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Hepatitis E virus (HEV) is an emerging zoonotic pathogen that exhibits great host diversity. The primary means of transmission of the virus in low- and middle-income countries is contaminated water, often due to a lack of access to proper sanitation, which leads to faecal contamination of water sources. Environmental surveillance is an important tool that can be used to monitor virus circulation and as an early warning system for outbreaks. This study was conducted to determine the prevalence and genetic diversity of HEV in wastewater, surface water (rivers and standpipe/ablution water), and effluent from a piggery in South Africa. A total of 536 water samples were screened for HEV using real-time reverse transcription-polymerase chain reaction. Overall, 21.8% (117/536) of the wastewater, river, and ablution water samples tested positive for HEV, whereas 74.4% (29/39) of the samples from the piggery tested positive. Genotyping revealed sequences belonging to HEV genotypes 3 (98%, 53/54) and 4 (2%, 1/54), with subtypes 3c, 3f, and 4b being identified. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Human bocavirus (HBoV) is known to be associated with a variety of clinical manifestation including acute gastroenteritis (AGE). Despite their global prevalence, no data is available on the epidemiology of HBoV associated with AGE in South Africa (SA). Between April 2009 and April 2015, 3765 stool specimens were collected from children less than 5 years of age hospitalized with diarrhea. Specimens were screened for selected enteric viruses by enzyme immunoassay and quantitative polymerase chain reaction, bacteria by culture and parasites by staining and microscopy. HBoV was detected in 5.63% (212 of 3765) of cases, the majority of which were children ≤2 years (92%, 195 of 212), and were common in the summer and autumn months (60%; 128 of 212). Further investigations of coinfections showed that bacteria (adjusted odds ratio [aOR] = 2.20; 95% confidence interval [CI], 1.41‐3.45; P =.001) and sapovirus (aOR = 2.05; 95% CI, 1.08‐3.86; P =.027) were significantly associated with HBoV in multivariate analysis. HBoV genotyping was successful in 191 of the 212 samples with HBoV‐1 being the most prevalent genotype observed (79.6%; 152 of 191) followed by HBoV‐3 (13.6%; 26 of 191), HBoV‐2 (5.2%; 10 of 191), and HBoV‐4 (1.6%; 3 of 191). The high prevalence of HBoV‐1, a virus known to be associated with respiratory infections, and the association between HBoV‐positive specimens and already established AGE agents, suggests that HBoV may play a limited role in the observed AGE cases in SA. Highlights: Human bocavirus was detected in 5.6% of hospitalized diarrhoea cases in children <5 years in South Africa between 2009 and 2015.Human bocavirus type 1 was the most common strain detected Human bocavirus may play a limited role in diarrhoeal disease burden in South Africa [ABSTRACT FROM AUTHOR]

Background: The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites. Method: Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case‐comparisons were investigated; HAstV‐positive and HAstV‐negative children, human immunodeficiency virus (HIV)‐infected and HIV‐uninfected (HAstV‐positive) children and HIV‐exposed and unexposed (HAstV‐positive HIV‐uninfected) children. Results: Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6‐month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1‐2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV‐uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV‐unexposed patients (P = 0.032). Conclusion: Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea‐free control groups. Future HAstV surveillance should include community‐based studies and children presenting at outpatient facilities. 1.Human astroviruses were identified in 7% of patients less than 5 years of age hospitalised for acute gastroenteritis and were detected frequently in the age group 7 to 12 months.2.The prevalence of human astroviruses was similar in HIV‐infected children as compared with HIV‐uninfected children with diarrhoea.3.Human astroviruses were detected more frequently among cases from homes that used outdoor water sources compared to indoor sources.4.More human astrovirus infections were detected in HIV‐uninfected patients that were exposed to HIV compared to HIV‐unexposed patients. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Hepatitis A virus (HAV) was detected, by real-time reverse transcription-polymerase chain reaction, in irrigation water from a dam on a commercial fresh produce farm in South Africa (SA). The virus was characterized by nucleotide sequence and phylogenetic analysis of a consensus sequence spanning the VP1 and VP1/P2B genomic regions. Amino acid sequence and phylogenetic analysis indicated that the HAV strain was closely related to HAV genotype V and possibly of simian origin. This suggests that a novel HAV may be circulating in SA and its presence in irrigation water highlights the potential for zoonotic or anthroponotic cross-species transmission via environmental food and water sources. J. Med. Virol. 88:734-737, 2016. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Sapoviruses (SaVs) were detected and quantified in 8/10 water samples collected from wastewater treatment works (WWTWs) and water sources impacted by these WWTWs in Limpopo Province, South Africa. The median SaV concentration was 2.45 x 106 copies/L and SaV genotypes I.2 and IV were characterised. This study provides new data on the high concentrations of clinically relevant SaVs in rivers and dams impacted by poor-performing WWTWs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. J. Med. Virol. 86:75-81, 2014. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Background. Data regarding the prevalence and molecular epidemiology of rotavirus infection in rural areas of Africa are limited. In this study the prevalence and genetic diversity of rotaviruses in a rural South African setting were investigated. Methods. During June 1998 to June 2000, 420 stool specimens were collected from children with acute diarrhea who visited primary health care clinics in the rural Vhembe region, Limpopo Province, South Africa. Group A rotaviruses were detected by enzyme-linked immunosorbent assay, and the G and P types were determined by reverse-transcription polymerase chain reaction. Results. Of the 420 specimens, 111 (26.4%) were positive for group A rotavirus; P[6]G1 strains predominated (32.4%), followed by P[8]G1 (13.5%), P[6]G9 (4.5%), P[4]G8 (3.6%), P[4]G1 (3.6%), P[6]G8 (3.6%), and P[6]G2 (2.7%). Dual infections, with >1 P type, were seen in 33 (37.1%) of the positive specimens. Conclusion. The unusual serotype and genotype combinations of rotavirus circulating in the rural communities of the Limpopo Province highlight the need for more studies to monitor the geographic distribution of rotavirus strains in rural African settings. [ABSTRACT FROM AUTHOR]

Human adenoviruses (HAdVs) cause a wide range of clinical syndromes and are classified in seven species, A-G, comprising 52 serotypes. HAdV-A31, -F40, and -F41 have been associated with diarrhea in infants and young children. In developing countries gastroenteritis is a major cause of morbidity and mortality in children and, in comparison to rotaviruses, there are no data on the HAdVs associated with diarrhea in pediatric patients in Kenya. This study investigates the prevalence and genotypes of HAdVs in 278 stool specimens (211 diarrheal; 67 non-diarrheal) from children ≤14 years of age in urban and rural areas in Kenya. Stool specimens were screened for HAdVs using a nested polymerase chain reaction and the HAdVs genotyped by sequence analysis of a conserved hexon gene fragment. HAdVs were detected in 104/278 (37.4%) of the stool specimens: 35/43 (81.4%) of diarrheal and 10/61 (16.4%) of non-diarrheal stool specimens from children in an urban hospice; 25/94 (26.6%) of diarrheal specimens from urban children and 34/80 (42.5%) of diarrheal specimens from children in a rural area. Species D HAdVs were identified as the most prevalent HAdV species in diarrheal stool specimens from urban children comprising 18/37 (48.6%) of the strains identified. In contrast HAdV species F predominated in pediatric diarrheal specimens from the rural area, being identified in 7/16 (43.8%) of the characterized strains. This study provides valuable new data on the prevalence and distribution of HAdV genotypes in diarrheal stool specimens in Kenya and Africa, and highlights the necessity for further investigations. J. Med. Virol. 82:77-84, 2010. © 2009 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The study aimed to determine the presence of mumps virus (MuV) in cerebrospinal fluid (CSF) specimens and to genetically characterise detected MuV strains. A real-time reverse transcription-polymerase chain reaction (RT-PCR) was used to detect the MuV F gene, and characterisation was performed by sequencing of the SH gene. Mumps virus was detected in 1.2% (3/260) of specimens. Phylogenetic analysis of one MuV strain revealed that it clustered with the Jeryl-Lynn and RIT4385 vaccine strains. As far as the authors could ascertain this is the first study to provide viral proof that these vaccine-like strains may be associated with aseptic meningitis. [ABSTRACT FROM AUTHOR]