Emerging norovirus GII.4 2008 variant detected in hospitalised paediatric patients in South Africa

Abstract

a b s t r a c tBackground: Noroviruses (NoVs) are important enteric pathogens that cause gastroenteritis worldwide. The first documented NoV outbreaks in South Africa (SA) were described in 1993. The current NoV prevalence and circulating genotypes are unknown. SA lacks NoV outbreak reporting systems and therefore the number and impact of NoV infections is underestimated. Objectives: This study aimed to determine the prevalence and genetic diversity of NoV infections in hospitalised paediatric patients with gastroenteritis in SA during 2008. Study design: Stool specimens referred for virological analysis from hospitalised children ≤13 years, with gastroenteritis, were screened for rotavirus, human adenovirus and human astrovirus by enzyme immunoassay and for NoV genogroup I (GI), II (GII) and sapovirus by real-time RT-PCR. NoV strains were genotyped, and variants identified, based on sequence and phylogenetic analyses of the 5 end or the full length of the capsid gene, respectively. Results: Rotavirus was the most prevalent virus detected in 24.2% (61/252) of specimens, followed by NoV in 14.3% (35/245) and adenovirus, astrovirus and sapovirus in 9.6%, 6.7% and 4% of specimens, respectively. NoVs were only detected in children ≤2 years. The GII NoVs (89%) predominated and eight types were identified with GII.4 (43%) detected most frequently. The emerging 2008 GII.4 variant represented 80% of the GII.4 strains. Conclusions: A diverse range of NoV genotypes were identified in hospitalised children with gastroenteritis. The 2008 GII.4 variant was the most frequently detected strain in the study. This is the first report of NoV GII.4 viruses in SA.

Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya

“…The GII.6 strains were the second most predominant strains identified and clustered together with strains from Sweden (JN183165) and Japan (AB818398). After NoV GII.4, NoV GII.6 has been shown to be the second most dominant strain in clinical studies in a number of countries namely, SA, Brazil, Japan, and Finland (Phan et al 2005;Mans et al, 2010;Ferreira et al 2010;Puustinen et al 2011;Chan-it et al 2012). Norovirus GII.6 strains were previously identified in clinical specimens from Kenya (Mans et al 2014), indicating the presence of clinically relevant strains in the water sources.…”

“…In Africa, the prevalence of NoVs has been investigated in both clinical (Mans et al 2010(Mans et al , 2014Hassine-Zaafrane et al 2013;Huynen et al 2013;) and environmental settings (Kamel et al 2010;Kiulia et al 2010;Sdiri-Loulizi et al 2010;Gibson 2011;Mans et al 2013;Murray et al 2013). Noroviruses have also been detected in shellfish collected along the Mediterranean Sea and Atlantic Coast of Morocco (Benabbes et al 2013).…”

Diverse norovirus genotypes identified in sewage-polluted river water in South Africa

“…There is little information on the seasonality of NoV outbreaks in the clinical setting in SA. In a 1-year study on sporadic paediatric gastroenteritis in the hospital setting in the northern region of Gauteng, NoV infections were observed throughout the year with an increase in the summer months [10]. Factors that may have masked a seasonal pattern include the relatively low efficiency of the recovery procedure, the presence of inhibitors in water samples and bias introduced by interruptions in the sampling schedule.…”

“…Nucleotide sequences were analysed as described previously [10]. A representative sequence of each set of clones was used for phylogenetic analyses.…”

“…A seroprevalence survey indicated widespread exposure to NoVs in a large portion of the population [9]. More recently a study in Gauteng province, SA indicated that after rotavirus (24 % prevalence), NoV was the most frequently detected viral pathogen in paediatric patients (14 % prevalence) hospitalized with viral gastroenteritis [10]. In spite of the evident importance of NoV infections, NoVs are not routinely tested for in diagnostic laboratories and NoV infections are probably underreported.…”