Assessment of selected environmental water samples in Kenya for the presence of clinically important enteric viruses

Abstract

Worldwide it is estimated that 1.1 billion people drink unsafe water and 1.7 million deaths are caused by drinking of unsafe water and poor sanitation. Enteric viruses are transmitted by the faecal-oral route and their spread has in part been attributed to the consumption of contaminated food and drinking water. Viruses are a major cause of waterborne disease but the health impact of waterborne viral infections is underestimated. Waterborne illness associated with viruses are more common than those caused by bacteria making it important to estimate the prevalence and diversity of enteric viruses in environmental water sources in order to assess the potential public health risks posed by the contaminated water sources. In Kenya, despite these risks data regarding the occurrence of the viruses in environmental water sources is limited, and in addition, data on the prevalence and molecular epidemiology of enteroviruses (EVs) and noroviruses (NoVs) in the clinical and environmental settings is lacking. Therefore, in this investigation the microbiological quality, the prevalence and molecular epidemiology of selected clinically relevant enteric viruses namely, EVs, NoVs and rotaviruses (RVs) in Kenyan urban and rural high risk water sources, namely the Mboone, Mutoine and Nairobi rivers and water from the Dadaab refugee camp, were investigated. Microbial indicator organisms, namely Escherichia. coli and total coliforms were detected at levels >200 cfu/mℓ in 100% (40/40) of the samples thereby exceeding the World Health Organization (WHO) recommended guidelines for drinking water (<1 most probable number/100 mℓ), suggesting that there is gross faecal contamination in these Kenyan water sources. The RVs were detected in 85% (34/40) of the samples and it was the most predominant virus detected being identified in 83% of the Mboone river samples, 100% of the Mutoine river samples, 83% of the Nairobi river samples and 50% of the household water from the Dadaab refugee camp. The G types detected were G1 and G9 and mixed G1+G9 being detected in the Nairobi river. The P types detected were, P[4], P[6] and P[8], with mixed P types P[4]+P[6], P[4]+P[8], P[6]+P[8] and P[4]+P[6]+P[8] being detected in the three surface water sources. Noroviruses were detected in 63% (25/40) of the selected water samples, with 60% (24/40) of the samples positive for NoV GII and 20% (8/40) for NoV GI. A number of genotypes were identified, namely, NoV GI.1, NoV GI.3 and NoV GI.9 and NoV GII.4, GII.6, GII.12, GII.16 and GII.17 with NoV GII.17 predominating. Enteroviruses were detected in 58% (23/40) of the samples by direct real-time reverse transcriptasepolymerase chain analysis of the recovered virus concentrates and were identified in the three rivers (Mboone, Mutoine and Nairobi rivers) accounting for 50%, 83% and 58% of water samples, respectively, but not in the borehole or household water from Dadaab. No polioviruses (PVs) were identified using the recommended WHO methods designed for identification of PVs and differentiation between vaccine-derived PVs and wild-type PVs in clinical specimens. In conclusion, this is the first comprehensive report on the molecular epidemiology of NoVs in Kenyan water sources. From this study it is evident that further nationwide studies are necessary to fully establish the prevalence, distribution and clinical relevance of enteric viruses in Kenyan water sources.