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Volume 41 Issue 4
August 2026
    Citation: Yuqing Zhou, Xiao Wang, Lu Zhang, Yang Yuan, Tianchun Liu, Yuqin Yang, Yingjie Zheng, Bing Zhao. Whole-genome evolutionary dynamics of human parainfluenza virus type 3 in Shanghai, China, 2016-2024 .VIROLOGICA SINICA, 2026, 41(4) : 993-998.  http://dx.doi.org/10.1016/j.virs.2026.07.005
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    Whole-genome evolutionary dynamics of human parainfluenza virus type 3 in Shanghai, China, 2016-2024

    • a. Shanghai Pudong New Area Center for Disease Control and Prevention (Shanghai Pudong New Area Health Supervision Institute), Shanghai 200136, China;

    • b. Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China;

    • c. Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China;

    • d. Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai 200032, China;

    • e. Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China

    • Highlights
      1 Fifty whole-genome sequencing revealed co-circulating HPIV-3 C3 sub-lineages C3f and C3a in Shanghai, China.
      2 Whole-genome phylogeny dated the HPIV-3 tMRCA to ~1925.6 and revealed two post-1990 demographic expansions.
      3 Recombination signals detected in the HN gene and other regions may lead to discordance in partial-gene phylogenies.
      4 The L gene showed the highest variability and harbored the largest number of putative positively selected sites.
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      10.1016j.virs.2026.07.005-ESM3.xlsx
      10.1016j.virs.2026.07.005-ESM1.docx
      10.1016j.virs.2026.07.005-ESM4.xlsx
      10.1016j.virs.2026.07.005-ESM2.xlsx

      1. Aso, J., Kimura, H., Ishii, H., Saraya, T., Kurai, D., Nagasawa, K., Matsushima, Y., Ryo, A., Takizawa, H., 2020. Molecular evolution of the hemagglutinin-neuraminidase (HN) gene in human respirovirus 3. Virus Res. 277, 197824.

      2. Bose, M.E., Shrivastava, S., He, J., Nelson, M.I., Bera, J., Fedorova, N., Halpin, R., Town, C.D., Lorenzi, H.A., Amedeo, P., Gupta, N., Noyola, D.E., Videla, C., Kok, T., Buys, A., Venter, M., Vabret, A., Cordey, S., Henrickson, K.J., 2019. Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes. PLOS ONE 14, e0220057.

      3. Elusah, J., Bulimo, W.D., Opanda, S.M., Symekher, S.L., Wamunyokoli, F., 2020. Genetic diversity and evolutionary analysis of human respirovirus type 3 strains isolated in Kenya using complete hemagglutinin-neuraminidase (HN) gene. PLOS ONE 15, e0229355.

      4. Godoy, C., Peremiquel-Trillas, P., Andres, C., Gimferrer, L., Uriona, S.M., Codina, M.G., Armadans, L., Martin, M.D.C., Fuentes, F., Esperalba, J., Campins, M., Pumarola, T., Anton, A., 2016. A molecular epidemiological study of human parainfluenza virus type 3 at a tertiary university hospital during 2013-2015 in Catalonia, Spain. Diagn. Microbiol. Infect. Dis. 86, 153-159.

      5. Greenbaum, B.D., Ghedin, E., 2015. Viral evolution: beyond drift and shift. Curr. Opin. Microbiol. 26, 109-115.

      6. Guo, Y., Li, L., Lai, Q., Wang, Y., Li, W., 2024. Molecular Epidemiology of Human Parainfluenza Virus Type 3 in Children With Acute Respiratory Tract Infection in Hangzhou. Influenza Other Respir. Viruses 18, e13351.

      7. Guo, Y.N., De, R., Wang, F.M., Han, Z.Z., Liu, L.Y., Sun, Y., Yao, Y., Ma, X.L., Liu, S., Zhu, C., Qu, D., Zhao, L.Q., 2025. Molecular Characterization of New Recombinant Human Adenoviruses Detected in Children with Acute Respiratory Tract Infections in Beijing, China, 2022-2023. Biomed. Environ. Sci. BES 38, 1071-1081.

      8. Han, J.Y., Suh, W., Han, S.B., 2022. Seasonal epidemiological and clinical characteristics of pediatric patients with human parainfluenza virus infection by serotype: a retrospective study. Virol. J. 19, 141.

      9. Lefkowitz, E.J., Dempsey, D.M., Hendrickson, R.C., Orton, R.J., Siddell, S.G., Smith, D.B., 2018. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res. 46, D708-D717.

      10. Matsumoto, Y., Ohta, K., Yumine, N., Goto, H., Nishio, M., 2015. Identification of two essential aspartates for polymerase activity in parainfluenza virus L protein by a minireplicon system expressing secretory luciferase. Microbiol. Immunol. 59, 676-683.

      11. Russell, C.J., Simoes, E.A.F., Hurwitz, J.L., 2018. Vaccines for the Paramyxoviruses and Pneumoviruses: Successes, Candidates, and Hurdles. Viral Immunol. 31, 133-141.

      12. Shao, N., Liu, B., Xiao, Y., Wang, X., Ren, L., Dong, J., Sun, L., Zhu, Y., Zhang, T., Yang, F., 2021. Genetic Characteristics of Human Parainfluenza Virus Types 1-4 From Patients With Clinical Respiratory Tract Infection in China. Front. Microbiol. 12, 679246.

      13. Stearns, K., Lampe, G., Hanan, R., Marcink, T., Niewiesk, S., Sternberg, S.H., Greninger, A.L., Porotto, M., Moscona, A., 2024. Human parainfluenza virus 3 field strains undergo extracellular fusion protein cleavage to activate entry. mBio 15, e0232724.

      14. Takahashi, M., Nagasawa, K., Saito, K., Maisawa, S.-I., Fujita, K., Murakami, K., Kuroda, M., Ryo, A., Kimura, H., 2018. Detailed genetic analyses of the HN gene in human respirovirus 3 detected in children with acute respiratory illness in the Iwate Prefecture, Japan. Infect. Genet. Evol. J. Mol. Epidemiol. Evol. Genet. Infect. Dis. 59, 155-162.

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      Whole-genome evolutionary dynamics of human parainfluenza virus type 3 in Shanghai, China, 2016-2024

        Corresponding author: Yingjie Zheng, yjzheng@fudan.edu.cn
        Corresponding author: Bing Zhao, zerg8424@hotmail.com
      • a. Shanghai Pudong New Area Center for Disease Control and Prevention (Shanghai Pudong New Area Health Supervision Institute), Shanghai 200136, China;
      • b. Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China;
      • c. Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200032, China;
      • d. Key Laboratory for Health Technology Assessment, National Commission of Health and Family Planning, Fudan University, Shanghai 200032, China;
      • e. Laboratory of Public Health Safety, Ministry of Education, School of Public Health, Fudan University, Shanghai 200032, China
      • Received Date: 24 December 2025
      • Accepted Date: 08 July 2026

      Abstract: Highlights
      1 Fifty whole-genome sequencing revealed co-circulating HPIV-3 C3 sub-lineages C3f and C3a in Shanghai, China.
      2 Whole-genome phylogeny dated the HPIV-3 tMRCA to ~1925.6 and revealed two post-1990 demographic expansions.
      3 Recombination signals detected in the HN gene and other regions may lead to discordance in partial-gene phylogenies.
      4 The L gene showed the highest variability and harbored the largest number of putative positively selected sites.

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