Enteric virome of Ethiopian children participating in a clean water intervention trial

Abstract

BackgroundThe enteric viruses shed by different populations can be influenced by multiple factors including access to clean drinking water. We describe here the eukaryotic viral genomes in the feces of Ethiopian children participating in a clean water intervention trial.Methodology/principal findingsFecal samples from 269 children with a mean age of 2.7 years were collected from 14 villages in the Amhara region of Ethiopia, half of which received a new hand-dug water well. Feces from these villages were then analyzed in 29 sample pools using viral metagenomics. A total of 127 different viruses belonging to 3 RNA and 3 DNA viral families were detected. Picornaviridae family sequence reads were the most commonly found, originating from 14 enterovirus and 6 parechovirus genotypes plus multiple members of four other picornavirus genera (cosaviruses, saliviruses, kobuviruses, and hepatoviruses). Picornaviruses with nearly identical capsid VP1 were detected in different pools reflecting recent spread of these viral strains. Next in read frequencies and positive pools were sequences from the Caliciviridae family including noroviruses GI and GII and sapoviruses. DNA viruses from multiple genera of the Parvoviridae family were detected (bocaviruses 1–4, bufavirus 3, and dependoparvoviruses), together with four species of adenoviruses and common anelloviruses shedding. RNA in the order Picornavirales and CRESS-DNA viral genomes, possibly originating from intestinal parasites or dietary sources, were also characterized. No significant difference was observed between the number of mammalian viruses shed from children from villages with and without a new water well.ConclusionsWe describe an approach to estimate the efficacy of potentially virus transmission-reducing interventions and the first complete (DNA and RNA viruses) description of the enteric viromes of East African children. A wide diversity of human enteric viruses was found in both intervention and control groups. Mammalian enteric virome diversity was not reduced in children from villages with a new water well. This population-based sampling also provides a baseline of the enteric viruses present in Northern Ethiopia against which to compare future viromes.

Genotyping of enteroviruses and human parechoviruses highlights their diversity in Northwest Ethiopia

“…This epidemiological information on the genetic diversity of EV contributes to the growing knowledge of genotypes circulating in Ethiopia. Most of the genotypes detected in this study were reported from previous studies in Ethiopia and other sub‐Saharan African countries 19‐24 . The frequent detection of EV‐B and EV‐C in this study is comparable with a previous study in Ethiopia in 2016 19 .…”

Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15

“…There are two possible reasons for limited worldwide HPeV15 detection: (i) silent transmission due to HPeV underdiagnosis explained by the lack of HPeV routine testing in clinical settings and lack of awareness among clinicians 1 , or (ii) localized geographical circulation of the virus in parts of Africa and Asia. However, in Africa, none of the studies conducted between 2002 and 2016 for HPeV detection in stool samples detected HPeV15 strains, neither in healthy nor in children with gastrointestinal symptoms [23][24][25][26] , except for one study from Ghanaian children in 2007-2008 11 . Nevertheless, these studies highlight the high genetic diversity of HPeVs in Africa, which include rare types like HPeV16, HPeV17 or the new type HPeV18 11,23,25,26 .…”

“…However, in Africa, none of the studies conducted between 2002 and 2016 for HPeV detection in stool samples detected HPeV15 strains, neither in healthy nor in children with gastrointestinal symptoms [23][24][25][26] , except for one study from Ghanaian children in 2007-2008 11 . Nevertheless, these studies highlight the high genetic diversity of HPeVs in Africa, which include rare types like HPeV16, HPeV17 or the new type HPeV18 11,23,25,26 . The studies that detected HPeVs in respiratory samples in African countries (Tunisia, Kenya and Gabon) did not perform type identification and therefore it is not possible to know whether type 15 was detected in these samples [27][28][29][30] .…”

“…In recent years, NGS has boosted identification of unsuspected and novel viruses and is becoming the standard for the discovery of viral pathogens 33,34 . It has been successfully used to identify or characterize full-genomes of new HPeVs like a HPeV1 variant 35 , type 4 31 , types 5 and 6 32 , type 7 36 , type 16 26 , type 17 37 , types 18 and 19 38 or to detect HPeVs in clinical specimens 25,26,[39][40][41] . Thanks to NGS, we were able to detect a mixed infection of HPeV15 and EV-A71 when using this technique to characterize the full genome sequence of EV-A71 13 .…”

Reference Echovirus 7 and 19 Genomes from Nigeria

“…The E7 genome is most similar to that of isolate Env_2016_Sep_E-7a (GenBank accession number MG451805 ), another E7 recovered from sewage in the United Kingdom in 2016, but has been suggested to be of sub-Saharan African origin ( 9 ). The E19 genome, on the other hand, is most similar to that of isolate ETH_P3/E19_2016 ( MF990292 ), an E19 recovered in April 2016 from the stool of a child in Ethiopia ( 10 ). Though EV-B genomic ends have been well characterized and the primers used in this study are based on conserved sequences ( 3 – 8 ), considering that the primers were used for amplification, the ends of the genomes might be of primer origin.…”