Group A rotaviruses (RVAs) are the most important etiological agent of acute gastroenteritis in children <5 years of age worldwide. The monovalent rotavirus vaccine Rotarix was introduced into the national Expanded Programme on Immunization (EPI) in Ghana in May 2012. However, there is a paucity of genetic and phylogenetic data on the complete genomes of human RVAs in circulation pre-vaccine introduction. The common bovine rotavirus VP7 genotype G8 has been sporadically detected in Ghanaian children, usually in combination with the VP4 genotype P[6]. To investigate the genomic constellations and phylogeny of RVA strains in circulation prior to vaccine introduction, the full genomes of two unusual G8P[6] strains, GH018-08 and GH019-08, detected during burden of disease surveillance, were characterized by Illumina MiSeq sequencing. The Ghanaian isolates, GH018-08 and GH019-08, exhibited the unusual, previously unreported genotype constellation G8-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H3. Phylogenetic analyses confirmed that 10 out of the 11 genes of GH018-08 and GH019-08 were identical/nearly identical, with significant variation detected only in their VP1 genes, and clearly established the occurrence of multiple independent interspecies transmission and reassortment events between co-circulating bovine/ovine/caprine rotaviruses and human DS-1-like RVA strains. These findings highlight the contribution of reassortment and interspecies transmission events to the high rotavirus diversity in this region of Africa, and justify the need for simultaneous monitoring of animal and human rotavirus strains.

Exposure to fecal contamination in public areas, especially in dense, urban environments, may significantly contribute to enteric infection risk. This study examined associations between sanitation and fecal contamination in public environments in four low-income neighborhoods in Accra, Ghana. Soil (n = 72) and open drain (n = 90) samples were tested for E. coli, adenovirus, and norovirus. Sanitation facilities in surveyed households (n = 793) were categorized by onsite fecal sludge containment (“contained” vs. “uncontained”) using previous Joint Monitoring Program infrastructure guidelines. Most sanitation facilities were shared by multiple households. Associations between spatial clustering of household sanitation coverage and fecal contamination were examined, controlling for neighborhood and population density (measured as enumeration areas in the 2010 census and spatially matched to sample locations). E. coli concentrations in drains within 50m of clusters of contained household sanitation were more than 3 log-units lower than those outside of clusters. Further, although results were not always statistically significant, E. coli concentrations in drains showed consistent trends with household sanitation coverage clusters: concentrations were lower in or near clusters of high coverage of household sanitation facilities—especially contained facilities—and vice versa. Virus detection in drains and E. coli concentrations in soil were not significantly associated with clustering of any type of household sanitation and did not exhibit consistent trends. Population density alone was not significantly associated with any of the fecal contamination outcomes by itself and was a significant, yet inconsistent, effect modifier of the association between sanitation clusters and E. coli concentrations. These findings suggest clustering of contained household sanitation, even when shared, may be associated with lower levels of fecal contamination within drains in the immediate public domain. Further research is needed to better quantify these relationships and examine impacts on health.

Rotavirus A (RVA) strains, a leading cause of severe gastroenteritis in children worldwide, commonly possess the Wa or DS-1 genotype constellations. During a hospital-based study conducted in Hanoi, Vietnam, in the 2012-2013 rotavirus season, G1P[8] strains with a virtually identical short RNA migration pattern were detected in 20 (14%) of 141 rotavirus-positive samples. Two representatives of these strains were shown by whole-genome sequencing to be double-gene reassortants possessing the genotype constellation of G1-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Sequencing and a database search revealed that these Vietnamese G1P[8] double-gene reassortant strains shared an immediate ancestor with a locally circulating G2P[4] strain in all of the inner-capsid and non-structural protein genes, whereas they were more closely related in the VP7 and VP4 genes to a Chinese G1P[8] strain and a Chinese G3P[8] strain, respectively, than to locally circulating G1P[8] strains. Despite the marked similarity between Japanese and Thai G1P[8] double-gene reassortant strains, phylogenetic analysis suggested that the Vietnamese and Japanese/Thai G1P[8] double-gene reassortant strains originated from independent reassortment events. Clinically, children infected with Vietnamese G1P[8] double-gene reassortant strains experienced severe diarrhoea, but it was not more severe than that in children infected with ordinary G1P[8] strains. In conclusion, Vietnamese G1P[8] double-gene reassortant strains originated from a locally circulating G2P[4] strain and caused severe diarrhoea, but there was no evidence of increased virulence.