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Sustainability

Anna Bernasconi edited this page Oct 31, 2022 · 5 revisions

The objective of EpiViruSurf is to offer a concrete public endpoint for research on the interplay of epitopes with current viral sequences; its sustainability depends on the timely provision of both sequences and epitope inputs, as well as on the interplay with the ViruSurf database and VirusViz visualization application.

SARS-CoV-2 sequence data are tentatively updated on EpiViruSurf and EpiViruSurf-GISAID every week.
The pipeline for downloading sequences has been in place since the start of our commitment with ViruSurf (submitted Jul-2020, published Oct-2020) and we expect to maintain both ViruSurf and EpiViruSurf for 5 years minimum. Below is the detail of our recent updates of GenBank/COG-UK and GISAID sequences.

Update date ViruSurf available seq. ViruSurf-GISAID available seq.
2021-03-15 432,767 764,761
2021-04-02 484,876 864,129
2021-04-12 517,303 1,029,971
2021-04-19 536,798 1,107,140
2021-04-26 579,185 1,221,746
2021-05-03 609,952 1,333,679
2021-05-10 721,030 1,451,375
2021-05-17 818,317 1,558,056
2021-05-24 885,516 1,589,888
2021-06-01 948,559 1,766,159
2021-06-07 987,743 1,854,602
2021-06-16 1,056,103 1,937,530
2021-06-21 1,091,677 2,012,563
2021-06-28 1,170,879 2,096,480
2021-07-07 1,219,757 2,201,242
2021-07-13 1,226,808 2,302,549

For what concerns IEDB, we update SARS-CoV-2 epitopes with the same frequency (as of 2021-07-13, epitopes are 6,117). We also periodically consider the other species (SARS-CoV, MERS, Dengue, and Ebola).