Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa

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dc.contributor.advisor Potgieter, N.
dc.contributor.advisor Traore, A. N.
dc.contributor.advisor Kabue, J. P.
dc.contributor.author Khumela, Ronewa
dc.date 2020
dc.date.accessioned 2020-09-30T08:33:53Z
dc.date.available 2020-09-30T08:33:53Z
dc.date.issued 2020-03
dc.identifier.citation Khumela, Ronewa (2020) Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa. University of Venda, South Africa..<http://hdl.handle.net/11602/1562>.
dc.identifier.uri http://hdl.handle.net/11602/1562
dc.description MSc (Microbiology) en_ZA
dc.description Department of Microbiology
dc.description.abstract Background: Globally, approximately 7,600,000 children under the age of 5 die annually due to diarrhea caused by viruses, bacteria and parasites. Human Astrovirus (HAstVs) has been identified as a causative agent of diarrheal disease worldwide especially in young children under five years of age. Recent reports in South Africa demonstrated HAstVs as a potential pathogen associated with diarrhea. The aim of this study was therefore to investigate the genetic characteristics of HAstVs in young children with diarrhea in rural communities of Vhembe District, Limpopo Province. Methodology: A total of 141 archived RNA, extracted from stool samples, were retrieved from -20°C storage. Using questionnaire, clinical data useful in the analysis of results were captured. The RIDA®GENE Viral Stool Panel I (PG1325) multiplex real-time RT-PCR assay was used for the detection of Astrovirus. Positive Astrovirus extracts were amplified by one-step ahead RT-PCR (cat no: 220213, (QIAGEN)) and one-step RT-PCR kit (cat no: 210212, (QIAGEN)) using specific primers targeting the viral capsid and polymerase regions. Amplified fragments were sequenced, and phylogenetic trees constructed by the neighbor-joining method using MEGA X (10.0.5) software. Results: HAstVs was detected in 10 (7%) of the 141 stool samples. A total of 9/10 (90%) HAstVs cases were from outpatients. The sequence analyses revealed HAstV genotype 1 and 2. A putative recombinant strain was found. Phylogenetic analysis revealed strain’s relatedness to others circulating in the African continent. Conclusion: This is the first study to characterize HAstVs from pediatric stool sample in the Vhembe district of Limpopo/South Africa. The study findings revealed the presence of HAstV type 1 and 2 in young children in the rural communities of the Vhembe District. Human Astrovirus genotype 1 and 2 are globally associated with diarrhea. Systematic surveillance to monitor HAstV strains circulation will help to understand the role of the pathogen in the study area. en_ZA
dc.description.sponsorship NRF en_ZA
dc.format.extent 1 online resource (xi, 66 leaves : some color illustrations, color map)
dc.language.iso en en_ZA
dc.rights University of Venda
dc.subject Acute gastroenteritis (AGE) en_ZA
dc.subject Children en_ZA
dc.subject Diarrhea en_ZA
dc.subject Human astrovirus en_ZA
dc.subject.ddc 362.198920968257
dc.subject.lcsh Diarrhea in children -- South Africa -- Limpopo
dc.subject.lcsh Diarrhea -- South Africa -- Limpopo
dc.subject.lcsh Children -- South Africa -- Limpopo
dc.subject.lcsh Gastroenteritis in children -- South Africa -- Limpopo
dc.subject.lcsh Pediatric gastroenterology -- South Africa -- Limpopo
dc.title Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa en_ZA
dc.type Dissertation en_ZA

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