Dataset Information

Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic.

ABSTRACT: We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility-based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6-8_R], with a genomic constellation of G4-P[6-8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3 were generated as a result of recombination between genogroup 1 rotavirus A1 human strain and a genotype A8 porcine strain and between genogroup 1 rotavirus T1 human strain and a genotype T7 bovine strain, respectively. Analyses of the RNA secondary structures of gene segment VP4, NSP1 and NSP3 showed that all the recombinant regions appear to start in a loop (single-stranded) region and terminate in a stem (double-stranded) structure. Also, the VP7 gene occupied lineage VII within the G4 genotypes consisting of mostly porcine or porcine-like G4 strains, suggesting the occurrence of reassortment. The remaining gene segments clustered phylogenetically with genogroup 1 strains. This exchange of whole or partial genetic materials between rotaviruses by recombination and reassortment contributes directly to their diversification, adaptation and evolution.

SUBMITTER: Esona MD

PROVIDER: S-EPMC5720362 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic.

Esona Mathew D MD Roy Sunando S Rungsrisuriyachai Kunchala K Sanchez Jacqueline J Vasquez Lina L Gomez Virgen V Rios Lourdes Aviles LA Bowen Michael D MD Vazquez Marietta M

The Journal of general virology 20170224 2

We report the genome of a novel human triple-recombinant G4P[6-8_R] mono-reassortant strain identified in a stool sample from the Dominican Republic during routine facility-based rotavirus strain surveillance. The strain was designated as RVA/Human-wt/DOM/2013840364/2013/G4P[6-8_R], with a genomic constellation of G4-P[6-8_R]-I1-R1-C1-M1-(A1-A8_R)-N1-(T1-T7_R)-E1-H1. Recombinant gene segments NSP1 and NSP3 were generated as a result of recombination between genogroup 1 rotavirus A1 human strain ...[more]

PMID: 27983480

Similar Datasets

Project description:BackgroundRotavirus G10P[11] strains have long been associated with asymptomatic neonatal infections in some parts of India. We have previously reported G10P[11] strains associated with both asymptomatic infections and severe gastrointestinal disease in neonates from Vellore in southern India, with >90% partial nucleotide and amino acid identity to the VP4, VP6, VP7 and NSP4 genes of the exclusively asymptomatic G10P[11] strain I321.ObjectivesIn this study, the whole genome of a G10P[11] isolate (N155) from a neonate with severe gastrointestinal disease was characterized to determine whether there were significant differences in its genetic makeup in comparison to G10P[11] strain I321 and to establish the origin of the G10P[11] strains in Vellore.Study designPCR amplification and complete genome sequencing was carried out for all 11 gene segments of symptomatic G10P[11] rotavirus isolate N155. Nucleotide and amino acid sequence similarity with I321, other human and bovine strains for each gene segment were determined. The origin of each gene was determined based on the degree of identity to bovine or human rotavirus strains.ResultsN155 was found to be a reassortant between human and bovine rotaviruses. With the exception of NSP2, gene sequences of strain N155 showed >90% identity to published sequences of I321. Gene segments encoding NSP1, 2 and 3 were of human rotavirus origin for both strains; however, phylogenetic analysis of NSP2 sequences indicated that the human parental strain that led to the origin of these bovine-human reassortant strains was different. There were no significant differences between NSP2 sequences of strains from symptomatic and asymptomatic neonates in the same setting.ConclusionsThe study shows that the difference in clinical presentations in neonates may not be due to the limited variability in the genome sequence of G10P[11] strains and that G10P[11] strains in different parts of India could have evolved through reassortment of different parental strains.

Project description:BACKGROUND:The island of Hispaniola, shared by Haiti and the Dominican Republic (DR), is the only remaining malaria-endemic island in the Caribbean and accounts for 95% of the lymphatic filariasis (LF) burden in the Americas. Both countries aim to eliminate the diseases by 2020. Migration from Haiti, where both diseases are more prevalent, may promote transmission in the DR. Historically, Haitian migrant labourers live in rural Dominican agricultural 'company towns' called bateyes, many of which received mass drug administration (MDA) for LF elimination. This study sought to determine the prevalence of malaria and LF in bateyes of the DR and to describe related risk factors for disease. METHODS:From March to April 2016, a cross-sectional, cluster survey was conducted across Dominican bateyes stratified into three regions: southwest, north and east. A household questionnaire (n = 776), captured demographics, ethnic origin, mobility patterns, malaria intervention coverage, and knowledge, and recent fever and treatment-seeking. Two individuals per household (n = 1418) were tested for malaria parasites by microscopy and rapid diagnostic test (RDT) and LF antigen by filariasis test strip (FTS). Population-level estimates and confidence intervals (CI) were computed adjusting for the survey design. Two-sided t-tests compared differences in knowledge scores. RESULTS:No (0%) blood sample was Plasmodium-positive by microscopy or RDT. Six individuals were FTS-positive (0.5%; 95% CI: 0.2-1.5), but none (0%) of these were microfilariae-positive. Most batey residents were born in the DR (57.8%), documented (85.0%), and permanent residents (85.1%). Very few respondents (9.4%) reported travel to Haiti in the past year. Overall, half (53.8%) of respondents owned a bed net, and 82.3% of net owners reported using it the previous night. Indoor residual spraying (IRS) differed by region (range: 4.7%-61.2%). Most of those with recent fever sought care (56.0%), yet only 30.5% of those seeking care were tested for malaria. Compared to Dominican-born populations, Haitian-born respondents more frequently reported recent fever, did not seek care for the fever, had not heard of malaria, and could not name symptoms or prevention methods. CONCLUSIONS:Malaria and LF transmission appear absent or extremely low in Dominican bateyes, which are a mixture of Haitian and Dominican residents. Travel to Haiti is rare, meaning risk of malaria and LF importation is low. Addressing identified gaps in intervention coverage, malaria knowledge, treatment seeking and service delivery will improve the quality of surveillance for these diseases, particularly among marginalized populations and promote island-wide elimination.

Dataset Information

Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic.

Publications

Characterization of a triple-recombinant, reassortant rotavirus strain from the Dominican Republic.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets