ABSTRACT
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.
Conclusions Our results highlight the introduction and spread of specific SARS-CoV-2 variants at very high frequency within a distinct geographic location that is important for clinical and public health perspectives in understanding the evolution and transmission of SARS-CoV-2.
Competing Interest Statement
The authors have declared no competing interest.
Funding Statement
Nevada IDeA Network of Biomedical Research Excellence (INBRE) from the National Institute of General Medical Sciences (GM 103440 and GM 104944) from the National Institutes of Health (NIH).
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
Yes
The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
Deidentified human specimens (nasal and nasopharyngeal swabs) were used for the extraction of viral RNA all the experiments were done in accordance with guidelines of the University of Nevada, Reno. The University of Nevada, Reno Institutional Review Board (IRB) reviewed this project and determined this study to be EXEMPT FROM IRB REVIEW according to federal regulations and University policy. The Environmental and Biological Safety committee of the University of Nevada, Reno, approved methods and techniques used in this study.
All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.
Yes
I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
Yes
I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.
Yes
Paper in collection COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv
The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, University of Washington, and Vrije Universiteit Amsterdam.
Subject Area
Reviews and Context
0
Comment
0
TRIP Peer Reviews
0
Community Reviews
0
Automated Services
0
Blogs/Media
Author Videos