High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses
Authors
Sahajpal, Nikhil S.Mondal, Ashis K.
Njau, Allan
Petty, Zachary
Chen, Jiani
Ananth, Sudha
Ahluwalia, Pankaj
Williams, Colin
Ross, Ted M.
Chaubey, Alka
DeSantis, Grace
Schroth, Gary P.
Bahl, Justin
Kolhe, Ravindra
Issue Date
2021-10-14
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Show full item recordAbstract
Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.Affiliation
Department of Pathologyae974a485f413a2113503eed53cd6c53
10.3390/v13102063
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Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0/