. doi: 10.1016/j.virs.2026.05.005
Citation: Shan Lu, Pei-Yu Zhen, Cai Bian, Ming-Zhu Zhang, Nan-Nan Yao, Xiao-Ling Su, Yu-Tong Huang, Chen Shan, Jia-Yi Pan, Lin Zhao, Yuan-Chun Zheng, Jia-Fu Jiang, Xiao-Min Zheng, Run-Ze Ye, Wu-Chun Cao. Identification and geographic evolutionary analysis of human pegivirus infection based on metatranscriptomic sequencing .VIROLOGICA SINICA, 2026, 41(3) : 711-715.  http://dx.doi.org/10.1016/j.virs.2026.05.005

基于宏转录组测序的人类Pegivirus感染鉴定与地理进化分析

  • Pegivirus hominis(HPgV)是一种单股正链RNA病毒,在人群中可与多种病毒共感染,但其遗传多样性和地理进化特征尚未充分阐明。本研究基于宏转录组测序,对中国黑龙江省人群中HPgV感染进行鉴定及系统发育分析。研究纳入了2023至2024年夏季在黑龙江省哨点医院主动监测患者的血清样本,通过宏转录组测序及基因组组装后进行系统发育分析,阳性病例经RT-PCR和Sanger测序确认。结合GenBank中公开发表的HPgV序列,对其进行地理进化和氨基酸变异特征分析。研究分别从5名受试者中获得了5条全长HPgV基因组,系统发育分析证实其均属于HPgV基因3型,该基因型主要分布于中国和日本等东亚地区。地理进化分析显示HPgV基因型存在空间聚集性,值得注意的是部分序列在NS4A区域并未与HPgV基因3型聚集。氨基酸比对鉴定出10个特异性突变位点。本研究为东亚地区HPgV的遗传多样性特征提供了新的见解。

Identification and geographic evolutionary analysis of human pegivirus infection based on metatranscriptomic sequencing

  • Highlights
    1 First report of HPgV genotype 3 strains in Heilongjiang, China, revealing its genetic diversity in East Asia.
    2 Phylogeographic analysis demonstrated spatial clustering in the distribution of human pegivirus genotypes 1-6.
    3 Identified an anomalous evolutionary branch in the NS4A region and ten specific amino acid mutation sites.
    4 Subgenomic alignments yield different lineage calls, necessitating full-length genomes for accurate genotyping.

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    1. Anggorowati, N., Yano, Y., Subronto, Y.W., Utsumi, T., Heriyanto, D.S., Mulya, D.P., Rinonce, H.T., Widasari, D.I., Lusida, M.I., Soetjipto, Hayashi, Y., 2013. GB virus C infection in Indonesian HIV-positive patients. Microbiol Immunol 57, 298-308.

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    3. Chivero, E.T., Stapleton, J.T., 2015. Tropism of human pegivirus (formerly known as GB virus C/hepatitis G virus) and host immunomodulation: insights into a highly successful viral infection. J Gen Virol 96, 1521-1532.

    4. Fama, A., Larson, M.C., Link, B.K., Habermann, T.M., Feldman, A.L., Call, T.G., Ansell, S.M., Liebow, M., Xiang, J., Maurer, M.J., Slager, S.L., Nowakowski, G.S., Stapleton, J.T., Cerhan, J.R., 2020. Human pegivirus infection and lymphoma risk: a systematic review and meta-analysis. Clin Infect Dis 71, 1221-1228.

    5. He, J., Yang, L., Niu, C., 2025. Human pegivirus detected in patient with reversible severe encephalitis and axillary lymphadenopathy: a case report. Diagn Pathol 20, 66.

    6. Nunnari, G., Nigro, L., Palermo, F., Attanasio, M., Berger, A., Doerr, H.W., Pomerantz, R.J., Cacopardo, B., 2003. Slower progression of HIV-1 infection in persons with GB virus C co-infection correlates with an intact T-helper 1 cytokine profile. Ann Intern Med 139, 26-30.

    7. Rey, D., Vidinic-Moularde, J., Meyer, P., Schmitt, C., Fritsch, S., Lang, J.M., Stoll-Keller, F., 2000. High prevalence of GB virus C/hepatitis G virus RNA and antibodies in patients infected with human immunodeficiency virus type 1. Eur J Clin Microbiol Infect Dis 19, 721-724.

    8. Simmonds, P., Butkovic, A., Grove, J., Mayne, R., Mifsud, J.C.O., Beer, M., Bukh, J., Drexler, J.F., Kapoor, A., Lohmann, V., Smith, D.B., Stapleton, J.T., Vasilakis, N., Kuhn, J.H., 2025. Taxonomic expansion and reorganization of Flaviviridae. Nat Microbiol 10, 3026-3037.

    9. Stapleton, J.T., Chaloner, K., Martenson, J.A., Zhang, J., Klinzman, D., Xiang, J., Sauter, W., Desai, S.N., Landay, A., 2012. GB virus C infection is associated with altered lymphocyte subset distribution and reduced T cell activation and proliferation in HIV-infected individuals. PLoS One 7, e50563.

    10. Takayama, S., Miura, T., Tominaga, T., Taki, M., Matsuo, S., Sugii, S., Shimotohno, K., 1999. Partial nucleotide sequencing of the NS3/helicase region of hepatitis G virus to prove vertical transmission. FEMS Microbiol Lett 175, 273-279.

    11. Tillmann, H.L., Manns, M.P., 2001. GB virus-C infection in patients infected with the human immunodeficiency virus. Antiviral Res 52, 83-90.

    12. Tuddenham, R., Eden, J.S., Gilbey, T., Dwyer, D.E., Jennings, Z., Holmes, E.C., Branley, J.M., 2020. Human pegivirus in brain tissue of a patient with encephalitis. Diagn Microbiol Infect Dis 96, 114898.

    13. Wang, T., Chen, J., Zhang, Q., Huang, X., Xie, N., Zhang, J., Cai, T., Zhang, Y., Xiong, H., 2019. Prevalence of hepatitis G virus infection among 67,348 blood donors in mainland China. BMC Public Health 19, 685.

    14. Yang, N., Dai, R., Zhang, X., 2020. Global prevalence of human pegivirus-1 in healthy volunteer blood donors: a systematic review and meta-analysis. Vox Sang 115, 107-119.

    15. Zhou, B., Ma, W., Wang, H., Fu, Y., Xu, L., Lu, L., Jiang, F., Peng, W., 1997. [Investigation on hepatitis G virus (HGV) infection among different populations in Shenzhen]. Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi 11, 348-351.

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    Identification and geographic evolutionary analysis of human pegivirus infection based on metatranscriptomic sequencing

      Corresponding author: Xiao-Min Zheng, hfbzxm@163.com
      Corresponding author: Run-Ze Ye, runze.ye@mail.sdu.edu.cn
      Corresponding author: Wu-Chun Cao, caowuchun@126.com
    • a. Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China;
    • b. Mudanjiang Forestry Central Hospital, Mudanjiang 157000, China;
    • c. State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China;
    • d. Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan 250012, China;
    • e. Shandong Provincial Key Laboratory of Intelligent Monitoring, Early Warning, Prevention and Control for Infectious Diseases, Jinan 250012, China

    Abstract: Highlights
    1 First report of HPgV genotype 3 strains in Heilongjiang, China, revealing its genetic diversity in East Asia.
    2 Phylogeographic analysis demonstrated spatial clustering in the distribution of human pegivirus genotypes 1-6.
    3 Identified an anomalous evolutionary branch in the NS4A region and ten specific amino acid mutation sites.
    4 Subgenomic alignments yield different lineage calls, necessitating full-length genomes for accurate genotyping.

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