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Norovirus (NoV) is the second most important cause of viral diarrheal disease in children worldwide after rotavirus and is estimated to be responsible for 17% of acute diarrhea in low-income countries. This study aimed to identify and report NoV genotypes in Mozambican children under the age of five years with acute diarrhea. Between May 2014 and December 2015, stool specimens were collected within the Mozambique Diarrhea National Surveillance (ViNaDia) and tested for NoV genogroups I (GI) and II (GII) using conventional reverse transcriptase-polymerase chain reaction (RT-PCR). Partial capsid and RNA-dependent RNA polymerase (RdRp) nucleotide sequences were aligned using the Muscle tool, and phylogenetic analyses were performed using MEGA X. A total of 204 stool specimens were tested for NoV. The detection rate of NoV was 14.2% (29/204). The presence of NoV was confirmed, by real-time RT-PCR (RT-qPCR), in 24/29 (82.8%) specimens, and NoV GII predominated (70.8%; 17/24). NoV GII.4 Sydney 2012[P31] was the predominant genotype/P-type combination detected (30.4%; 7/23). This is the first study which highlights the high genetic diversity of NoV in Mozambican children and the need to establish a continuous NoV surveillance system.

This study assessed the risks posed by noroviruses (NoVs) in surface water used for drinking, domestic, and recreational purposes in South Africa (SA), using a quantitative microbial risk assessment (QMRA) methodology that took a probabilistic approach coupling an exposure assessment with four dose-response models to account for uncertainty. Water samples from three rivers were found to be contaminated with NoV GI (80-1,900 gc/L) and GII (420-9,760 gc/L) leading to risk estimates that were lower for GI than GII. The volume of water consumed and the probabilities of infection were lower for domestic (2.91 × 10 -8 to 5.19 × 10 -1 ) than drinking water exposures (1.04 × 10 -5 to 7.24 × 10 -1 ). The annual probabilities of illness varied depending on the type of recreational water exposure with boating (3.91 × 10 -6 to 5.43 × 10 -1 ) and swimming (6.20 × 10 -6 to 6.42 × 10 -1 ) being slightly greater than playing next to/in the river (5.30 × 10 -7 to 5.48 × 10 -1 ). The QMRA was sensitive to the choice of dose-response model. The risk of NoV infection or illness from contaminated surface water is extremely high in SA, especially for lower socioeconomic individuals, but is similar to reported risks from limited international studies.

Background: Although sapovirus (SaV) has been detected in 2.2-12.7% of gastroenteritis cases globally, there are limited data on SaV epidemiology., Objectives: Describe the epidemiology, clinical characteristics and factors associated with SaV gastroenteritis in hospitalised children <5 years of age in South Africa., Study Design: Between 2009 and 2013 during prospective diarrhoeal surveillance, stool specimens were collected from four sites and screened for SaVs and associated enteric pathogens using ELISA, microscopy, conventional and real-time PCR. Epidemiological and clinical data were compared in patients with or without SaV. Odds ratios were assessed by bivariate and stepwise multivariable logistic regression analysis., Results: Sapoviruses were detected in 7.7% (238/3103) of children admitted to hospital and 11.4% (9/79) of deaths. Sapovirus was detected more commonly in children 19-24 months compared to<6months (aOR=2.3; p=0.018) and in males (aOR=2.0; p=0.001). Additional factors associated with SaV detection included residing with≥7 inhabitants compared to ≤3 (aOR=2.2; p=0.011) and concomitant norovirus infections (aOR=3.0; p=0.003). HIV-infected children with SaV were more likely to have bloody stools (aOR=16.8; p<0.001), low birth weight (<2.5kg; aOR=5.8; p=0.007) and live in environments without flush toilets (aOR=8.1; p=0.003) compared to HIV-uninfected children., Conclusions: Sapoviruses, which are perceived to cause mild diarrhoea, were detected in hospitalised children and diarrhoeal deaths in South Africa. Determinants increasing the odds of SaV included overcrowding and concomitant infections while HIV-infected children with SaV displayed bloody stools, low birth weight and reduced access to proper sanitation. Mitigation strategies against SaV infections include improved sanitation., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Norovirus (NoV) is recognised as a leading cause of gastroenteritis worldwide across all age groups. The prevalence and diversity of NoVs in many African countries is still unknown, although early sero-prevalence studies indicated widespread early infection. Reports on NoVs in Africa vary widely in terms of study duration, population groups and size, inclusion of asymptomatic controls, as well as genotyping information. This review provides an estimate of NoV prevalence and distribution of genotypes of NoVs in Africa. Inclusion criteria for the review were study duration of at least 6 months, population size of >50 and diagnosis by RT-PCR. As regions used for genotyping varied, or genotyping was not always performed, this was not considered as an inclusion criteria. A literature search containing the terms norovirus+Africa yielded 74 publications. Of these 19 studies from 14 out of the 54 countries in Africa met the inclusion criteria. Data from studies not meeting the inclusion criteria, based on sample size or short duration, were included as discussion points. The majority of studies published focused on children, under five years of age, hospitalised with acute gastroenteritis. The mean overall prevalence was 13.5% (range 0.8-25.5%) in children with gastroenteritis and 9.7% (range 7-31%) in asymptomatic controls, where tested. NoV GII.4 was the predominant genotype identified in most of the studies that presented genotyping data. Other prevalent genotypes detected included GII.3 and GII.6. In conclusion, NoV is a common pathogen in children with diarrhoea in Africa, with considerable carriage in asymptomatic children. There is however, a paucity of data on NoV infection in adults.

Background: Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. However, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of current long-term studies., Objective: To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in South Africa (SA)., Study Design: From April 2009 to December 2013, SaVs were characterised from stool specimens from children hospitalised with gastroenteritis in four provinces of SA., Results: Fourteen different SaV genotypes were identified from the 221 strains that were characterised. Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other identified genotypes included six belonging to GI (GI.1-GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII (GII.1-GII.7)., Conclusion: This study has provided the first comprehensive data on the genetic diversity of SaVs in a clinical setting in SA, contributing to the global knowledge of this virus., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Background: Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA)., Results: Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x2 analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa., Conclusions: Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses.

The human caliciviruses (HuCVs) are important causes of gastroenteritis worldwide. Norovirus (NoV) and sapovirus (SaV) have been detected in HIV-seropositive children but the genetic diversity of HuCVs circulating in these individuals is largely unknown. In this study the prevalence and genotype diversity of HuCVs circulating in Kenyan HIV-positive children, with or without diarrhea, from the year 1999 to 2000 was investigated. The overall prevalence of HuCVs was 19% with NoV predominating at 17% (18/105) and SaV present in 5.7% (6/105) of specimens. Human CVs were detected in both symptomatic (24%) and asymptomatic (16%) children. Co-infections with other enteric viruses were detected in 21.6% of children with diarrhea but only in 4.4% of children without diarrhea. Remarkable genetic diversity was observed with 12 genotypes (7 NoV, 5 SaV) being identified in 20 HuCV-infected children. NoV genogroup II (GII) strains predominated with GII.2 and GII.4 each representing 27% of the NoV-positive strains. The GII.4 strain was most closely related to the nonepidemic GII.4 Kaiso 2003 variant. Other NoV genotypes detected were GI.3, GII.6, GII.12, GII.14, and GII.17. Five different SaV genotypes (GI.2, GI.6, GII.1, GII.2, and GII.4) were characterized from six specimens. Diarrheal symptoms were not associated with any specific HuCV genotype. Overall the HuCV genotype distribution detected in this study reflects those in other studies worldwide. The strains detected are closely related to genotypes that have circulated on several continents since the year 2000., (© 2013 Wiley Periodicals, Inc.)

Background: 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., (Copyright © 2010 Elsevier B.V. All rights reserved.)