Molecular detection and characterisation of sapoviruses and noroviruses in outpatient children with diarrhoea in Northwest Ethiopia

Abstract

Childhood morbidity and mortality of diarrhoeal diseases are high, particularly in low-income countries and noroviruses and sapoviruses are among the most frequent causes worldwide. Their epidemiology and diversity remain not well studied in many African countries. To assess the positivity rate and the diversity of sapoviruses and noroviruses in Northwest Ethiopia, during November 2015 and April 2016, a total of 450 faecal samples were collected from outpatient children aged <5 years who presented with diarrhoea. Samples were screened for noroviruses and sapoviruses by real-time RT-PCR. Partial VP1 genes were sequenced, genotyped and phylogenetically analysed. Norovirus and sapovirus stool positivity rate was 13.3% and 10.0%, respectively. Noroviruses included GII.4 (35%), GII.6 (20%), GII.17 (13.3%), GII.10 (10%), GII.2 (6.7%), GII.16 (5%), GII.7 (3.3%), GII.9, GII.13, GII.20 and GI.3 (1.7% each) strains. For sapoviruses, GI.1, GII.1 (20.0% each), GII.6 (13.3%), GI.2 (8.9%), GII.2 (11.1%), GV.1 (8.9%), GIV.1 (6.7%), GI.3 and GII.4 (2.2% each) genotypes were detected. This study demonstrates a high genetic diversity of noroviruses and sapoviruses in Northwest Ethiopia. The positivity rate in stool samples from young children with diarrhoea was high for both caliciviruses. Continued monitoring is recommended to identify trends in genetic diversity and seasonal variations.

Keywords: Childhood diarrhoea; genotyping; low-income country; molecular epidemiology; northwest Ethiopia.

Fig. 1.

Map of sampling sites. Stools were sampled in the cities Gondar and Bahir Dar, which are both situated in the Amhara National Regional State (grey) in Northwest Ethiopia. Previous data on sapoviruses and/or noroviruses are available from the nearby rural Goncha Siso Enese region, the capital Addis Ababa and the city of Awassa.

Fig. 2.

Monthly positivity rate of stool samples (PR) and distribution of sapovirus (A) and norovirus (B) genotypes in Gondar and Bahir Dar.

Fig. 3.

Phylogenetic analysis of sapoviruses (A, B and C) and noroviruses (D) based on Maximum Likelihood estimations of partial VP1 gene nucleic acid sequences. Numbers at each node represents bootstrap values obtained with 1000 replicates (>80 are shown). Strains from the present study are labelled with a black circle (Gondar) and black diamond (Bahir Dar). Grey triangles indicate previously reported strains from Ethiopia.