Genotyping and whole genome classification of group A rotaviruses originating from an urban and rural site in Mozambique

English: In 2015, a study by Nhampossa and co-workers reported that rotaviruses are among the leading causes of severe gastroenteritis in children in Mozambique. However, there is not much published information on rotavirus surveillance in this country. In addition, currently there has not been any published information on the genotypes of strains circulating in Mozambique. In 2012, Dr Nilsa de Deus (National Institute of Health, INS) initiated a rotavirus surveillance project at Manhiça Health Research Centre (CISM) where the aim was to study the prevalence as well as the genotypes of strains circulating in two regions of the country i.e Manhiça and Mavalane, rural and urban site, respectively. The work done in the current study is part of a collaborative project on Mozambican rotavirus strain characterisation, molecular epidemiology and rotavirus strain evolution between the research groups of Dr de Deus at INS/CISM and the University of the Free State (UFS). The aims were to use reverse-transcriptase polymerase chain reaction (RT-PCR) and Sanger sequencing to confirm the genotypes obtained by the Mozambican researchers with genotyping PCR and to use next generation sequencing (NGS) to determine genotypes of rotavirus previously typed as mixed genotypes or untypeable with genotyping PCR. The Mozambican reseachers collected stool specimens of children with severe diarrhoea seeking medical attention in hospitals in Mavalane and Manhiça. Positive specimens for the rotavirus antigen were typed by genotyping PCR and were sent to UFS. RNA was successfully extracted from 40/58 specimens received. From the 40 RNA positive specimens, characterisation of strains into P and G genotypes using RT-PCR and Sanger sequencing was performed for 30 specimens. Phylogenetic analysis of strains whose genotypes could be determined by RT-PCR and Sanger sequencing showed that strains circulating in Mozambique were similar to strains circulating in the low income countries in southern Africa and India. In Mozambique, the genotypes detected included G2P[4], G12P[6], G8P[4] and G12P[8]. Whole genome sequencing of nine selected Mozambican samples using NGS was successful and samples which were previously typed as mixed by genotyping PCR appeared as single infections. Interestingly, one specimen that was previously typed with genotyping PCR as G12P[NT], and subsequently as G12P[6] with RT-PCR in combination with Sanger sequencing was typed as a mixed genotype with NGS, revealing a relatively rare P[14] genotype. Phylogenetic analysis of specimens characterised with NGS indicated that Mozambican rotavirus strains are similar to strains circulating in southern Africa, India and Bangladesh. Rotavirus infections are a problem in low-income countries such as Mozambique as their rate of detection is high, with various genotypes circulating and making continual surveillance a necessity before and after the introduction of vaccines.