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Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008

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Abstract

Rotavirus A strains detected in diarrhoeal children commonly possess any one of the genotypes G1, G2, G3, G4, and G9, with a recent increase in G12 detection globally. G12P[6] strains possessing short RNA (DS-1-like) and long RNA (Wa-like) migration patterns accounted for 27 % of the strains circulating in Blantyre, Malawi, between 2007 and 2008. To understand how the G12P[6] strains with two distinct genetic backgrounds emerged in Malawi, we conducted whole-genome analysis of two long-RNA and two short-RNA strains. While the former had a typical Wa-like genotype constellation of G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, the latter was found to have G12-P[6]-I2-R2-C2-M1-A2-N2-T2-E2-H2: a VP3 gene mono-reassortant on the DS-1-like backbone. Phylogenetic and Bayesian Markov chain Monte Carlo analyses showed that the short-RNA G12P[6] strains were generated around 2006 by reassortment between an African Wa-like G12P[6] strain donating three genes (the VP7, VP4, and VP3 genes) and a G2P[4] strain similar to the one circulating in Thailand or the United States of America that donated the remaining eight genes. On the other hand, the long-RNA strains were generated as a result of reassortment events within Wa-like G12 and non-G12 strains commonly circulating in Africa; only the VP4 gene was from a Malawian G8P[6] strain. In conclusion, this study uncovered the evolutionary pathways through which two distinct G12P[6] strains emerged in Malawi.

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Acknowledgments

The clinical trial of Rotarix® in Malawi, through which the strains characterised in this study were identified, was supported by PATH’s Rotavirus Vaccine Program (funded by GAVI) and by GlaxoSmithKline Biologicals. This study was performed under the Agreement on Academic Partnership between The University of Liverpool and Nagasaki University.

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Author notes

  1. L. P. Do

    Present address: Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam

  2. Y. H. Doan

    Present address: Department of Virology 2, National Institute of Infectious Diseases, Tokyo, Japan

Authors and Affiliations

  1. Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan

    T. Nakagomi, L. P. Do, C. A. Agbemabiese, M. Kaneko, P. Gauchan, Y. H. Doan & O. Nakagomi

  2. Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK

    T. Nakagomi, K. C. Jere, M. Iturriza-Gomara, O. Nakagomi & N. A. Cunliffe

  3. Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi

    K. C. Jere

  4. Vaccines and Immunization, PATH, Seattle, WA, 98121, USA

    A. D. Steele

  5. MRC Diarrhoeal Pathogens Research Unit, MEDUNSA, University of Limpopo, Pretoria, South Africa

    A. D. Steele

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  1. T. Nakagomi
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Correspondence to T. Nakagomi.

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Funding

This study was supported by a Grant-in-aid for overseas scientific research from Japan Society for the Promotion of Science awarded to Toyoko Nakagomi (No. 22406014). This study was also supported by the Global Centre of Excellence Program on Integrated Global Control Strategy for Tropical and Emerging Infectious Diseases from the Ministry of Education, Culture, Sports, Science and Technology, Japan.

Conflict of interest

The authors declare that they have no conflict of interest regarding this study.

Ethical approval and informed consent

This study was performed in accordance with the ethical standards of the review boards of all relevant institutions. Informed consent was obtained from the parents/guardians of all individual participants included in the original study. The use of specimens for this study was also approved by both PATH and GlaxoSmithKline Biologicals.

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Nakagomi, T., Do, L.P., Agbemabiese, C.A. et al. Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008. Arch Virol 162, 213–226 (2017). https://doi.org/10.1007/s00705-016-3103-5

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