This repo contains wet-lab evaluated and non-evaluated primer schemes for full-viral genome sequencing of highly diverse viral pathogens designed with varVAMP.
Primers can contain ambiguous characters in order to achieve pan-specificity. We recommend using a One-Step-RTPCR Protocol at 60°C primer annealing for 35 to 40 cycles. Due to the variability of some viruses, we can not garantuee that the primers will work for every sample you are trying to sequence but for the large majority they should perform resonably well. Happy sequencing!
| Virus | Genotypes | Amplicon Size | GenomeRecovery | Evaluated | Primers | Input alignment | Full varVAMP output |
|---|---|---|---|---|---|---|---|
| HEV | 3 (f, e) | 1000-1500 | 99.0 % | ✅ | tsv | aln | output |
| HEV | 3 (c, h1, m, i, uc, l) | 1000-1500 | 99.3 % | ✅ | tsv | aln | output |
| ratHEV | all | 1200-1700 | 97.4 % | ✅ | tsv | aln | output |
| Polio | 1-3 | 1000-1400 | 99.6 % | ✅ | tsv | aln | output |
| HAV | all | 1000-1600 | 95.6 % | ✅ | tsv | aln | output |
| BoDV | all | 400-550 | 98.6 % | ✅ | tsv | aln | output |
| SARS-CoV-2 | B.1-XBB | 260-365 | 99.7 % | 🔲 | tsv | aln | output |
| SARS-CoV-2 | B.1-XBB | 700-800 | 99.7 % | ✅ | tsv | aln | output |
| Norovirus | non-G.II.4 G.II | 1500-2000 | 99.0 % | 🔲 | tsv | aln | output |
| Norovirus | G.II.4 | 1200-1600 | 99.6 % | 🔲 | tsv | aln | output |
| Virus | Genotypes | Evaluated | Primers | Input alignment | Full varVAMP output |
|---|---|---|---|---|---|
| Polio | 1 | ✅ | tsv | aln | output |
| Polio | 2 | ✅ | tsv | aln | output |
| Polio | 3 | ✅ | tsv | aln | output |
| Polio | 1-3 | ✅ | tsv | aln | output |
If you just want to use the primers, just go for the tsv files in the primer section. If you are interested in the full varVAMP output (here you can also find additional non-used primers) have a look at the input alignment to get a feeling for the variability and have a look here for an explanation on the output files. If you want to design primers yourself, the outputs can also help you in understanding how the software works and how to prepare the data and set the parameters for a successful scheme design.
...to all the people to have contributed to these primer designs by providing input alignments 🍺, did primer designs 🍷 and wet-lab evaluated primer schemes 🍸
- Mathias Schemmerer (Universitätsklinikum Regensburg, Germany): HAV 🍺🍸, HEV 🍺, ratHEV 🍺, BoDV 🍺🍸
- Johanna Kleine (Universitätsklinikum Freiburg, Germany): HEV 🍸🍷🍺
- Sindy Böttcher, Julian Kreibich (Robert Koch Institute, Berlin, Germany): Polio 🍸
- Martin Hölzer (Robert Koch Institute, Berlin, Germany): SARS-CoV-2 🍺
If you designed and/or wet-lab evaluated primer schemes that we should include here, just contribute via an issue or pull request!
If you use primers from this repository please cite:
varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens.
(paper currently under preparation)