Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Apr 17;25(1):378.
doi: 10.1186/s12864-024-10246-w.

Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022

Qiang Yin  1 , Wei Liu  1 , Yajuan Jiang  1 , Qiang Feng  2 , Xiaoyu Wang  1 , Huixin Dou  1 , Zanzan Liu  1 , Feifei He  3 , Yingying Fan  4 , Baihai Jiao  5 , Boyan Jiao  6
Affiliations

Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022

Qiang Yin et al. BMC Genomics. .

Abstract

Objective: This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China.

Methods: Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites.

Results: All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites.

Conclusion: SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.

Keywords: Molecular features; Omicron; SARS-CoV-2; Termination mutation; Whole genome sequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
.
Fig. 2
Fig. 2
.
Fig. 3
Fig. 3
.
Fig. 4
Fig. 4
.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Vallee A. Geoepidemiological perspective on COVID-19 pandemic review, an insight into the global impact. Front Public Health. 2023;11:1242891. doi: 10.3389/fpubh.2023.1242891. - DOI - PMC - PubMed
    1. Koelle K, Martin MA, Antia R, Lopman B, Dean NE. The changing epidemiology of SARS-CoV-2. Science. 2022;375(6585):1116–21. doi: 10.1126/science.abm4915. - DOI - PMC - PubMed
    1. Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, et al. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci. 2023;14(23):6149–206. doi: 10.1039/d2sc06665c. - DOI - PMC - PubMed
    1. Ghosh N, Nandi S, Saha I. A review on evolution of emerging SARS-CoV-2 variants based on spike glycoprotein. Int Immunopharmacol. 2022;105:108565. doi: 10.1016/j.intimp.2022.108565. - DOI - PMC - PubMed
    1. Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. 2022;603(7902):679–86. doi: 10.1038/s41586-022-04411-y. - DOI - PMC - PubMed

Supplementary concepts