Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing

• DOI: 10.3389/fimmu.2022.814806
• Publication Date: 2022-04-04T06:30:13Z
• Authors: Yanan Wang; Duo Chen; Chaofeng Zhu; Zhenhua Zhao; Shanshan Gao; Jianjun Gou; Yongjun Guo; Xiangdong Kong
• Keywords: Coronavirus; Amplicon; Multiplex

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays crucial role in virus surveillance evolutionary analysis. In this study, five sequences of SARS-CoV-2 were obtained from nasopharyngeal swab samples Zhengzhou, China. Following RNA extraction cDNA synthesis, multiplex PCR was performed with two primer pools produce the overlapped amplicons ~1,200 bp. viral genomes 96% coverage using nanopore sequencing. Forty-five missense nucleotide mutations identified; out these, 5 located at Nsp2, Nsp3, Nsp14, ORF10 genes occurred <0.1% frequency global dataset. On basis mutation profiles, clustered into sublineages (B.1.617.2 AY.31) or subclades (21A 21I). phylogenetic analysis several regions China Myanmar revealed that patients had different transmission chains. Taken together, we established platform for genetic identified variants circulating Zhengzhou during August 2021. Our study provided support government policymaking prevention control COVID-19.