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Next generation sequencing of SARS-CoV-2 from patient specimens of Nevada reveals occurrence of specific nucleotide variants at high frequency

Background: SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19), which has a wide range of disease manifestations, including relatively mild respiratory illness to severe disease requiring hospitalization. Patients with signs of COVID-19 (fever, coughing, shortness of breath) were tested for the virus by targeting specific SARS-COV-2 genomic loci via RT-PCR using RNA extracted from nasopharyngeal/nasal swabs specimens. However, this testing does not yield genetic information required for identifying viral evolution or variants. Therefore, we sequenced 200 specimens from positively identified cases in Nevada through our robust protocol for sequencing SARS-CoV-2 genomes directly from patient's nasopharyngeal/nasal swabs. This protocol enabled identification of specific nucleotide variants including those for D614G and clade defining mutations. Additionally, these sequences were used to determine the phylogenetic relationships of SARS-CoV-2 genomes of public health importance occurring in the state of Nevada. Results: Our study reports a novel finding of a variant in the nsp12 (RdRp) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-1). This 323F variant is found at a very high frequency in Northern Nevada compared to other geographic areas. Structural modeling of the RdRP interface domain indicates the P323F variant did not significantly change the protein conformation. Conclusions: Our results highlight the introduction and spread of specific SARS-CoV-2 variants at a very high frequency within a distinct geographic location. This is important for clinical and public health perspectives in understanding the transmission and evolution of SARS-CoV-2 as it circulates in humans.