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Genome sequencing and phylogenetic reconstruction reveal a potential fourth rhinovirus species and its worldwide distribution

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Abstract

Genome sequences of members of a potential fourth rhinovirus (RV) species, provisionally denoted as rhinovirus A clade D, from patients with acute respiratory infection were determined. Bayesian coalescent analysis estimated that clade D emerged around the 1940s and diverged further around 2006-2007 into two distinctive sublineages (RV-A8-like and RV-A45-like) that harbored unique “clade-defining” substitutions. Similarity plots and bootscan mapping revealed a recombination breakpoint located in the 5ʹ-UTR region of members of the RV-A8-like sublineage. Phylogenetic reconstruction revealed the distribution of clade D viruses in the Asia Pacific region and in Europe, underlining its worldwide distribution.

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Acknowledgements

This work was supported in part by grants from the Ministry of Higher Education, Malaysia: High Impact Research UM.C/625/1/HIR/MOE/CHAN/02/02 to K.K.T and Postgraduate Research Fund (PG097-2015A) to K.T.N. We would like to thank Ann C. Palmenberg (University of Wisconsin) for discussion and advice.

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Authors and Affiliations

  1. Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

    Kim Tien Ng & Adeeba Kamarulzaman

  2. Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore

    Kim Tien Ng

  3. Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

    Yutaka Takebe & Kok Keng Tee

  4. AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan

    Yutaka Takebe

  5. School of Healthcare and Medical Sciences, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia

    Kok Keng Tee

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  1. Kim Tien Ng
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  2. Yutaka Takebe
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Correspondence to Kok Keng Tee.

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Ng, K.T., Takebe, Y., Kamarulzaman, A. et al. Genome sequencing and phylogenetic reconstruction reveal a potential fourth rhinovirus species and its worldwide distribution. Arch Virol 166, 225–229 (2021). https://doi.org/10.1007/s00705-020-04855-5

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  • DOI: https://doi.org/10.1007/s00705-020-04855-5

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