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

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.