Enteric viruses isolates and rotavirus genotypes during the seasonal surge of acute watery childhood diarrhoea in South-Eastern Nigeria

Diarrhoea remains one of the top three causes of death in Africa. However, data on the molecular epidemiology of enteric viruses in Nigeria is rare. Two hundred and forty three infants and children below the age of 5 years with acute watery diarrhoea were evaluated for the presence of enteric viruses in stool by real-time PCR (rtPCR) during the dry months of December to April 2017, which correspond to diarrhoea season in South-East Nigeria. At least one viral pathogen was detected in 95.1% (231/243) of the study population. Rotavirus, 231(95.1%) was the most common followed by adenovirus, 103(42.4%) and enterovirus 32(13.2%). Other viruses seen in the stool samples include astrovirus 7.3 % (11/151), parechovirus 3.5 % (4/113), sapovirus, 2.8 % (4/145), bocavirus 6.8% (5/73) and human coronavirus 13.9% (10/73). Norovirus and hepatitis A and E viruses were not detected. Children that consumed factory packaged water had the lowest prevalence of rotavirus infection (p=0.044). A significant association between the viral pathogen and home treatment of drinking water or exclusive breastfeeding was not observed. Randomly selected 46 samples were genotyped for rotavirus, which showed that G3P[6] (39.1%) was the most common, followed by G1P[8] (15.2%), G9P[8] (13.0%), G12P[8] (6.5%), G9P[6]P[8] (2.2%), and G12P[6] (2.2%). This was the highest rotavirus prevalence in any published African study, and may be a reflection of inadequate water sanitation/hygiene in the study area, a peculiar epidemiological situation and/or the sensitivity of the diagnostic method used. The present study suggests that the burden of rotavirus is bigger than previously reported; and that morbidity can be greatly reduced if rotavirus vaccine is included in Nigerian national immunization policy.