Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Autor: Connor R; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Shakya M; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Yarmosh DA; American Type Culture Collection, Manassas, VA 20110, USA.; BEI Resources, Manassas, VA 20110, USA., Maier W; Galaxy Europe Team, University of Freiburg, 79085 Freiburg, Germany., Martin R; Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA., Bradford R; American Type Culture Collection, Manassas, VA 20110, USA.; BEI Resources, Manassas, VA 20110, USA., Brister JR; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Chain PSG; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Copeland CA; Deloitte Consulting LLP, Rosslyn, VA 22209, USA., di Iulio J; Vir Biotechnology Inc., San Francisco, CA 94158, USA., Hu B; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Ebert P; Eli Lilly and Company, Indianapolis, IN 46225, USA., Gunti J; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Jin Y; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Katz KS; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Kochergin A; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., LaRosa T; Deloitte Consulting LLP, Rosslyn, VA 22209, USA., Li J; Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA., Li PE; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Lo CC; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Rashid S; American Type Culture Collection, Manassas, VA 20110, USA., Maiorova ES; Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA., Xiao C; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Zalunin V; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Purcell L; Vir Biotechnology Inc., San Francisco, CA 94158, USA., Pruitt KD; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Jazyk: angličtina
Zdroj: Viruses [Viruses] 2024 Mar 11; Vol. 16 (3). Date of Electronic Publication: 2024 Mar 11.
DOI: 10.3390/v16030430
Abstrakt: Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.
Databáze: MEDLINE
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