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 five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four 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 in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.
Highlights
Toward the end of 2019, several individuals with signs of pneumonia reported to hospitals in Wuhan, the capital of Hubei Province in Central China
We sequenced five SARS-CoV-2 genomes from clinical samples collected from Oklahoma, United States between March and July 2020
Presence of D614G mutation in the S gene was found in all the isolates
Summary
Toward the end of 2019, several individuals with signs of pneumonia reported to hospitals in Wuhan, the capital of Hubei Province in Central China. The etiological agent was identified to be a novel coronavirus (SARS-CoV-2/nCoV-19) on 7th January 2020 (Zheng, 2020). By the end of January 2020, WHO declared a “public health emergency of international concern” (Statement on the second meeting of the International Health Regulations 2005, 2020). Numerous coronaviruses infecting different animal species including humans have been identified. Other previously identified coronaviruses known to infect humans include SARS-CoV-1, MERS-CoV, HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1 (Graat et al, 2003; Van Elden et al, 2004; Mackay et al, 2012; Annan et al, 2013; Owusu et al, 2014; Corman et al, 2018)
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