Genomic surveillance revealed prevalence of unique SARS-CoV-2 variants bearing mutation in the RdRp gene among Nevada patients

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. However, this testing does not yield genetic information required for identifying viral evolution or variants.

Methods: We sequenced 200 specimens from positively identified cases in Nevada through our robust protocol for sequencing SARS-CoV-2 genomes directly from patients 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 the finding of a novel variant in the nsp12 (RdRp-RNA dependent RNA Polymerase) 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 suggesting for a founder effect. Structural modeling of the RdRP with P323F mutation did not show any significant difference in protein conformation but the phenotypic effect is unknown and an area of active investigation.