SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States

Mindy Leelawong; Stephanie L Mitchell; Randal C Fowler; Edimarlyn Gonzalez; Scott Hughes; Marissa P Griffith; Jane W Marsh; Lee H Harrison; Jennifer L Rakeman

doi:10.1016/j.diagmicrobio.2021.115468

SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States

Diagn Microbiol Infect Dis. 2021 Nov;101(3):115468. doi: 10.1016/j.diagmicrobio.2021.115468. Epub 2021 Jul 5.

Authors

Mindy Leelawong¹, Stephanie L Mitchell², Randal C Fowler¹, Edimarlyn Gonzalez¹, Scott Hughes¹, Marissa P Griffith³, Jane W Marsh³, Lee H Harrison³, Jennifer L Rakeman⁴

Affiliations

¹ New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
² Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
³ Center for Genomic Epidemiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
⁴ New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA. Electronic address: jrakeman@health.nyc.gov.

Abstract

Nasal and nasopharyngeal swab specimens tested by the Cepheid Xpert Xpress SARS-CoV-2 were analyzed by whole-genome sequencing based on impaired detection of the N2 target. Each viral genome had at least one mutation in the N gene, which likely arose independently in the New York City and Pittsburgh study sites.

Keywords: COVID-19; Cepheid XpertXpress; SARS-CoV-2; SARS-CoV-2 diagnostic testing; single nucleotide polymorphisms.

MeSH terms

COVID-19 / epidemiology*
COVID-19 / virology*
Cities / epidemiology
Coronavirus Nucleocapsid Proteins / genetics*
Databases, Genetic
Genome, Viral
Humans
Mutation
Phosphoproteins / genetics
SARS-CoV-2 / genetics*
United States / epidemiology

Substances

Coronavirus Nucleocapsid Proteins
Phosphoproteins
nucleocapsid phosphoprotein, SARS-CoV-2