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Iturriza-Gomara M.,Public Health England | Esona M.D.,Gastroenteritis and Respiratory Viruses Laboratory Branch | Gray J.,Norwich University
Journal of Medical Virology

Annually 20-70% of all hospital admissions and 20% of fatal diarrhea cases among children less than 5 years of age occur due to severe rotavirus diarrhea. Universal immunization is the major strategy aimed at controlling rotavirus infection. The main objective of the present study was to elucidate the evolutionary relationships of the most common rotavirus strains co-circulating in Bulgaria. The sequence and phylogenetic analysis revealed strain diversity and circulation of different rotavirus variants belonging to a single genotype. A mutated G4P[8] strain with the insertion of an asparagine residue in position 76; G2, G9, and G1 variants with amino acid substitutions in the antigenic regions A, B, and/or C were all identified in this study in the absence of an immunization program. Rotavirus strain surveillance in both the pre- and post-vaccine eras is of increasing importance in order to assess the effectiveness of the rotavirus vaccines for protection against disease associated with a diverse population of rotavirus strains. © 2010 Wiley-Liss, Inc. Source

Nyaga M.M.,University of South Africa | Jere K.C.,University of South Africa | Jere K.C.,University of Liverpool | Esona M.D.,University of South Africa | And 17 more authors.
Infection, Genetics and Evolution

Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5. years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed rotavirus-positive human stool samples (. n=. 13) obtained from hospitalised children under the age of 5. years who presented with acute gastroenteritis at sentinel hospital sites in six African countries, as well as bovine and porcine stool samples (. n=. 1 each), to gain insights into rotavirus diversity and evolution. Polyacrylamide gel electrophoresis (PAGE) analysis and genotyping with G-(VP7) and P-specific (VP4) typing primers suggested that 13 of the 15 samples contained more than 11 segments and/or mixed G/P genotypes. Full-length amplicons for each segment were generated using RVA-specific primers and sequenced using the Ion Torrent and/or Illumina MiSeq next-generation sequencing platforms. Sequencing detected at least one segment in each sample for which duplicate sequences, often having distinct genotypes, existed. This supported and extended the PAGE and RT-PCR genotyping findings that suggested these samples were collected from individuals that had mixed rotavirus infections. The study reports the first porcine (MRC-DPRU1567) and bovine (MRC-DPRU3010) mixed infections. We also report a unique genome segment 9 (VP7), whose G9 genotype belongs to lineage VI and clusters with porcine reference strains. Previously, African G9 strains have all been in lineage III. Furthermore, additional RVA segments isolated from humans have a clear evolutionary relationship with porcine, bovine and ovine rotavirus sequences, indicating relatively recent interspecies transmission and reassortment. Thus, multiple RVA strains from sub-Saharan Africa are infecting mammalian hosts with unpredictable variations in their gene segment combinations. Whole-genome sequence analyses of mixed RVA strains underscore the considerable diversity of rotavirus sequences and genome segment combinations that result from a complex evolutionary history involving multiple host species. © 2015 Elsevier B.V. Source

Magagula N.B.,University of Limpopo | Esona M.D.,University of Limpopo | Esona M.D.,Gastroenteritis and Respiratory Viruses Laboratory Branch | Nyaga M.M.,University of Limpopo | And 8 more authors.
Journal of Medical Virology

Group A rotaviruses (RVAs) are the leading cause of severe gastroenteritis and eventually death among infants and young children worldwide, and disease prevention and management through vaccination is a public health priority. In August 2009, Rotarix™ was introduced in the South African Expanded Programme on Immunisation. As a result, substantial reductions in RVA disease burden have been reported among children younger than 5 years old. Rotavirus strain surveillance post-vaccination is crucial to, inter alia, monitor and study the evolution of vaccine escape strains. Here, full-genome sequence data for the 11 gene segments from 11 South African G1P[8] rotavirus strains were generated, including 5 strains collected from non-vaccinated children during the 2004-2009 rotavirus seasons and 6 strains collected from vaccinated children during the 2010 rotavirus season. These data were analyzed to gain insights into the overall genetic makeup and evolution of South African G1P[8] rotavirus strains and to compare their genetic backbones with those of common human Wa-like RVAs from other countries, as well as with the Rotarix™ and RotaTeq™ G1P[8] vaccine components. All 11 South African G1P[8] strains revealed a complete Wa-like genotype constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. On the basis of sequence similarities, the South African G1P[8] strains (with the exception of strain RVA/Human-wt/ZAF/1262/2004/G1P[8]) were closely related to each other (96-100% identity in all gene segments). Comparison to the Rotarix™ and RotaTeq™ G1P[8] vaccine components revealed a moderate nucleotide identity of 89-96% and 93-95%, respectively. The results indicated that none of the gene segments of these 11 South African G1P[8] strains were vaccine-derived. This study illustrates that large-scale next generation sequencing will provide crucial information on the influence of the vaccination program on evolution of rotavirus strains. This is the first report to describe full genomic analyses of G1P[8] RVA strains collected from both non-vaccinated and vaccinated children in South Africa. © 2014 Wiley Periodicals, Inc. Source

Nyaga M.M.,University of Limpopo | Stucker K.M.,J. Craig Venter Institute | Esona M.D.,University of Limpopo | Esona M.D.,Gastroenteritis and Respiratory Viruses Laboratory Branch | And 18 more authors.
Virus Genes

Group A rotaviruses (RVAs) with distinct G and P genotype combinations have been reported globally. We report the genome composition and possible origin of seven G8P[4] and five G2P[4] human RVA strains based on the genetic evolution of all 11 genome segments at the nucleotide level. Twelve RVA ELISA positive stool samples collected in the representative countries of Eastern, Southern and West Africa during the 2007–2012 surveillance seasons were subjected to sequencing using the Ion Torrent PGM and Illumina MiSeq platforms. A reference-based assembly was performed using CLC Bio’s clc_ref_assemble_long program, and full-genome consensus sequences were obtained. With the exception of the neutralising antigen, VP7, all study strains exhibited the DS-1-like genome constellation (P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and clustered phylogenetically with reference strains having a DS-1-like genetic backbone. Comparison of the nucleotide and amino acid sequences with selected global cognate genome segments revealed nucleotide and amino acid sequence identities of 81.7–100 % and 90.6–100 %, respectively, with NSP4 gene segment showing the most diversity among the strains. Bayesian analyses of all gene sequences to estimate the time of divergence of the lineage indicated that divergence times ranged from 16 to 44 years, except for the NSP4 gene where the lineage seemed to arise in the more distant past at an estimated 203 years ago. However, the long-term effects of changes found within the NSP4 genome segment should be further explored, and thus we recommend continued whole-genome analyses from larger sample sets to determine the evolutionary mechanisms of the DS-1-like strains collected in Africa. © 2014, Springer Science+Business Media New York. Source

Moon S.,Gastroenteritis and Respiratory Viruses Laboratory Branch | Moon S.,Korea University | Humphrey C.D.,Centers for Disease Control and Prevention | Kim J.S.,Korea University | And 4 more authors.
Clinical Microbiology and Infection

Group C rotavirus (GpC RV) causes sporadic cases and outbreaks of acute diarrhoea in humans worldwide, but has not been detected among children in South Korea. The present study aimed to detect GpC RV among children hospitalized with gastroenteritis in South Korea and to perform a molecular characterization of GpC RV strains. From November 2003 to January 2006, 434 faecal samples were collected from children <10years of age who were hospitalized for treatment of acute diarrhoea and screened for group C and A rotaviruses by enzyme immunoassay. GpC RV strains were characterized by sequence and phylogenetic analysis.Of the 434 samples screened, two were positive for GpC RV and one had a mixed GpC and GpA RV infection. One of the strains, Icheon, shared high sequence conservation in VP4, VP6 and VP7 genes with other published GpC RV. This is the first report describing the molecular characteristics of GpC RV among children in South Korea. Additional surveillance is needed to determine the burden of GpC RV gastroenteritis. © 2010 European Society of Clinical Microbiology and Infectious Diseases. No claim to original US government works. Source

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