Whole-genome sequencing and genetic characterization of 200 novel coronavirus cases in Baiyin city in 2023

Yanbo WANG; Hongdong MA; Yaqian YANG; Xiaomei ZHANG; Dan SONG; Baodi LI

doi:10.11847/zgggws1143980

Zhongguo gonggong weisheng (Aug 2024)

Whole-genome sequencing and genetic characterization of 200 novel coronavirus cases in Baiyin city in 2023

Yanbo WANG,
Hongdong MA,
Yaqian YANG,
Xiaomei ZHANG,
Dan SONG,
Baodi LI

Affiliations

Yanbo WANG: Department of Laboratory Testing, Baiyin Municipal Center for Disease Control and Prevention, Baiyin 730900, China
Hongdong MA: Department of Laboratory Testing, Baiyin Municipal Center for Disease Control and Prevention, Baiyin 730900, China
Yaqian YANG: Department of Laboratory Testing, Baiyin Municipal Center for Disease Control and Prevention, Baiyin 730900, China
Xiaomei ZHANG: Department of Laboratory Testing, Baiyin Municipal Center for Disease Control and Prevention, Baiyin 730900, China
Dan SONG: Department of Laboratory Testing, Baiyin Municipal Center for Disease Control and Prevention, Baiyin 730900, China
Baodi LI: Gansu Provincial Key Laboratory of Pathogen for Infectious Diseases, Gansu Provincial Center for Disease Control and Prevention, Lanzhou 730000, China

DOI: https://doi.org/10.11847/zgggws1143980
Journal volume & issue: Vol. 40, no. 8
pp. 1006 – 1012

Abstract

Read online

ObjectiveTo analyze the prevalence and genetic variations of SARS-CoV-2 variants in Baiyin city, Gansu province in 2023, and provide scientific basis for epidemic prevention and control and vaccine development. MethodsA total of 200 nasal/oropharyngeal swab samples were collected from COVID-19 cases who visited medical institutions, were hospitalized, or under monitoring in Baiyin city, Gansu province from January to September 2023. Next-generation sequencing technology was used for whole-genome sequencing. MGI metargetCOVID software was used for sequence assembly analysis and Pangolin platform for typing. FREEBAYES was used to detect mutation sites, and annotation was performed based on NIRVANA. MAFFT software was used for multiple sequence alignment, and IQTREE was used to construct the phylogenetic tree. GGTREE and GGTREEEXTRA software were used for visualization analysis of the phylogenetic tree and related clinical information. ResultsFrom January to September 2023, all detected SARS-CoV-2 in Baiyin city were Omicron variants, with BA.5.2 (32 cases, 100.00%) in the first quarter (January-March), mainly XBB (56 cases, 62.92%) and FL (20 cases, 22.47%) families in the second quarter (April-June), and mainly dominated by EG.5.1.1 (52 cases, 65.82%) in the third quarter (July-September). Forty-two mutation sites were significantly enriched in moderate cases, including 25 mutations in the ORF1ab gene, 9 mutations in the S gene, 3 mutations each in the ORF3a and ORF8 genes, and 2 mutations in the N gene. ConclusionThe SARS-CoV-2 genomes circulating in Baiyin city were in different branches from the Wuhan reference strain and were basically consistent with the Pangolin typing lineages and input time. There were genetic associations between different clinical symptoms, and the association of vaccination and previous infection with the phylogenetic tree was not significant.

Published in Zhongguo gonggong weisheng

ISSN: 1001-0580 (Print)
Publisher: Editorial Office of Chinese Journal of Public Health
Country of publisher: China
LCC subjects: Medicine: Public aspects of medicine
Website: https://www.zgggws.com/indexen.htm

About the journal

Abstract

Keywords