Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023
文献类型：期刊论文
| 作者 | Shah, Pir Tariq4,5; Ejaz, Mohammad3; Tamanna, Kosar2; Riaz, Muhammad Nasir2; Wu, Zhenyong1,4; Wu, Chengjun5 |
| 刊名 | VIRUS RESEARCH
 |
| 出版日期 | 2024-08-01 |
| 卷号 | 346页码:12 |
| 关键词 | JC polyomavirus Classification Clustering Recombination Variation |
| ISSN号 | 0168-1702 |
| DOI | 10.1016/j.virusres.2024.199414 |
| 通讯作者 | Wu, Zhenyong(wuzhenyong@simm.ac.cn) ; Wu, Chengjun(wcj5532@dlut.edu.cn) |
| 英文摘要 | The human JC polyomavirus (JCV) is a widespread, neurotropic, opportunistic pathogen responsible for progressive multifocal leukoencephalopathy (PML) as well as other diseases in immunosuppressed individuals, including granule cell neuronopathy, JCV-associated nephropathy, encephalitis, and meningitis in rare cases. JCV classification is still unclear, where the ICTV (International Committee on Taxonomy of Viruses) has grouped all the strains into human polyomavirus 2, with no classification on clade and subclade levels. Therefore, JCV strains were previously classified using different genomic regions, e.g., full-length, VP1, and the V-T intergenic region etc., and the strains were grouped into several types related to various geographic locations and human ethnicities. However, neither of these classifications and nomenclature contemplates all the groups described so far. Herein, we evaluated all the available full-length coding genomes, VP1, and large T antigen nucleotide sequences of JCV reported during 1993-2023 and classified them into four major phylogenetic clades, i.e., GI-GIV, where GI is further grouped into two types GI.1 and GI.2 with five sub-clades each (GI.1/GI.2 a-e), GII into three (GII a-c), GIII as a separate clade, and GIV into seven sub-clades (GIV a-g). Similarly, the phylogeographic network analysis indicated four major clusters corresponding to GI-GIV clades, each with multiple subclusters and mutational sub-branches corresponding to the subclades. GI and GIV clusters are connected via GI.1-e reported from Europe and America, GII, GIII and GIV clusters are connected by GII-b and GII-c strains reported from Africa, while GIV cluster strains are connected to the Russia-Italy JCV haplotype. Furthermore, we identified JCV-variant-GS/B-Germany-1997 (GenBank ID: AF004350.1) as an inter-genotype recombinant having major and minor parents in the GI.1-e and GII-a clades, respectively. Additionally, the amino acid variability analysis revealed high entropy across all proteins. The large T antigen exhibited the highest variability, while the small t antigen showed the lowest variability. Our phylogenetic and phylogeographic analyses provide a new approach to genotyping and sub-genotyping and present a comprehensive classification system of JCV strains based on their genetic characteristics and geographic distribution, while the genetic recombination and amino acid variability can help identify pathogenicity and develop effective preventive and control measures against JCV infections. |
| WOS关键词 | PROGRESSIVE MULTIFOCAL LEUKOENCEPHALOPATHY ; VIRUS-DNA ; CONTROL REGION ; EVOLUTION ; ARCHETYPAL ; BRAIN ; EPIDEMIOLOGY ; POPULATION ; PREVALENCE ; ANTIBODIES |
| 资助项目 | National Natural Science Foundation of China[82072287] ; National Natural Science Foundation of China[32371283] ; Taishan Scholars Program[E31108R0Y5] ; Special Supporting Funds for Leading Talents at or above the Provincial level in Yantai City[E32012R0Y5] |
| WOS研究方向 | Virology |
| 语种 | 英语 |
| WOS记录号 | WOS:001253274300001 |
| 出版者 | ELSEVIER |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/312026]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Wu, Zhenyong; Wu, Chengjun |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Mat Med, Shanghai 201203, Peoples R China 2.Hazara Univ, Dept Microbiol, Mansehra 21300, Pakistan 3.Govt Postgrad Coll Mandian, Dept Microbiol, Abbottabad, Pakistan 4.Bohai Rim Adv Res Inst Drug Discovery, Shandong Lab Yantai Drug Discovery, Yantai 264000, Shandong, Peoples R China 5.Dalian Univ Technol, Fac Med, Sch Basic Med, 2 Linggong Rd, Dalian 116024, Liaoning, Peoples R China |
| 推荐引用方式 GB/T 7714 | Shah, Pir Tariq,Ejaz, Mohammad,Tamanna, Kosar,et al. Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023[J]. VIRUS RESEARCH,2024,346:12. |
| APA | Shah, Pir Tariq,Ejaz, Mohammad,Tamanna, Kosar,Riaz, Muhammad Nasir,Wu, Zhenyong,&Wu, Chengjun.(2024).Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023.VIRUS RESEARCH,346,12. |
| MLA | Shah, Pir Tariq,et al."Insights into the genetic characteristics, clustering patterns, and phylogeographic dynamics of the JC polyomavirus, 1993 to 2023".VIRUS RESEARCH 346(2024):12. |
入库方式： OAI收割
来源：上海药物研究所
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