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

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Journal of Genetics and Genomics 2021年第1期48卷 40-51页

作者： Paul D.Hartley Richard L.Tillett David P.AuCoin Joel R.Sevinsky Yanji Xu Andrew Gorzalski Mark Pandori Erin Buttery Holly Hansen Michael A.Picker Cyprian C.Rossetto Subhash C.Verma Nevada Genomics Center RenoNV 89557USA University of Nevada RenoRenoNV 89557USA Nevada Institute of Personalized Medicine University of NevadaLas VegasNV 89154USA Department of Microbiology&Immunology University of NevadaReno School of MedicineRenoNV 89557USA Theiagen Consulting LLCHighlands RanchCO 80128USA Nevada Center for Bioinformatics RenoNV 89557USA Nevada State Public Health Laboratory RenoNV 89503USA Southern Nevada Public Health Laboratory of the Southern Nevada Health District Las VegasNV 89107USA

Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal *** determine the variants of SARS-CoV-2 circulating in the state of Nevada,specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform,which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads,without the need of culture-based *** genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the *** report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine(F) from proline (P),in the first reported isolate of SARS-CoV-2,*** 323F variant was present at a very high frequency in Northern *** modeling determined this mutation in the interface domain,which is important for the association of accessory proteins required for the *** conclusion,we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations,which is important for understanding the evolution and circulation of SARS-CoV-2variants of public health importance,while it circulates in humans.

关键词： SARS-CoV-2 COVID-19 genome enrichment nsp12 RdRp orf1b 314

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