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为了解安徽省新型冠状病毒（SARS-CoV-2）奥密克戎变异株流行趋势和进化规律，本研究选取了2023年3月至9月安徽省皖北、皖中和皖南地区共计365份本土新冠病毒感染确诊病例，利用高通量测序技术开展SARS-CoV-2全基因组测序。将获得的高质量序列通过Pangolin和Nextclade网站对SARS-CoV-2分型和突变位点进行统计分析。监测期间安徽省不同区域奥密克戎变异株构成存在时间差异：在监测前期到中期，皖北地区优势株由XBB.1.16及其亚分支发展为XBB.1.22及其亚分支；皖中地区由BA.5.2及其亚分支发展为FE.1及其亚分支；而皖南地区由XBB.1.22及其亚分支发展为FE.1及其亚分支，在监测后期不同区域优势株均以EG.5及其亚分支占主导。受到地理文化气候等多因素影响，不同区域的变异株构成也存在空间差异，合肥市和亳州市的奥密克戎变异株亚型相对更多。安徽省不同区域奥密克戎变异株基因组平均核苷酸突变位点数随时间逐渐增加，主要伴随着S蛋白的突变。本研究结合安徽省区域特征分析了奥密克戎变异株的流行特征，为新冠病毒感染防控措施的制定提供重要理论支持。
Abstract：To understand the epidemiological trends and evolutionary dynamics of SARS-CoV-2 Omicronvariants in Anhui Province, this study analyzed 365 confirmed local COVID-19 cases from northern, central andsouthern Anhui Province, China between March and September 2023. Whole genome sequencing of SARS-CoV-2 was performed using high-throughput sequencing technology. The high-quality sequences obtained wereanalyzed variant typing and mutation sites through the Pangolin and Nextclade platforms. Temporal differencesin the composition of Omicron variants were observed across different regions of Anhui Province, China duringthe monitoring period. In the early to middle stages, the dominant strain in northern Anhui evolved fromXBB.1.16 and its sub-lineages to XBB.1.22 and its sub-lineages. In central Anhui, the dominant strain evolvedfrom BA.5.2 and its sub-lineages to FE.1 and its sub-lineages. In southern Anhui, the dominant strain evolvedfrom XBB.1.22 and its sub-lineages to FE.1 and its sub-lineages. By the late stage, EG.5 and its sub-lineagesbecame the dominant strains across all regions. Geographic, cultural, and climatic factors contributed to spatialdifferences in the composition of Omicron variants, with Hefei and Bozhou, China exhibiting a greater diversityof subtypes. The average number of nucleotide mutations in Omicron variant genomes from different regionsincreased over time, primarily driven by mutations in the spike(S) protein. This study based on the regionalcharacteristics of Anhui Province, analyzed the epidemiological features of Omicron variants, providingimportant theoretical support for the development of COVID-19 preventive and control measures.
[1] Kim D, Lee JY, Yang JS, et al. The architecture of SARS-CoV-2 transcriptome[J]. Cell, 2020, 181(4):914-921. e10. DOI:10. 1016/j. cell. 2020. 04. 011.
[2] Abu Turab Naqvi A, Fatima K, Mohammad T, et al.Insights into SARS-CoV-2 genome, structure,evolution, pathogenesis and therapies:structural genomics approach[J]. Biochim Biophys Acta Mol Basis Dis, 2020, 1866(10):165878. DOI:10. 1016/j.bbadis. 2020. 165878.
[3] Telenti A, Arvin A, Corey L, et al. After the pandemic:perspectives on the future trajectory of COVID-19[J]. Nature, 2021, 596:495-504. DOI:10. 1038/s41586-021-03792-w.
[4] Zhang Y, Zhang H, Zhang W. SARS-CoV-2 variants,immune escape, and countermeasures[J]. Front Med,2022, 16(2):196-207. DOI:10. 1007/s11684-021-0906-x.
[5] World Health Organization. Classification of Omicron(B. 1. 1. 529):SARS-CoV-2 Variant of Concern[EB/OL].(2021-11-26)[2024-05-22]. https：//www. who.int/news/item/26-11-2021-classification-of-omicron-（b. 1. 1. 529）-sars-cov-2-variant-of-concern
[6] Kandeel M, Mohamed MEM, Abd El-Lateef HM, et al. Omicron variant genome evolution and phylogenetics[J]. J Med Virol, 2022, 94(4):1627-1632. DOI:10. 1002/jmv. 27515.
[7]吴俣，刘珏，刘民，等.新型冠状病毒Omicron变异株的流行病学特征及其科学防控建议[J].中华疾病控制杂志，2022, 26(5):497-501. DOI:10. 16462/j. cnki.zhjbkz. 2022. 05. 001.
[8] Pan Y, Wang L, Feng Z, et al. Characterisation of SARS-CoV-2 variants in Beijing during 2022:an epidemiological and phylogenetic analysis[J]. Lancet,2023, 401(10377):664-672. DOI:10. 1016/s0140-6736(23)00129-0.
[9]国家卫生健康委员会．关于进一步优化落实新冠肺炎疫情防控措施的通知[EB/OL].(2022-12-07)[2024-05-22]. http：//www. nhc. gov. cn/xcs/gzzcwj/202212/8278e7a7aee34e5bb378f0e0fc94e0f0. shtml.
[10]国家卫生健康委员会．关于印发《新型冠状病毒感染“乙类乙管”疫情监测方案》等5个文件的通知[EB/OL].(2022-12-26)[2024-05-22]. http：//www. nhc.gov. cn/xcs/zhengcwj/202212/ce0210b36e314e4e846a940bd859b828. shtml.
[11]PangoNetwork. Cov-Lineages[EB/OL].(2024-05-20)[2024-05-22]. https：//cov-lineages. org/lineage_list.html.
[12]Dejnirattisai W, Huo J, Zhou D, et al. SARS-CoV-2Omicron-B. 1. 1. 529 leads to widespread escape from neutralizing antibody responses[J]. Cell, 2022, 185(3):467-484. e15. DOI:10. 1016/j.cell. 2021. 12. 046.
[13]Lu R, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus:implications for virus origins and receptor binding[J].Lancet, 2020, 395(10224):565-574. DOI:10. 1016/S0140-6736(20)30251-8.
[14]Worobey M, Pekar J, Larsen BB, et al. The emergence of SARS-CoV-2 in Europe and North America[J]. Science, 2020, 370(6516):564-570.DOI:10. 1126/science. abc8169.
[15]Hadfield J, Megill C, Bell SM, et al. Nextstrain:realtime tracking of pathogen evolution[J]. Bioinformatics,2018, 34(23):4121-4123. DOI:10. 1093/bioinformatics/bty407.
[16]刘晓瑜，魏永伟. SARS-CoV-2 S蛋白：研究进展与挑战[J].病毒学报，2020, 36(6):1157-1164. DOI:10. 13242/j. cnki. bingduxuebao. 003787.
[17]Hulswit RJ, de Haan CA, Bosch BJ. Coronavirus spike protein and tropism changes[J]. Adv Virus Res, 2016,96:29-57. DOI:10. 1016/bs. aivir. 2016. 08. 004.
[18]Chen J, Wang R, Hozumi Y, et al. Emerging dominant SARS-CoV-2 variants[J]. J Chem Inf Model, 2023, 63(1):335-342. DOI:10. 1021/acs. jcim. 2c01352.
[19]Zhang L, Mann M, Syed ZA, et al. Furin cleavage of the SARS-CoV-2 spike is modulated by O-glycosylation[J]. Proc Natl Acad Sci U S A, 2021, 118(47):e2109905118. DOI:10. 1073/pnas. 2109905118.
[20]Gupta R. SARS-CoV-2 Omicron spike mediated immune escape and tropism shift[J]. Res Sq, 2022.DOI:10. 21203/rs. 3. rs-1191837/v1.
[21]Gangavarapu K, Abdel Latif A, Mullen JL, et al.Outbreak. info genomic reports:scalable and dynamic surveillance of SARS-CoV-2 variants and mutations[J].Res Sq, 2022. DOI:10. 21203/rs. 3. rs-1723829/v1.
基本信息:
DOI：10.13242/j.cnki.bingduxuebao.004629
中图分类号:R373
引用信息:
[1]刘涓涓,吴小珉,宋永庆等.安徽省不同区域新冠病毒奥密克戎变异株分子流行病学特征分析[J].病毒学报,2025,41(03):693-701.DOI:10.13242/j.cnki.bingduxuebao.004629.
基金信息:
2022年度安徽省卫生健康委科研项目(项目号:AHWJ2022b016),题目:基于超分支滚环等温扩增介导荧光偏振双模态新冠病毒精准检测及单碱基变异筛查技术研究; 安徽省新型冠状病毒肺炎疫情应急科研攻关(项目号:202004a07020004),题目:新型冠状病毒基因分子变异与进化研究; 安徽农业大学茶树生物学与资源利用国家重点实验室开放基金资助项目(项目号:SKLTOF20200131),题目:EGCG及其氧化产物对新型冠状病毒抑制作用研究~~