Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
Department of Pathology, Aga Khan University Hospital, Nairobi 30270-00100, Kenya.
Viruses. 2021 Oct 14;13(10):2063. doi: 10.3390/v13102063.
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.
在当前的 COVID-19 大流行中出现了两个严重的公共卫生挑战，即 SARS-CoV-2 变体监测不足和忽视其他同时传播的呼吸道病毒。此外，还需要准确评估疫情的演变、范围和动态，以了解病毒的传播。为了应对这些挑战，我们使用了一种高通量下一代测序（NGS）呼吸道病毒面板（RVP）评估了 533 个样本，该面板包含 40 种病毒病原体。性能指标显示，PPA、NPA 和准确性分别为 95.98%、85.96%和 94.4%。在佐治亚州，美国，含有某些远距离变体的穿山甲谱系 B 的分支，包括 ORF1ab 中的 P4715L、ORF3a 中的 Q57H 和 ORF8 中的 S84L，与 D614G 刺突蛋白突变共变，是大流行早期最常见的。来自同一县的分离株形成并系群，表明县与县之间存在病毒传播。该研究表明，NGS-RVP 可用于识别新型变体，从而提供可采取行动的信息，以预防或减轻新出现的病毒威胁，并提供有关病毒传播模式的模型，以预测区域疫情的传播/复发，并提供有关可能是导致全球疾病负担的独立因素的同时传播的呼吸道病毒的关键信息。
