Whole genome sequencing reveals genetic heterogeneity of G3P[8] rotaviruses circulating in Italy |
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| Institution: | 1. Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy;2. Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy;3. Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary;1. Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan;2. Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam;3. Centre for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan;4. Dairy Hygiene Research Division, Hokkaido Research Station, National Institute of Animal Health, Sapporo, Hokkaido, Japan;1. Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam;2. Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan;3. Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan;4. Vietnam Research Station, National Institute of Hygiene and Epideimmiology-Nagasaki University, Hanoi, Viet Nam;5. Vietnam Research Station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan;6. Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam |
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| Abstract: | After a sporadic detection in 1990s, G3P8] rotaviruses emerged as a predominant genotype during recent years in many areas worldwide, including parts of Italy. The present study describes the molecular epidemiology and evolution of G3P8] rotaviruses detected in Italian children with gastroenteritis during two survey periods (2004–2005 and 2008–2013). Whole genome of selected G3P8] strains was determined and antigenic differences between these strains and rotavirus vaccine strains were analyzed. Among 819 (271 in 2004–2005 and 548 in 2008–2013) rotaviruses genotyped during the survey periods, the number of G3P8] rotavirus markedly varied over the years (0/83 in 2004, 30/188 in 2005 and 0/96 in 2008, 6/88 in 2009, 4/97 in 2010, 0/83 in 2011, 9/82 in 2012, 56/102 cases in 2013). The genotypes of the 11 gene segments of 15 selected strains were assigned to G3-P8]-I1-R1-C1-M1-A1-N1-T1-E1-H1; thus all strains belonged to the Wa genogroup. Phylogenetic analysis of the Italian G3P8] strains showed a peculiar picture of segregation with a 2012 lineage for VP1-VP3, NSP1, NSP2, NSP4 and NSP5 genes and a 2013 lineage for VP6, NSP1 and NSP3 genes, with a 1.3–20.2% nucleotide difference from the oldest Italian G3P8] strains. The genetic variability of the Italian G3P8] observed in comparison with sequences of rotaviruses available in GenBank suggested a process of selection acting on a global scale, rather than the emergence of local strains, as several lineages were already circulating globally. Compared with the vaccine strains, the Italian G3P8] rotaviruses segregated in different lineages (5–5.3% and 7.2–11.4% nucleotide differences in the VP7 and VP4, respectively) with some mismatches in the putative neutralizing epitopes of VP7 and VP4 antigens. The accumulation of point mutations and amino acid differences between vaccine strains and currently circulating rotaviruses might generate, over the years, vaccine-resistant variants. |
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