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Open AccessArticle

Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA

1
Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, India
2
Talwar and Talwar Consultants, Mohali 160055, India
3
Department of Microbiology and Immunology, University of Nevada, Reno, NV 89557, USA
4
Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008 Tatarstan, Russia
*
Authors to whom correspondence should be addressed.
Authors had equal contribution.
Pathogens 2020, 9(7), 565; https://doi.org/10.3390/pathogens9070565
Received: 10 June 2020 / Revised: 7 July 2020 / Accepted: 11 July 2020 / Published: 13 July 2020
(This article belongs to the Special Issue SARS-CoV Infections)
SARS-CoV-2 has spread very quickly from its first reported case on 19 January 2020 in the United Stated of America, leading WHO to declare pandemic by 11 March 2020. RNA viruses accumulate mutations following replication and passage in human population, which prompted us to determine the rate and the regions (hotspots) of the viral genome with high rates of mutation. We analyzed the rate of mutation accumulation over a period of 11 weeks (submitted between 19th January to 15 April 2020) in USA SARS-CoV-2 genome. Our analysis identified that majority of the viral genes accumulated mutations, although with varying rates and these included NSP2, NSP3, RdRp, helicase, Spike, ORF3a, ORF8, and Nucleocapsid protein. Sixteen mutations accumulated in Spike protein in which four mutations are located in the receptor binding domain. Intriguingly, we identified a fair number of viral proteins (NSP7, NSP9, NSP10, NSP11, Envelop, ORF6, and ORF7b proteins), which did not accumulate any mutation. Limited changes in these proteins may suggest that they have conserved functions, which are essential for virus propagation. This provides a basis for a better understanding of the genetic variation in SARS-CoV-2 circulating in the US, which could help in identifying potential therapeutic targets for controlling COVID-19. View Full-Text
Keywords: SARS-CoV2; genome; mutation; bioinformatics SARS-CoV2; genome; mutation; bioinformatics
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MDPI and ACS Style

Kaushal, N.; Gupta, Y.; Goyal, M.; Khaiboullina, S.F.; Baranwal, M.; Verma, S.C. Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA. Pathogens 2020, 9, 565. https://doi.org/10.3390/pathogens9070565

AMA Style

Kaushal N, Gupta Y, Goyal M, Khaiboullina SF, Baranwal M, Verma SC. Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA. Pathogens. 2020; 9(7):565. https://doi.org/10.3390/pathogens9070565

Chicago/Turabian Style

Kaushal, Neha; Gupta, Yogita; Goyal, Mehendi; Khaiboullina, Svetlana F.; Baranwal, Manoj; Verma, Subhash C. 2020. "Mutational Frequencies of SARS-CoV-2 Genome during the Beginning Months of the Outbreak in USA" Pathogens 9, no. 7: 565. https://doi.org/10.3390/pathogens9070565

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