Potgieter, N.Traore, A. N.Kabue, J. P.Khumela, Ronewa2020-09-302020-09-302020-03Khumela, 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>.http://hdl.handle.net/11602/1562MSc (Microbiology)Department of MicrobiologyBackground: 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.1 online resource (xi, 66 leaves : some color illustrations, color map)enUniversity of VendaAcute gastroenteritis (AGE)UCTDChildrenDiarrheaHuman astrovirus362.198920968257Diarrhea in children -- South Africa -- LimpopoDiarrhea -- South Africa -- LimpopoChildren -- South Africa -- LimpopoGastroenteritis in children -- South Africa -- LimpopoPediatric gastroenterology -- South Africa -- LimpopoDissertationKhumela R. Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa. []. , 2020 [cited yyyy month dd]. Available from: http://hdl.handle.net/11602/1562Khumela, R. (2020). <i>Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa</i>. (). . Retrieved from http://hdl.handle.net/11602/1562Khumela, Ronewa. <i>"Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa."</i> ., , 2020. http://hdl.handle.net/11602/1562TY - Dissertation AU - Khumela, Ronewa AB - 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. DA - 2020-03 DB - ResearchSpace DP - Univen KW - Acute gastroenteritis (AGE) KW - Children KW - Diarrhea KW - Human astrovirus LK - https://univendspace.univen.ac.za PY - 2020 T1 - Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa TI - Characterization of human astrovirus in pediatric patients with diarrhea from rural communities of Limpopo South Africa UR - http://hdl.handle.net/11602/1562 ER -