US National Institutes of Health Prioritization of SARS-CoV-2 Variants

Abstract

Since late 2020, SARS-CoV-2 variants have regularly emerged with competitive and phenotypic differences from previously circulating strains, sometimes with the potential to escape from immunity produced by prior exposure and infection. The Early Detection group is one of the constituent groups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution program. The group uses bioinformatic methods to monitor the emergence, spread, and potential phenotypic properties of emerging and circulating strains to identify the most relevant variants for experimental groups within the program to phenotypically characterize. Since April 2021, the group has prioritized variants monthly. Prioritization successes include rapidly identifying most major variants of SARS-CoV-2 and providing experimental groups within the National Institutes of Health program easy access to regularly updated information on the recent evolution and epidemiology of SARS-CoV-2 that can be used to guide phenotypic investigations.

Keywords: 2019 novel coronavirus disease; COVID-19; SARS-CoV-2; SARS-CoV-2 variants; US National Institute of Allergy and Infectious Diseases; US National Institutes of Health; computational biology; coronavirus disease; epidemiological monitoring; epidemiology; pandemic prevention and control; respiratory infections; severe acute respiratory syndrome coronavirus 2; viruses; zoonoses.

Figure 1

US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution Early Detection consortium prioritization of variant rankings from February 2023, produced by taking the consensus of rankings provided by the consortium subgroups. The lineages are shown on the right, split into different functional categories. The colored bars indicate priority categories 1, 2, and 3. This prioritization, and all future prioritizations, can be accessed with supporting information (6) (Appendix 1).

Figure 2

Comparison of rankings provided by 7 of the subgroups of the US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution consortium for the February 2023 prioritization. Lighter colors indicate a higher ranking and darker colors a lower ranking; gray indicates that the group deferred or did not provide a ranking for that lineage. Two groups (Broad Institute team, Walter Reed Army Institute of Research team) were not able to provide rankings for the February 2023 prioritization. Appendix 3 Figure 1 shows tangle plots comparing rankings between all pairs of consortium subgroups. BGU/NIBN, Ben Gurion University of the Negev, The National Institute for Biotechnology in the Negev; BV-BRC, Bacterial and Viral Bioinformatics Resource Center; CU, Cambridge University; LANL, Los Alamos National Laboratory; ISMMS, Icahn School of Medicine at Mt. Sinai; UC-R, University of California-Riverside School of Medicine; UoM, University of Missouri.

Figure 3

Gantt chart showing the priority category (denoted by colored rectangles) for each SARS-CoV-2 lineage at each monthly prioritization between May 2022 and February 2023. The frequency of each lineage in global surveillance data is shown with black circles for each month. For lineages with a frequency <0.1%, but which are observed at least once in a given month, a small black point is shown. Exact matches to sequence definitions as provided in US National Institutes of Health National Institute of Allergy and Infectious Diseases SARS-CoV-2 Assessment of Viral Evolution Early Detection consortium prioritization spreadsheets are required for a sequence to count as a match to a lineage. Appendix 3 Figure 3 is an analogous figure for all 21 monthly prioritizations, back to April 2021.