in the vaccine group, and the efficacy appears to remain high in patients with sequenced variants of concern
• Safety and efficacy of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine: an interim analysis of a randomised controlled phase 3 trial in Russia presents the first phase 3 results for the Sputnik V vaccine, with an estimated efficacy of 91.6%, and no serious adverse effects associated with vaccination
• GSK and CureVac to develop next generation mRNA COVID-19 vaccines and CureVac and UK Government to collaborate on development of vaccines against SARS-CoV-2 variants open the road to multi-variant mRNA vaccines by these companies
• CureVac Provides Update on Phase 2b/3 Trial of First-Generation COVID-19 Vaccine Candidate, CVnCoV where the primary efficacy endpoint is not met, with only 47% efficacy although the majority of cases were caused by variants of concern

Diagnostics

• SARS-CoV-2 diagnostic pipeline is an extensive list of available tests, searchable and exportable by type, as well as an independent validation of SARS-CoV-2 assays with results for molecular (PCR) tests as well as preliminary results for antigen ("quick") and antibody tests
• COVID-19 In Vitro Diagnostic Devices and Test Methods Database by the European Commission
• EUA Authorized Serology Test Performance, compiled by the FDA, lists sensitivity and specificity for a number of antibody tests approved for emergency use in the US
• Antigen-Tests zum direkten Erregernachweis des Coronavirus SARS-CoV-2 is an extensive list of antigen tests with manufacturer-provided information about them by the German medicine agency, while a Comparative evaluation of the sensitivities of SARSCoV-2 antigen rapid tests is provided with own evaluation by the Paul-Ehrlich-Institut based on sensitivity to three known cycle thresholds
• Comparison of seven commercial SARS-CoV-2 rapid Point-of-Care Antigen tests validates a few tests trying to determine their specificity and sensitivity

Epidemiology

Country	Sereprevalence	Highest-hit area	In health workers	Asymptomatics	Seroconversion	Source
England	6%	London (13%)	11.7%	32%	96.2%	Imperial
Italy	2.5%	Lombardy (7.5%)	5.6%	27.3%	N/A	Ministry of Health
Spain	5%	Madrid (>10%)	10.2%	32.7%	91.8%	Lancet

• ECDC's COVID-19 surveillance report, updated on a weekly basis with detail data on the evolution of the epidemic in Europe
• Short-term Mortality Fluctuations by the Human Mortality Database, providing excess mortality visualizations and raw data from 25 countries
• EuroMoMo, publishing bulletins and detailed graphs of excess mortality in European countries, and the CDC's Excess Deaths Associated with COVID-19 page has a similar visualization for the US during the pandemic
• The Economist and the New York Times have articles on excess mortality, with the former in particular looking at specific regions like Lombardy, Madrid and New York City and offering an infographic covering a number of countries and cities
• National data that feed into EuroMoMo are available for Spain and Italy (pages in the respective languages)
• Report on Weekly Deaths in South Africa from all causes as well as COVID-19 deaths, for each region
• Investigation of SARS-CoV-2 variants of concern: variant risk assessments by the UK government
• SeroTracker is a dashboard and data platform for SARS-CoV-2 serosurveys, with a map as well as graphs and raw data for serological surveys around the world, with the ability to filter them according to various parameters, including the type of source and the estimated risk of bias, the type of test used and antibodies detected, as well as demographics and date ranges assessed
• O impacto da pandemia de Covid-19 na mortalidade no Brasil provides excess mortality data for Brazil, globally or by state
• Assessing the age specificity of infection fatality rates for COVID-19: systematic review, meta-analysis, and public policy implications finds that the IFR is very low for children and younger adults to 1.4% at age 65, 4.6% at age 75, and 15% at age 85, and that most variation worldwide reflects difference in the population's age profiles
• COVID-19 Deaths by Demographic and Geographic Characteristics provided by the CDC for the US
• Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2 finds that the virus replicates poorly in dogs, pigs, chickens, and ducks, but ferrets and cats are permissive to infection, including airborne for cats; SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study finds that bats and ferrets are susceptible but pigs and chickens are not; Experimental infection of cattle with SARS-CoV-2 finds that cattle are not susceptible; Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates analyzes the ACE2 receptors in many species of animals to estimate the risk of susceptibility to infection
• Imperial College's comparison of containment vs mitigation strategies mainly with a view on the UK and US
• Inferring the effectiveness of government interventions against COVID-19 and The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries try to measure the effectiveness of various non-pharmaceutical interventions by correlating them with spread in countries that implemented them
• Unexpected detection of SARS-CoV-2 antibodies in the prepandemic period in Italy shows that an amount of people in Italy, and especially Lombardy, had SARS-CoV-2 antibodies back in October (possibly September) 2019, confirmed first by an ELISA assay and then by a cytopathic effect (CPE)–based live virus microneutralization assay, on blood samples of people who had previously participated in a study on lung cancer
• SARS-CoV-2 has been circulating in northern Italy since December 2019: Evidence from environmental monitoring was published on Nature and finds presence of viral RNA from wastewater in parts of northern Italy (Milan, Turin), with published partial sequences of the isolated RNA
• Sentinel surveillance of SARS-CoV-2 in wastewater anticipates the occurrence of COVID-19 cases is a preprint finding that SARS-CoV-2 was detected in Barcelona sewage long before the declaration of the first COVID-19 case, indicating that the infection was present in the population before the first imported case was reported; however, the identified RNA was not sequenced, and an unlikely positive in March 2019 raises the question of false positives
• Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study on more than 60000 participants selected by random sampling find a seroprevalence of about 5%, with 10% in the Madrid area and 3% on the coasts, and a seroprevalence of around 90% in people who had previously tested positive by PCR; most participants were asymptomatic, but among the symptomatic participants, only around 20% had been PCR-tested before
• Suppression of COVID-19 outbreak in the municipality of Vo, Italy, a study showing that in a fully locked-down town of around 3000 people, all of which were tested multiple times, 43% of the total cases were asymptomatic, but could infect others
• The early phase of the COVID-19 outbreak in Lombardy, Italy analyzes nearly 6000 laboratory-confirmed cases and determines the epidemic started much earlier than the first recognized case of February 22, with the first patient showing symptoms on January 1, and correctly predicts that "the number of critical cases may become largely unsustainable for the healthcare system in a very short-time horizon"
• Effective containment explains subexponential growth in recent confirmed COVID-19 cases in China, published on 8 April 2020
• CMMID traveller screening effectiveness simulator
• CMMID repository of COVID-19 research
• Curated updates from the International Society for Infectious Diseases
• Evolutionary history of SARS-COV-2, a paper published on Nature
• Relationship between the ABO Blood Group and the COVID-19 Susceptibility has been studied by Chinese researchers first, but a paper on The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis echoed its finding that type A blood carries the highest risk while type O carries the lowest (although one is about risk of contracting and one about severity); finally 23andMe finds evidence that blood type plays a role in COVID-19 in preliminary results on a 750000-partecipant study that is now published, again finding that type O is protective, while finding no significant differences among the other types, but no correlation was found in Association of Sociodemographic Factors and Blood Group Type With Risk of COVID-19 in a US Population, a case-control study including more than 11000 people who tested positive for COVID in the United States
• Two metres or one: what is the evidence for physical distancing in covid-19? notes that distancing rules are based on very outdated notions, a false dichotomy between big and small droplets, and therefore proposed a more nuanced "red/yellow/green" risk model for various situations
• Origin and evolution of SARS-CoV-2 proposed presence of two clades with distinct behaviors, but a Response to “On the origin and continuing evolution of SARS-CoV-2 rebutted that claim, which is now discredited
• Preliminary evidence of association with temperature, where a correlation with lower temperatures is found but not conclusively and not very significantly, and Seasonal variation in SARS-CoV-2 transmission in temperate climates which finds in June 2021 that when adjusting for non-pharmaceutical interventions, there is a seasonal variation of the rate of transmission in European countries with its minimum in early July and its maximum in early January
• Paper on demographics and intergenerational contact in Italy and South Korea and their influence on COVID-19 epidemics
• Fighting COVID-19: the heterogeneous transmission thesis, arguing that vulnerable people should be isolated while younger people at low risk and fit to work should be allowed work and socialization to limit total deaths
• High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2, a modelling based on Chinese case data, predicting an R0 between 3.8 and 8.9, hence much higher than previously suggested 2.2–2.7
• Airborne transmission of SARS-CoV-2: the world should face the reality, an opinion paper, substantiated by references, claiming there is no reason to assume this virus isn't as airborne as SARS-CoV-1 proved to be
• Interview on Icelandic genetic sequencing project showing children don’t seem to infect parents
• Sharing a household with children and risk of COVID-19: a study of over 300,000 adults living in healthcare worker households in Scotland suggests that among healthcare workers, parents of young children are more likely to be protected from COVID-19, hypothizing that if the difference in children "are due to differential exposure to non-SARS-CoV-2 infectious agents, adults who are close contacts of children may partly share in this protection"
• Antibody surveys suggesting vast undercount of coronavirus infections may be unreliable, a ScienceMag article critical of the methodologies and conclusions of a few of the large-sample antibody assays done recently around the world, while also describing them to the extent it's possible (since a few gave their results to the press before publishing papers)
• Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults was found as part of the REACT2 study, echoing findings from seroprevalence in blood donors in England (see pages 41 to 44)
• SARS-CoV-2 seroprevalence trends in healthy blood donors during the COVID-19 Milan outbreak, finding that among blood donors in Milan, Lombardy, around 4.6% were positive to IgG at the "start of the outbreak" on February 24, and around 7.1% by April 8, using a test with 98.3% specificity, yielding similar prevalence as a Seroprevalence of SARS-CoV-2 in Hong Kong and in residents evacuated from Hubei province, China: a multicohort study despite different specificity and sensitivity of tests
• Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals, published on Cell, finds that T-cells from uninfected individuals respond to SARS-CoV-2, "suggesting cross-reactive recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2", echoing a previous preprint Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors; however, a newer preprint claims Pre-COVID-19 humoral immunity to common coronaviruses does not confer cross-protection against SARS-CoV-2
• SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis finds that mean duration of RNA shedding is 17 days, but no study detected live virus beyond day 9 of illness, despite persistently high viral loads from RT-PCR cycles
• Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant looks at 167 Delta (B.1.617.2) infections in mainland China that could all be traced to one origin case, and finds through PCR testing that the viral loads were, on average, 1000 times higher than previously seen levels from Alpha or Beta variants

Follow-up

This section includes information about so-called "long COVID".

• Post-hospitalisation COVID-19 study (PHOSP-COVID), recruiting 10,000 patients who have been hospitalised with COVID-19 in the UK
• CORAL Study, trying to understanding the impact of COVID-19 on young people, adults, pregnant women and older people to predict need for mental health support
• Study to identify markers that could predict COVID-19 outcome by the University of Bristol finds that Three quarters of patients report long-term effects of coronavius
• Evolution of antibody immunity to SARS-CoV-2 finds that in a cohort of 87 patients 10% of which needed hospital care, 44% reported long-term symptoms after 6 months, and it also suggests that there may still be replicating virus in the intestine (gut) of about half of infected individuals at least 90 days after infection (see also this tweet commenting about that)
• Persistent Symptoms in Patients After Acute COVID-19, an Italian study on patients that were hospitalized, after around 60 days
• The prevalence of long COVID symptoms and COVID-19 complications, by the British Office for National Statistics, has plans for estimating the prevalence of, and risk factors for, "long COVID" symptoms and health complications following coronavirus (COVID-19) infection, and early data
• Prevalence of Symptoms More Than Seven Months After Diagnosis of Symptomatic COVID-19 in an Outpatient Setting reports on a survey of non-hospitalized patients at Geneva University Hospitals under the CoviCare follow-up program, finding that 39% still reported some symptoms after 7 to 9 months, mainly fatigue, loss of smell, or taste, dyspnea and headache
• Outcomes of Cardiovascular Magnetic Resonance Imaging in Patients Recently Recovered From Coronavirus Disease 2019 (COVID-19), a study on 100 "unselected" patients in Germany (median age 49), finds that 78% had cardiac involved, and 60% ongoing myocardial inflammation
• As Their Numbers Grow, COVID-19 “Long Haulers” Stump Experts with a few examples of studies showing a large proportion of cases suffer long-term symptoms, most often cough but also frequently more complex and reminescent of ME/CFS
• BNONews COVID-19 reinfection tracker keeps track of patients who likely had COVID-19 more than once, with their location, age, sex, interval before re-infection, severity of both cases, and a link to more details
• Cognitive deficits in people who have recovered from COVID-19 looked at cognitive test data from 84,285 people in the UK and found that among those who had recovered from COVID (with or without lingering symptoms, and particularly but not solely in hospitalized subjects), there were substantial deficits that couldn't adequately be explained by other differences, and concluded that COVID has cognitive symptoms that persist in the "early-chronic phase"
• Persistent self-reported changes in hearing and tinnitus in post-hospitalisation COVID-19 cases finds that in 1 out of 10 of those cases, changes in hearing or tinnitus are reported at 8 weeks after discharge from hospital
• Preliminary evidence on long COVID in children looked at children below 18 years of age (median age 11.4) in Italy who developed persistent symptoms, and found that 42.6% were still "distressed" by symptoms 120 days or more after initial assessment

Models

• IHME COVID-19 Projections currently offers a SEIR model with unpublished assumptions for the US and many other countries
• EpiForecasts Temporal variation in transmission during the COVID-19 outbreak produces "daily estimates of the time-varying reproduction number" based on an open source model for the world, countries by continent, as well as subnational units of some countries (Belgium, Brazil, Canada, Colombia, India, Italy, Germany, UK, USA), with case and death notification data as input
• Covid ActNow, "America’s COVID warning system", has an alternative model as well as a detailed tracker for the US, although it's also SEIR
• Event Horizon - COVID-19 by the Brockmann lab at RKI, with predictions for several countries
• neherlab@biozentrum COVID-19 Scenarios, a customizable parametric modeller of COVID-19 outbreaks in various conditions with accounting for hospital and ICU bed availability
• Ontario's COVID-19 Technical Briefing
• Modelling the COVID-19 epidemic and implementation of population-wide interventions in Italy, published on Nature
• COVID-19 Daily Epidemic Forecasting by the Institute of Global Health, Faculty of Medicine, University of Geneva and the Swiss Data Science Center, ETH Zürich-EPFL
• Covasim is available from the Institute for Disease Modeling's COVID InfoHub as a stochastic agent-based simulator for COVID-19 epidemic analyses, described in its paper
• Epidemic Calculator is an elaboration on the SEIR model that simulates the disease's progression at a higher resolution, subdividing patients into mild, moderate and fatal, with source code available

Masks

There is mixed advice on the use of masks by the general public, and the advice from political authorities appears to be changing in various parts of the world depending on the availability of masks and the state of the pandemic. Here are some scientific articles or papers trying to determine the usefulness of masks, and behaviors such as re-use of masks.

• Face Masks for the General Public by the Royal Society DELVE initiative, answering many basic question on mask use, making, re-use, cleaning and appropriateness backed by a number of references
• Mask testing data by Aaron Collins, a list of single-use respirators (N95, KF94, KN95, FFP2 masks) for adults and children with measurements of filtration efficacy, pressure drop (measured by an amateur, so not to be taken as professional measurements) and other characteristics like size and strap types
• Rational use of face masks in the COVID-19 pandemic, a review of mask-related advice from authorities published on The Lancet
• Risk of SARS-CoV-2 transmission by aerosols, the rational use of masks, and protection of healthcare workers from COVID-19 is more recent than the above and concludes that no mask type completely avoids transmission, but it's possible high-quality surgical masks may be as effective as FFP2 respirators
• Community Use of Cloth Masks to Control the Spread of SARS-CoV-2 is a document by the CDC describing the espected benefits of mask wearing, especially multi-layered cloth masks for community use
• BBC: Coronavirus Expert panel to assess face mask use by public covers the WHO "reopening discussion" on the matter, and scientific literature on the aerosolization of cough and sneezes
• N95DECON, a scientific consortium for data-driven study of N95 filtering facepiece respirator decontamination
• Turbulent Gas Clouds and Respiratory Pathogen Emissions: Potential Implications for Reducing Transmission of COVID-19, a paper published on JAMA on aerosolization and characteristics of respiratory emissions like coughs and sneezes
• BBC: US 'considers cloth face masks for public', discussing an internal memo from the CDC where widespread use of many types of masks may be suggested
• Professional and Home-Made Face Masks Reduce Exposure to Respiratory Infections among the General Population, a study on the effectiveness of various types of masks on protecting from respiratory infections
• Papers about effectiveness of basic masks #masks4all a collection of scientific literature on the use of masks, though itself clearly biased in favor of using them
• Addressing COVID-19 mask shortages, a paper published at Stanford evaluating the filtering efficacy of many non-standard types of masks, and effective way to disinfect and re-use single-use masks
• Effect of various decontamination procedures on disposable N95 mask integrity and SARS-CoV-2 infectivity, testing vaporized hydrogen peroxide, ultraviolet light, and 70% ethanol for decontamination of N95 masks while assessing the viability of any remaining virus and the integrity of the masks after decontamination
• Face Masks Against COVID-19: An Evidence Review, a preprint covering COVID-19 transmission characteristics, characteristis and efficacy of masks, estimated impacts of widespread use, and sociological considerations for policy-making
• Critical levels of mask efficiency and of mask adoption that theoretically extinguish respiratory virus epidemics, a preprint that calculates that for R0=2.5, at minimum 80% of the population must wear masks with 50% filtration efficiency (below N95/FPP2) for extinction
• Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis concludes that all three intervention result in a significant reduction of risk

Syndrome in children

• An outbreak of severe Kawasaki-like disease at the Italian epicentre of the SARS-CoV-2 epidemic: an observational cohort study
• This Week In Virology 611 podcast section in which the Kawasaki-like syndrome is discussed

Prior research

• Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor, a 2013 study published on Nature
• A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence, a 2015 study published on Nature
• How China’s “Bat Woman” Hunted Down Viruses from SARS to the New Coronavirus, an article on Scientific American

News

Note: news and press releases about vaccines may be in their respective Vaccines sections rather than here.

• Info and live news updates from The Guardian
• Our transcription of speeches and press conferences related to COVID-19
• https://www.scmp.com/news/china/society/article/3049623/coronavirus-hubei-province-reports-81-new-deaths-and-2841 aerosol transmission, "viral pneumonia"
• https://arstechnica.com/science/2020/02/quarantine-camps-door-to-door-searches-in-wuhan-as-coronavirus-rampages-on/ quarantine camps
• https://www.theguardian.com/world/2020/feb/10/coronavirus-who-warns-spread-by-people-who-had-not-visited-china-could-be-tip-of-the-iceberg creepy
• https://www.lbc.co.uk/news/coronavirus-residents-welded-inside-their-own-home/ creepier
• American President Trump suspends travel from the EU
• WHO reverses course on use of face masks by the general public and home-made masks, an article by the SCMP which details changing attitudes towards face masks by the WHO and various governments
• Some doctors moving away from ventilators for virus patients, reports MedicalXpress, amid shortage of ventilators
• Blood tests show 14% of people are now immune to covid-19 in one town in Germany using antibody tests on a sample of 500 people
• New York antibody study estimates 13.9% of residents have had the coronavirus, Gov. Cuomo says, meaning at least 2.7 million New Yorkers have been infected as of April 23 ago, if this sampling of people going to grocery stores and shopping loations is representative
• First known U.S. coronavirus death occurred on Feb. 6 in Santa Clara County, San Francisco Chronicle article describing post-mortem confirmed cases predating earliest known deaths in California, and (https://www.scmp.com/news/world/united-states-canada/article/3081330/coronavirus-covid-19-us-earlier-first-thought-and), an SCMP article also covering that with discussion of implications given prevalence shown by antibody tests in the state of New York
• NIH halts clinical trial of hydroxychloroquine: study shows treatment does no harm, but provides no benefit
• Mysterious Covid-linked disease 'no longer expected to be fatal' in children after treatment breakthrough after increases of Kawasaki-like syndromes had seemed to appear in children with COVID-19
• Face masks to become mandatory in shops in England and France, while CDC study recommends mask mandates to battle coronavirus, claiming it could get it under control in one to two months if everyone wears a mask
• Experimental COVID-19 vaccine safe, generates immune response in the NIH-sponsored Phase 1 trial tested mRNA vaccine co-developed with Moderna
• Denmark to restrict North Jutland borders due to mink coronavirus outbreak from a mutated strain that may be less susceptible to current antibodies or vaccines
• SARS-CoV-2 spike mutations arising in Danish mink and their spread to humans, preliminary paper by the Danish Statens Serum Institut on the mink strains and human spill-back, following an earlier WHO statement on the matter and later a risk assessment paper by the ECDC
• COG-UK update on SARS-CoV-2 Spike mutations of special interest comes after the UK government announces a mutation gaining prevalence in South-East England, including London, which appears to spread more easily than pre-existing ones, according to the government's NERVTAG meeting on SARS-CoV-2 variant under investigation VUI-202012/01, which dubs it "Variant of Concern 202012/01" (VOC), and as shown in a Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations; the ECDC released a report on this variant on December 20, Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom, and London's Imperial College later released a report on Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data; a later NERVTAG document confirms increased disease severity in the VOC, now also commonly known as variant B.1.1.7, while noting inevitable limitations in the datasets used to assess that; Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1 is a matched cohort study published in March 202 finding that in a relatively young cohort in the UK, the variant increases the mortality risk by 64%
• Pfizer and BioNTech Announce Vaccine Candidate Against COVID-19 Achieved Success in First Interim Analysis from Phase 3 Study in a press release where they state that their BNT162b2 vaccine has more than 90% efficacy, based on 94 participant who got COVID-19 during the trial, without any serious safety concerns; the article Vaccine Efficacy Data! by Derek Lowe provides an early opinion on these results
• Moderna’s COVID-19 Vaccine Candidate Meets its Primary Efficacy Endpoint in the First Interim Analysis of the Phase 3 COVE Study, announces the company in a press release claiming a first interim analysis of 95 COVID cases showed an efficacy of 94.5% for their mRNA-1273 vaccine, and severe cases only in the control arm, during their COVE Phase 3 trial
• Oxford University and AstraZeneca both issue press releases on interim efficacy assessment of their ChAdOx1 nCoV-2019 vaccine, showing overall 70% efficacy but divided into 62% for a group that received two full doses, and 90% for a group receiving a half dose followed by a full-dose booster, and Derek Lowe discusses these results and the methodological differences compared to Pfizer and Moderna in Oxford/AZ Vaccine Efficacy Data
• Second interim analysis of clinical trial data showed a 91.4% efficacy for the Sputnik V vaccine on day 28 after the first dose; vaccine efficacy is over 95% 42 days after the first dose, as announced by Gamaleya in a press release, where it was also specified that no significant adverse reactions have occurred; the international price for this vaccine was stated as being below $10
• Moderna Announces Primary Efficacy Analysis in Phase 3 COVE Study for Its COVID-19 Vaccine Candidate and Filing Today with U.S. FDA for Emergency Use Authorization in a press release where efficacy is put at 94.1%, with 100% efficacy against "severe" cases, after 196 COVID cases have developed within the trial participants, and after more than two months of follow-up
• The Wuhan files — Leaked documents reveal China's mishandling of the early stages of Covid-19 is a CNN release of excerpts of private documents from the Chinese government supposedly showing cover-ups of facts about the epidemic, including a 20-fold increase of what was thought to be influenza in Hubei during December 2019
• Pfizer-BioNTech COVID-19 vaccine and related biological product advisory committee briefing document announces that this vaccine meets the FDA success criteria, with vaccine efficacy after the booster dose at 95.0%, counting 8 COVID-19 cases in the vaccine group compared to 162 COVID-19 cases in the placebo group, with a 95% credible interval of 90.3% to 97.6%
• UK says new coronavirus strain is more infectious, but vaccines should still work is also covered in Britain says new coronavirus variant up to 70% more transmissible, a quick fact sheet by The Straits Times
• New COVID-19 variant identified in South Africa is allegedly not only spreading fast but more dangerous, causing more severe illness in younger patients who do not suffer from other medical conditions and driven by new Covid-19 mutation that affects younger people although this is, for now, only media analysis; ScienceMag states Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear
• Sanofi, in unusual move, to help Pfizer, BioNTech make coronavirus vaccine doses, with the earliest batches to be made available by August 2021, after setbacks and delays in the development of its own vaccine candidates, after demand for existing vaccines has widely outstripped supply as immunization campaigns have kicked off in the US, UK and Europe
• Confidential European Commission documents seen by a German media team show a majority of EU member states wanted "traditional" vaccines and were "very little interested" in new-type jabs from BioNTech-Pfizer and Moderna, published on Deutsche Welle, states that considerations of unknown efficacy, price, and logistical complexity of the mRNA vaccines made most EU state push for other, better-known types
• EU hails deals to get more vaccine shots, tackle variants with a new contract for 150 million Moderna doses in 2021 and another 150 million in 2022 (see EU press release), and more doses of Pfizer/BioNTech secured
• COVID: Several European countries halt use of AstraZeneca vaccine with at least two batches under scrutiny after deaths and throbosis-related events in Austria, Italy and Denmark, which have not so far conclusively linked to the vaccine, but invesigation is in progress
• Covid-19 vaccine linked to a reduction in transmission in a Scottish study, not yet published, examining around 300000 healthcare workers, and finding that compared to unvaccinated workers, vaccination results in a 30% reducting in COVID-19 among members of the vaccinated workers' households after the first shot, and 54% after the second, nothing that this of course underestimates protection because household members can also be infected from other sources
• After 10 March 2021, several European countries suspended administration of the AstraZeneca COVID-19 vaccine, following some unusual blood clotting events. Statements in English are available from the Norwegian Medicines Agency and the German Paul Ehrlich Institute. Later on 15 March, Germany suspends use of AstraZeneca vaccine, along with Italy, France, Spain despite the Italian Medicines Agency having stated the previous day Unjustified alarm on safety of AstraZeneca vaccine
• PHE to provide genomic sequencing support to partners across the world, as part of the New Variant Assessment Platform program, with current or previously participating countries as of July 2021 being Brazil, Ethiopia, Kenya, Nigeria, Pakistan, Singapore, Ukraine, Kyrgyzstan, Tajikistan, and Albania, and the Africa Centre for Disease Control and Prevention
• US to Advise Boosters for Most Americans 8 Months After Vaccination is revealed by the New York Times, in advance of an official announcement, in August 2021, while the WHO expresses opposition to the plan due to the need for a worldwide vaccine supply
• Merck and Ridgeback’s Investigational Oral Antiviral Molnupiravir Reduced the Risk of Hospitalization or Death by Approximately 50 Percent Compared to Placebo for Patients with Mild or Moderate COVID-19 in Positive Interim Analysis of Phase 3 Study and the phase 3 of the MOVe-OUT trial was stopped early due to effectiveness, of what could be the first oral treatment with substantial effectiveness on non-hospitalized patients with risk factors
• Heavily mutated coronavirus variant puts scientists on alert as they determine whether a fast-spreading variant in South Africa poses a threat to COVID vaccines' effectiveness, and the WHO calls special meeting to discuss new Covid variant found in South Africa with ‘a large number of mutations’, while in the UK, Coronavirus variant fear sparks Africa travel curbs, with countries added back to the "red list" of restricted travel in a swift reaction to what appears to be perceived as a very threatening variant

API and feeds

• John Hopkins daily data in CSV format
• CoronaDataScraper provides much more extensive daily data by getting it from each government, although it's being replaced with Li which is to be run locally
• ZBMed preVIEW API
• outbreak.info has a comprehensive API, mainly divided into epidemiological information (cases, etc) and resources such as publications, trials, and datasets
• Vaccine Spotter API with vaccine availability information for the US in JSON format; source code for the API and website on GitHub
• Australian Department of Health emergency alert
• https://www.reddit.com/live/14d816ty1ylvo.rss
• https://www.globaltimes.cn/rss/outbrain.xml
• https://www.globaltimes.cn/content/1177737.shtml real time updates
• https://tools.cdc.gov/api/v2/resources/media/403372.rss
• https://www.cnbc.com/2020/02/10/coronavirus-latest-updates-china-hubei.html
• CNBC Health feed
• Fever Monitor CSV from RKI's Fever Monitor
• SurvStat@RKI 2.0 lets you create arbitrary queries on official German case data, with the query format described here
• RAPS COVID-19 vaccine tracker approved vaccines CSV and vaccines candidates in development CSV

Italy

• Vital links from Reddit
• Civil Protection Open COVID-19 Data licensed under Creative Commons Attribution 4.0, and their associated ArcGIS tracker
• Detailed daily data by the Ministry of Health
• La Repubblica's live updates are reasonably up to date
• Map of the areas currently under lockdown
• PM Conte's press conference about the lockdown
• Emergency decree instituting the lockdown
• Il Segnalatore's COVID-19 articles, covering the epidemic in general and with daily updated sets of graphs based on official data but including predictions of future trends
• LiveNewsMap is not about the coronavirus in particular, but right now mostly is
• ISTAT mortality data covering the first 4 months of 2020 compared to 2015-2019, in various formats and broken down by age and gender
• Age statistics for Lombardy
• LeccoNotizie's map and statistics for the cases and deaths in Lombardy
• ISS press release concerning fatality by age groups 1
• ISS press release concerning fatality by age groups 2
• SIAARTI recommendations for treatment choice in case of lacks of beds suggesting to exclude older age groups from treatment
• Paper estimating real infected population in Italy
• Ministry of Interior self-certification form for movement within the quarantine area which needs to be filled in whenever leaving one's residence with information on where you're going and why
• Covid-19, ecco cosa spiega lo studio effettuato a Vo', un articolo pubblicato dall'Università di Padova
• CoVid-19: il virus era presente in Lombardia già il 1° gennaio 2020, ancora dall'Università di Padova, su uno studio effettuato su quasi 6000 pazienti positivi
• Free online services for the quarantined areas
• Immuni: tutte le immagini disponibili su Github, announcing the publication of documentation for Italy's contact tracing app on GitHub, with screenshots; subsequent article discusses the security issues brought up by COPASIR
• Coronavirus warning from Italy: Effects of COVID-19 could be worse than first thought , warns an article trying to raise awareness that COVID isn't a "you either die or recover completely" kind of deal
• Translated Civil Protection press conferences and Prime Minister speeches
• Covid-19, illustrati i risultati dell'indagine di sieroprevalenza presents preliminary results of the countrywide seroprevalence survey, with an initial expected sample of 150000 but only around 65000 actual responses, estimating 2.5% of the population has antibodies, half of which in Lombardy (7.5%), around 27% asymptomatic
• Report Vaccini Anti COVID-19 by region

(For history and diffs of this document, see its GitHub page)