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Characteristics of viral specimens collected from asymptomatic and fatal cases of COVID-19

The Journal of Biomedical Research 2020年第6期34卷 431-436页

作者： andrew J.gorzalski Paul Hartley Chris Laverdure Heather Kerwin Richard Tillett Subhash Verma Cyprian Rossetto Sergey Morzunov Stephanie Van Hooser Mark W.Pandori Nevada State Public Health Laboratory RenoNV 89597USA Nevada Genomics Center RenoNV 89557USA Washoe County Health District RenoNV 89512USA Nevada Institute of Personalized Medicine University of Nevada Las VegasLas VegasNV 89154-4022USA Nevada Center for Bioinformatics University of Nevada RenoRenoNV 89557USA Department of Microbiology and Immunology University of NevadaReno School of MedicineRenoNV 89557USA. Department of Pathology and Laboratory Medicine University of NevadaReno School of MedicineRenoNV 89557USA.

We sought to determine the characteristics of viral specimens associated with fatal cases,asymptomatic cases and non-fatal symptomatic cases of *** included the analysis of 1264 specimens found reactive for at least two SARS-CoV-2 specific loci from people screened for infection in Northern Nevada in March-May of *** these,30 were specimens from fatal cases,while 23 were from positive,asymptomatic *** assessed the relative amounts of SARS-CoV-2 RNA from sample swabs by real-time PCR and use of the threshold crossing value(Ct).Moreover,we compared the amount of human RNase P found on the same swabs.A considerably higher viral load was found to be associated with swabs from cases involving fatality and the difference was found to be strongly statistically *** this difference,we sought to assess whether any genetic correlation could be found in association with virus from fatal cases using whole genome *** no common genetic elements were discerned,one branch of epidemiologically linked fatal cases did have two point mutations,which no other of 156 sequenced cases from northern Nevada *** mutations caused amino acid changes in the 3′-5′exonuclease protein,and the product of the gene,orf8.

关键词： COVID-19 SARS-COV-2 real-time PCR Ct value viral load

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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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