SARS-CoV-2 genomes from Oklahoma, USA

Abstract

Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study we sequenced SARS-CoV-2 from 5 clinical samples obtained in Oklahoma, USA during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and 4 during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected such as G1167V in S gene, A6269S and P3371S in ORF1ab, T28I in ORF7b, G96R in ORF8. Phylogenetic analysis of the genomes showed similarity to viruses from across the globe. These novel mutations and phylogenetic analysis emphasize the contagious nature of the virus.

First detection and report of SARS-CoV-2 Spike protein N501Y mutations in Oklahoma USA

“…Q27Stop mutation in ORF 8 was detected in 3 out of these 4 samples. N501Y and the previously described D614G mutations (14,15) were detected in all 6 samples (Table 2).…”

“…Annotated genes and the whole genomes were aligned using MUSCLE aligner in MEGA-X (12). The genome sequences were submitted to GISAID (1) and their GISAID classification and PANGO lineages (13) (14,15) were detected in all 6 samples (Table 2).…”

Sword of Damocles or choosing well. Population genetics sheds light into the future of the COVID-19 pandemic and SARS-CoV-2 new mutant strains

“…Due to Covid-19's pandemic magnitude, an immense effort to sequence SARS-CoV-2 genetic variants and its relations to clinical and epidemiological findings has been made worldwide. There are nearly a thousand preprints available about genetic variants, published in https://www.medrxiv.org 1 , https://www.biorxiv.org 2 and some other preprint platforms, which promote the rapid data exchange about SARS-CoV-2 genetic sequences [3][4][5][6][7][8][9][10] , infectivity and lethality (https://nextstrain.org/sars-cov-2/; https://www.ncbi.nlm.nih.gov; https://www.gisaid.org; https://covid.pages.uni.lu; https://www.covid19dataportal.org) [11][12][13][14][15] . Updated mutations on any sequence can be tested in different countries and time periods.…”

SARS-CoV-2 Genomes From Oklahoma, United States

“…PA acknowledges a grant from NIGMS under award number GM105978. This manuscript has been released as pre-print at medRxiv ( Narayanan et al, 2020 ).…”