Richard L. Tillett
David P. AuCoin
Joel R. Sevinsky
Yanji Xu
Andrew Gorzalski
Mark Pandori
Erin Buttery
Holly Hansen
Michael A. Picker
Cyprian C. Rossetto
Subhash C. Verma
aNevada Genomics Center, Reno, NV 89557, USA
bUniversity of Nevada, Reno, Reno, NV 89557, USA
cNevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
dDepartment of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
eTheiagen Consulting, LLC, Highlands Ranch, CO 80128, USA
fNevada Center for Bioinformatics, Reno, NV 89557, USA
gNevada State Public Health Laboratory, Reno, NV 89503, USA
hSouthern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
More InformationCorresponding author: E-mail address: crossetto@med.unr.edu (Cyprian C. Rossetto);E-mail address: scverma@med.unr.edu (Subhash C. Verma)
Publish Date:2021-01-20
Abstract
Abstract
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification. High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak. We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine (F) from proline (P), in the first reported isolate of SARS-CoV-2, Wuhan-Hu-1. This 323F variant was present at a very high frequency in Northern Nevada. Structural modeling determined this mutation in the interface domain, which is important for the association of accessory proteins required for the polymerase. In conclusion, we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations, which is important for understanding the evolution and circulation of SARS-CoV-2 variants of public health importance, while it circulates in humans.Keywords: SARS-CoV-2,
COVID-19,
Genome enrichment,
nsp12,
RdRp,
orf1b 314
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http://www.jgenetgenomics.org/article/exportPdf?id=b94925b9-abd9-435d-9c36-ebcacdbed182&language=en
