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

[摘要] English: In 2015, a study by Nhampossa and co-workers reported that rotaviruses are among the leadingcauses of severe gastroenteritis in children in Mozambique. However, there is not muchpublished information on rotavirus surveillance in this country. In addition, currently there hasnot been any published information on the genotypes of strains circulating in Mozambique. In2012, Dr Nilsa de Deus (National Institute of Health, INS) initiated a rotavirus surveillanceproject at Manhiça Health Research Centre (CISM) where the aim was to study the prevalenceas well as the genotypes of strains circulating in two regions of the country i.e Manhiça andMavalane, rural and urban site, respectively.The work done in the current study is part of a collaborative project on Mozambican rotavirusstrain characterisation, molecular epidemiology and rotavirus strain evolution between theresearch groups of Dr de Deus at INS/CISM and the University of the Free State (UFS). Theaims were to use reverse-transcriptase polymerase chain reaction (RT-PCR) and Sangersequencing to confirm the genotypes obtained by the Mozambican researchers with genotypingPCR and to use next generation sequencing (NGS) to determine genotypes of rotaviruspreviously typed as mixed genotypes or untypeable with genotyping PCR.The Mozambican reseachers collected stool specimens of children with severe diarrhoeaseeking medical attention in hospitals in Mavalane and Manhiça. Positive specimens for therotavirus antigen were typed by genotyping PCR and were sent to UFS. RNA was successfullyextracted 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 wasperformed for 30 specimens. Phylogenetic analysis of strains whose genotypes could bedetermined by RT-PCR and Sanger sequencing showed that strains circulating in Mozambiquewere similar to strains circulating in the low income countries in southern Africa and India. InMozambique, the genotypes detected included G2P[4], G12P[6], G8P[4] and G12P[8].Whole genome sequencing of nine selected Mozambican samples using NGS was successfuland samples which were previously typed as mixed by genotyping PCR appeared as singleinfections. Interestingly, one specimen that was previously typed with genotyping PCR asG12P[NT], and subsequently as G12P[6] with RT-PCR in combination with Sangersequencing 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 andBangladesh. Rotavirus infections are a problem in low-income countries such as Mozambiqueas their rate of detection is high, with various genotypes circulating and making continualsurveillance a necessity before and after the introduction of vaccines.

[发布机构] University of the Free State