Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay.

DOI: https://doi.org/10.1101/2020.08.25.265074
Manu Vanaerschot, Sabrina Mann, James T. Webber, Jack Kamm, Sidney M. Bell, John Bell, Si Noon Hong, Minh Nguyen, Lienna Chan, Karan Bhatt, Michelle Tan, Angela Detweiler, Wesley Wu, Joshua Batson, David Dynerman, CLIAHUB Consortium, Debra Wadford, Andreas S. Puschnik, Norma Neff, Vida Ahyong, Steve Miller, Patrick Ayscue, Simon Paul, Amy Kistler, Joe L. DeRisi, Emily D. Crawford
_{Chan Zuckerberg Biohub, San Francisco, California, USA (Manu Vanaerschot, Sabrina Mann, James T. Webber, Jack Kamm, Lienna Chan, Karan Bhatt, Michelle Tan, Angela Detweiler, Wesley Wu, Josh Batson, David Dynerman, Andreas S. Puschnik, Vida Ahyong, Norma Neff, Patrick Ayscue, Amy Kistler, Joe L. DeRisi, E. D. Crawford)
Chan Zuckerberg Initiative, Redwood City, California, USA (Sidney M. Bell) California Department of Public Health, Richmond, California, USA (John Bell, Debra Wadford)
Department of Public Health, Madera, California, USA (Si Noon Hong, Minh Nguyen, Simon Paul)
University of California, San Francisco, California, USA (Sabrina Mann, Steve Miller, Joe L. DeRisi, Emily D. Crawford)}

Abstract

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly-used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for SARS-CoV-2 diagnosis.

Methods

Sequence Data

./data/sequence_metadata.tsv contains the accession numbers of all sequences used in this analysis. Per GISAID terms of service, these can be downloaded via gisaid.org.

qPCR values

See ./data/Figure1*_rawdata.tsv.

Analysis and Figures

The tree was generated via Nextstrain's augur, v10.0.0, via the workflow specified in nextstrain/ncov at the linked commit. The config files used are located in tree/nextstrain-config/.

Figure 1 was generated in PRISM. Figure 2 was generated using the code found in figures/.

Additional citations

Our work is possible because of the computational tools developed by the research community. We gratefully acknowledge their contributions, and regret the journal-imposed limitation on the number of citations.

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