Genomic Epidemiology of Imported Cases of COVID-19 in Guangdong Province,China,October 2020–May 2021

摘要

Objective The pandemic of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2) has been engendering enormous hazards to the world. We obtained the complete genome sequences of SARSCo V-2 from imported cases admitted to the Guangzhou Eighth People’s Hospital, which was appointed by the Guangdong provincial government to treat coronavirus disease 2019(COVID-19). The SARS-Co V-2 diversity was analyzed, and the mutation characteristics, time, and regional trend of variant emergence were evaluated.Methods In total, 177 throat swab samples were obtained from COVID-19 patients(from October2020 to May 2021). High-throughput sequencing technology was used to detect the viral sequences of patients infected with SARS-Co V-2. Phylogenetic and molecular evolutionary analyses were used to evaluate the mutation characteristics and the time and regional trends of variants.Results We observed that the imported cases mainly occurred after January 2021, peaking in May2021, with the highest proportion observed from cases originating from the United States. The main lineages were found in Europe, Africa, and North America, and B.1.1.7 and B.1.351 were the two major sublineages. Sublineage B.1.618 was the Asian lineage(Indian) found in this study, and B.1.1.228 was not included in the lineage list of the Pangolin web. A reasonably high homology was observed among all samples. The total frequency of mutations showed that the open reading frame 1 a(ORF1 a) protein had the highest mutation density at the nucleotide level, and the D614 G mutation in the spike protein was the commonest at the amino acid level. Most importantly, we identified some amino acid mutations in positions S, ORF7 b, and ORF9 b, and they have neither been reported on the Global Initiative of Sharing All Influenza Data nor published in Pub Med among all missense mutations.Conclusion These results suggested the diversity of lineages and sublineages and the high homology at the amino acid level among imported cases infected with SARS-Co V-2 in Guangdong Province, China.