Multiple genomic sequences of SARS-CoV-2 from all over the world have since been deposited in public databases such as GenBank and GISAID (Global Initiative on Sharing All Influenza Data 1) ( Elbe and Buckland-Merrett, 2017). The first genome sequence of SARS-CoV-2 was made available on January 10th (GenBank ID: MN908947.3) ( Wu et al., 2020). and can also be critical in source attribution and determining microbial provenance ( van Dorp et al., 2020). It can shed light on pathogenicity, virulence, drug/vaccine targets, mutation sites etc. Genomic sequence data is important in identifying, characterizing and understanding pathogens ( Rambaut et al., 2008 Salipante et al., 2015). 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). Based on genomic sequence analysis, it is reported to have originated from bats ( Hu et al., 2015) and pangolins ( Zhang et al., 2020a, b). SARS-CoV-2 is an enveloped positive-sense single-stranded RNA virus belonging to the genus Betacoronavirus (subgenus Sarbecovirus) in the Coronaviridae family (order: Nidovirales). Numerous coronaviruses infecting different animal species including humans have been identified. As of December 22nd, 2020, a total of 78,263,502 confirmed patients and 1,722,307 deaths have been reported worldwide ( Dong et al., 2020) and 2,65,620 registered cases and over 2,240 deaths in the state of Oklahoma, United States ( OSDH-Covid-19 Tracker, 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). Human to human transmission was recorded around the same time ( Nishiura et al., 2020). The etiological agent was identified to be a novel coronavirus (SARS-CoV-2/nCoV-19) on 7th January 2020 ( Zheng, 2020). Toward the end of 2019, several individuals with signs of pneumonia reported to hospitals in Wuhan, the capital of Hubei Province in Central China. 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. Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). 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. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced.
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. 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. Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 5High-Performance Computing Center, Oklahoma State University, Stillwater, OK, United States.4Center for Health Sciences, Oklahoma State University, Tulsa, OK, United States.3Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States.2Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States.1Oklahoma Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, United States.Agarwal 3,5 and Akhilesh Ramachandran 1,2* Ritchey 1, Girish Patil 1, Teluguakula Narasaraju 1, Sunil More 2, Jerry Malayer 3, Jeremiah Saliki 1, Anil Kaul 4, Pratul K.
0 kommentar(er)
