Important notice!

Primer schemes have now been migrated to labs.primalscheme. Rather then contributing to this repo, we now encourage that you contribute primer schemes designed with varVAMP to primerschemes. Use primal-page to create correctly formatted input data.

ViralPrimerSchemes

This repo contains wet-lab evaluated and non-evaluated primer schemes for full-viral genome sequencing of highly diverse viral pathogens designed with varVAMP.

Tiled schemes

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

qPCR schemes

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

Which files should I check?

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.

Large THANK you...

...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 🍺

Contributing

If you designed and/or wet-lab evaluated primer schemes that we should include here, just contribute via an issue or pull request!

Citing this repo

If you use primers from this repository please cite.