RT Journal Article
SR Electronic
T1 Early Computational Detection of Potential High Risk SARS-CoV-2 Variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.12.24.474095
DO 10.1101/2021.12.24.474095
A1 Beguir, Karim
A1 Skwark, Marcin J.
A1 Fu, Yunguan
A1 Pierrot, Thomas
A1 Lopez Carranza, Nicolas
A1 Laterre, Alexandre
A1 Kadri, Ibtissem
A1 Lui, Bonny Gaby
A1 Sänger, Bianca
A1 Liu, Yunpeng
A1 Poran, Asaf
A1 Muik, Alexander
A1 Sahin, Ugur
YR 2021
UL http://biorxiv.org/content/early/2021/12/27/2021.12.24.474095.abstract
AB The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants on a daily basis. While most variants do not impact the course of the pandemic, some variants pose significantly increased risk when the acquired mutations allow better evasion of antibody neutralisation in previously infected or vaccinated subjects, or increased transmissibility. Early detection of such high risk variants (HRVs) is paramount for the proper management of the pandemic. However, experimental assays to determine immune evasion and transmissibility characteristics of new variants are resource-intensive and time-consuming, potentially leading to delayed appropriate responses by decision makers. Here we present a novel in silico approach combining Spike protein structure modelling and large protein transformer language models on Spike protein sequences, to accurately rank SARS-CoV-2 variants for immune escape and fitness potential. We validate our immune escape and fitness metrics with in vitro pVNT and binding assays. These metrics can be combined into an automated Early Warning System (EWS) capable of evaluating new variants in minutes and risk monitoring variant lineages in near real-time. The EWS flagged 12 out of 13 variants, designated by the World Health Organisation (WHO, Alpha-Omicron) as potentially dangerous, on average two months ahead of them being designated as such, demonstrating its ability to help increase preparedness against future variants. Omicron was flagged by the EWS on the day its sequence was made available, with immune evasion and binding metrics subsequently confirmed through our in vitro experiments.One-Sentence Summary A COVID-19 Early Warning System combining structural modelling with AI to detect and monitor high risk SARS-CoV-2 variants, identifying >90% of WHO designated variants on average two months in advance.Competing Interest StatementU.S. is a management board member and employee at BioNTech SE. A.M., B.G.L. and B.S. are employees at BioNTech SE. A.P. and Y. L. are employees at BioNTech US. U.S. and A.M. are inventors on patents and patent applications related to RNA technology and the COVID-19 vaccine. U.S., A.M., B.G.L., and B.S. have securities from BioNTech SE. K.B. is a management board member and employee at InstaDeep Ltd. M.J.S., Y.F., T.P., N.L.C., A.L. and I.K. are employees of InstaDeep Ltd or its subsidiaries. K.B., M.J.S., Y.F., T.P., N.L.C., and A.L. are inventors on patents and patent applications related to AI technology. K.B., M.J.S., Y.F., T.P., N.L.C., and A.L. have securities from InstaDeep Ltd.