Next Article in Journal
Development of Glycyrrhizinic Acid-Based Lipid Nanoparticle (LNP-GA) as An Adjuvant That Improves the Immune Response to Porcine Epidemic Diarrhea Virus Spike Recombinant Protein
Previous Article in Journal
Impact of Nonpharmaceutical Interventions during the COVID-19 Pandemic on the Prevalence of Respiratory Syncytial Virus in Hospitalized Children with Lower Respiratory Tract Infections: A Systematic Review and Meta-Analysis
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Viruses
Volume 16
Issue 3
10.3390/v16030430
viruses-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

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

by
Ryan Connor
1,†,
Migun Shakya
2,†,
David A. Yarmosh
3,4,
Wolfgang Maier
5,
Ross Martin
6,
Rebecca Bradford
3,4,
J. Rodney Brister
1,
Patrick S. G. Chain
2,
Courtney A. Copeland
7,
Julia di Iulio
8,
Bin Hu
2,
Philip Ebert
9,
Jonathan Gunti
1,
Yumi Jin
1,
Kenneth S. Katz
1,
Andrey Kochergin
1,
Tré LaRosa
7,
Jiani Li
6,
Po-E Li
2,
Chien-Chi Lo
2,
Sujatha Rashid
3,
Evguenia S. Maiorova
6,
Chunlin Xiao
1,
Vadim Zalunin
1,
Lisa Purcell
8 and
Kim D. Pruitt
1,*add Show full author list remove Hide full author list
1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
2
Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
3
American Type Culture Collection, Manassas, VA 20110, USA
4
BEI Resources, Manassas, VA 20110, USA
5
Galaxy Europe Team, University of Freiburg, 79085 Freiburg, Germany
6
Clinical Virology Department, Gilead Sciences, Foster City, CA 94404, USA
7
Deloitte Consulting LLP, Rosslyn, VA 22209, USA
8
Vir Biotechnology Inc., San Francisco, CA 94158, USA
9
Eli Lilly and Company, Indianapolis, IN 46225, USA
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Viruses 2024, 16(3), 430; https://doi.org/10.3390/v16030430
Submission received: 5 December 2023 / Revised: 12 February 2024 / Accepted: 16 February 2024 / Published: 11 March 2024
(This article belongs to the Special Issue Molecular and Computational Studies in Epidemiology and Evolution of Pandemic Virus)
Browse Figures
Versions Notes

Abstract

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.
Keywords: SARS-CoV-2; variant calling SARS-CoV-2; variant calling

Share and Cite

MDPI and ACS Style

Connor, R.; Shakya, M.; Yarmosh, D.A.; Maier, W.; Martin, R.; Bradford, R.; Brister, J.R.; Chain, P.S.G.; Copeland, C.A.; di Iulio, J.; et al. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses 2024, 16, 430. https://doi.org/10.3390/v16030430

AMA Style

Connor R, Shakya M, Yarmosh DA, Maier W, Martin R, Bradford R, Brister JR, Chain PSG, Copeland CA, di Iulio J, et al. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses. 2024; 16(3):430. https://doi.org/10.3390/v16030430

Chicago/Turabian Style

Connor, Ryan, Migun Shakya, David A. Yarmosh, Wolfgang Maier, Ross Martin, Rebecca Bradford, J. Rodney Brister, Patrick S. G. Chain, Courtney A. Copeland, Julia di Iulio, and et al. 2024. "Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows" Viruses 16, no. 3: 430. https://doi.org/10.3390/v16030430

APA Style

Connor, R., Shakya, M., Yarmosh, D. A., Maier, W., Martin, R., Bradford, R., Brister, J. R., Chain, P. S. G., Copeland, C. A., di Iulio, J., Hu, B., Ebert, P., Gunti, J., Jin, Y., Katz, K. S., Kochergin, A., LaRosa, T., Li, J., Li, P.-E., ... Pruitt, K. D. (2024). Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows. Viruses, 16(3), 430. https://doi.org/10.3390/v16030430

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop