JCVI: Research / Projects / Rotavirus Genomics and Metagenomics of African Stool Samples / Overview
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Rotavirus Genomics and Metagenomics of African Stool Samples


Pediatric diarrheal diseases remain a significant cause of childhood morbidity and mortality in developing countries. Various pathogenic organisms can contribute to diarrheal diseases, including viruses, bacteria, and parasites. However, close to half of all diarrheal cases worldwide in children less than 5 years of age are caused by rotaviruses. These pediatric rotaviral cases result in more than 500,000 deaths annually, with the majority occurring in developing countries. 

However, as for all infectious diseases, the development of diarrheal diseases depends not only on the pathogen but also on a number of host and environmental factors. These include the host immune response, various other susceptibility/resistance genotypes of the host, the microbiome composition of the host, and environmental conditions, such as the diet and nutritional status of the host. Understanding how all of these factors interact to contribute to the development, pathogenesis and outcome of pediatric diarrheal diseases remains an active area of research that will hopefully lead to novel strategies for the prevention and treatment of these diseases.

To this end, the overall goal of this research project is to advance our understanding of pediatric diarrheal diseases in sub-Saharan Africa using various next generation sequencing strategies to evaluate enteric community relationships among rotaviruses, other diarrheal pathogens, and commensal microbiota. A core group of approximately 300 rotavirus-positive samples has been selected for analysis from a large archive of diarrheal stool samples collected from children less than 5 years of age between 1998 and 2010 in sub-Saharan Africa. This archive was established as part of the African Rotavirus Surveillance Network and is maintained by the WHO Rotavirus Regional Reference Laboratory for Africa, MRC/UL Diarrhoeal Pathogens Research Unit, Department of Virology, University of Limpopo Medunsa Campus, South Africa. In addition, rotavirus-negative diarrheal stool samples and normal stool samples from children in similar geographic locations will be evaluated for comparison of their microbiome composition with that of the core sample group. 

For the microbiome analysis, 16S ribosomal DNA markers from all samples will be sequenced and used to determine their bacterial compositions, which will be compared between rotavirus-positive and rotavirus-negative diarrheal stool samples, between diarrheal and normal stool samples, and between diarrheal stool samples containing specific strains of rotavirus. For a subset of approximately 60 samples, full metagenomic analyses will be performed to identify all organisms present in each sample, in addition to bacteria and rotavirus. 

Rotaviral sequencing of these samples will provide insights into the diversity of rotaviruses circulating in sub-Saharan Africa. Of particular interest are samples that spanned the period before and after the introduction of rotavirus vaccination programs in some of the sampled countries, allowing for the evaluation of possible vaccination effects on rotaviral evolution and diversity. The use of rotavirus vaccines to reduce the number of pediatric diarrheal cases is an important strategy being used to address the fourth Millenium Development Goal of the United Nations, which aims to reduce child mortality. However, the effectiveness of these vaccines must be monitored and new vaccines developed as needed to best protect against the circulating strains of rotavirus. 


National Institute of Allergy and Infectious Diseases (NIAID) Genome Sequencing Centers for Infectious Diseases (GSCID)

Principal Investigators

David Wentworth

Karen Nelson


M. Jeffrey Mphahlele
Medical Research Council, University of Limpopo, Medunsa Campus, Pretoria, South Africa