Genetic characterization of norovirus strains in hospitalized children from Pakistan

Abstract

Norovirus is one of the most common causes of acute gastroenteritis among children in developing countries. No data on the prevalence and genetic variability of norovirus are available for Pakistan, where early childhood mortality due to acute gastroenteritis is common. We tested 255 fecal specimens from children under 5 years of age hospitalized between April 2006 and March 2008 with severe acute gastroenteritis in five hospitals in the four largest cities in Pakistan for norovirus by real-time RT-PCR. Positive samples were further genotyped by conventional RTPCR targeting the 5′-end of the capsid gene followed by sequencing of the positive PCR products. Overall, 41 (16.1%) samples tested positive for norovirus with an equal frequency in rotavirus-positive and rotavirus-negative samples. Nine (22%) samples were genogroup (G)I positive, 30 (73%) GII positive and two (5%) samples contained a mixture of GI and GII viruses. Sequence analyses demonstrated co-circulation of 14 norovirus genotypes including four GI genotypes (GI.3, GI.5, GI.7, GI.8) and 10 GII genotypes (GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.9, GII.13, GII.16, and GII.21). The most prevalent genotypes were GI.7 and GII.4 both causing 12.2% of the infections. This report confirms the presence of multiple norovirus genotypes in hospitalized children with acute gastroenteritis in Pakistan and a lack of clear predominance of GII.4 viruses.

The Comparative Molecular Epidemiology of GII.P7_GII.6 and GII.P7_GII.7 Norovirus Outbreaks in Victoria, Australia, 2012-2014

“…Although GII.6 (ORF 2) and GII.7 (ORF 2) noroviruses have been documented in various studies [6,7,8] and GII.6 (ORF 2) has been noted to be a relatively common norovirus in some settings [9,10,11,12], detailed molecular epidemiological analysis of these viruses is lacking. Furthermore, although a link between GII.6 and GII.7 noroviruses has been documented, in that both can be linked to GII.P7 [13,14,15,16], the precise relationship between GII.P7_GII.6 and GII.P7_GII.7 does not appear to have been examined.…”

Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013–2015

“…Its symptoms include nausea, diarrhoea, vomiting, stomach cramps and fever [ 2 ]. While these symptoms can be self-limiting in healthy individuals, children, elderly and immune-compromised individuals often experience prolonged symptoms [ 3 , 4 ]. The shedding of norovirus has also been shown in asymptomatic individuals [ 5 ], and its transmission occurs mainly by the faecal-oral route, through either contaminated food or water sources [ 6 ], person to person contact or through aerosols [ 7 ].…”

A systematic review and meta-analysis of the prevalence of norovirus in cases of gastroenteritis in developing countries

“…[ 6 , 7 ] Although 7 genogroups of NoV (GI–GVII) have been identified, [ 8 ] 2 genogroups (GI and GII) are the main causes of NoV-associated gastroenteritis; a recent increase in NoV GII-associated gastroenteritis was reported not only in developed countries [ 9 – 13 ] but also in developing countries. [ 14 , 15 ]…”