title: Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008.
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.
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. tnakagom@nagasaki-u.ac.jp.|Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. tnakagom@nagasaki-u.ac.jp.
authors.forename: T
authors.initials: T
authors.lastname: Nakagomi
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.|Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
authors.forename: L P
authors.initials: LP
authors.lastname: Do
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
authors.forename: C A
authors.initials: CA
authors.lastname: Agbemabiese
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Kaneko
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
authors.forename: P
authors.initials: P
authors.lastname: Gauchan
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.|Department of Virology 2, National Institute of Infectious Diseases, Tokyo, Japan.
authors.forename: Y H
authors.initials: YH
authors.lastname: Doan
authors.affiliation: Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.|Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi.
authors.forename: K C
authors.initials: KC
authors.lastname: Jere
authors.affiliation: Vaccines and Immunization, PATH, Seattle, WA, 98121, USA.|MRC Diarrhoeal Pathogens Research Unit, MEDUNSA, University of Limpopo, Pretoria, South Africa.
authors.forename: A D
authors.initials: AD
authors.lastname: Steele
authors.affiliation: Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: M
authors.initials: M
authors.lastname: Iturriza-Gomara
authors.affiliation: Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.|Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: O
authors.initials: O
authors.lastname: Nakagomi
authors.affiliation: Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
authors.forename: N A
authors.initials: NA
authors.lastname: Cunliffe
mesh_terms: D016000:Cluster Analysis; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D008295:Malawi; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D016865:Reassortant Viruses / Q000235:genetics; D012401:Rotavirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D012400:Rotavirus Infections / Q000821:virology*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral