Surveillance of acute flaccid paralysis often identifies enteroviruses not typeable by virus neutralization in cell culture. During 2000 and 2001, 186 isolates from 138 children with acute flaccid paralysis in the Democratic Republic of the Congo were sent for typing to the National Reference Centre for Enteroviruses in Lyon, France. The 5' UTR of the viral genome could be amplified by PCR for 158 isolates from 114 patients. Isolates from 89 patients were neutralizable, and contained non-polio enterovirus types. Seventeen children were infected with more than one entero- or adenovirus; another three were co-infected with both these viruses. Serological typing failed with 19 isolates from 13 (9%) patients. The VP1 region of these strains could be amplified by PCR and sequenced, which revealed that five children were infected with CV-A17, EV-70, EV-76, EV-77, or CV-A13. Two patients were doubly infected, one with CV-A24 and E-9, and another with E-27 and EV-81. Isolates from six children contained strains with divergent VP1 region. The amino acid sequences of these complete VP1 regions diverged >or=28% from published types indicating that they represented two new enterovirus types, tentatively designated EV-93 belonging to HEV-B and EV-94 within HEV-D. The latter enterovirus has in parallel been isolated from sewage in Egypt. In conclusion, there was a high frequency of "untypable" enterovirus isolates from cases with acute flaccid paralysis in the Democratic Republic of the Congo. Six of these were shown to represent two enteroviruses not previously described.

Background Sapovirus (SV) infection is a public health concern which plays an important role in the burden of diarrhoeal diseases, causing acute gastroenteritis in people of all ages in both outbreaks and sporadic cases worldwide. Objective/Study Design The purpose of this report is to summarise the available data on the detection of human SV in low and middle income countries. A systematic search on PubMed and ScienceDirect database for SV studies published between 2004 and 2017 in low and middle income countries was done. Studies of SV in stool and water samples were part of the inclusion criteria. Results From 19 low and middle income countries, 45 published studies were identified. The prevalence rate for SV was 6.5%. A significant difference (P=0) in SV prevalent rate was observed between low income and middle income countries. Thirty-three (78.6%) of the studies reported on children and 8 (19%) studies reported on all age groups with diarrhoea. The majority (66.7%) of studies reported on hospitalised patients with acute gastroenteritis. Sapovirus GI was shown as the dominant genogroup, followed by SV-GII. Conclusion The detection of human SV in low and middle income countries is evident; however the reports on its prevalence are limited. There is therefore a need for systematic surveillance of the circulation of SV, and their role in diarrhoeal disease and outbreaks, especially in low and middle income countries.

Abstractobjectives To assess the contribution of Human Norovirus to diarrhoeal diseases in Africa. methods We conducted a systematic review of the PubMed and EMBASE databases for published articles of Human Norovirus in Africa between 1990 and 2013. Data were extracted from selected studies and analysed.results A total of 208 eligible studies were identified, of which 55 (from 19 countries) met the inclusion criteria. Many cases were of sporadic gastroenteritis (70.9%) in children (82%), 65.4% of which were seen in an outpatient setting. Over half (59.4%) of the affected children were under 5 years of age. The pooled prevalence rate of Human NoV was 11% (95% CI 8-14%), and the meta-analysis indicated significant heterogeneity between the studies. However, the conditional negative binomial regression could not clearly find the factors affecting the Human NoV prevalence rates reported. A close relationship was found between Human Norovirus strains from environmental and clinical samples.

HighlightsNoV detection rates in cases and controls from children in Rural South Africa were not significantly different.Estimated GII viral load significantly higher in symptomatic than in asymptomatic children.First report on the difference between cases and controls with NoV in rural African population related to the viral load of NoV genogroups.

Background Human Bocavirus (HBoV) is an emerging virus discovered in 2005 from individuals suffering gastroenteritis and respiratory tract infections. Numerous studies related to the epidemiology and pathogenesis of HBoV have been conducted worldwide. This review reports on HBoV studies in individuals with acute gastroenteritis, with and without respiratory tract infections in Africa between 2005 and 2016. Material and Method The search engines of PubMed, Google Scholar, and Embase database for published articles of HBoV were used to obtain data between 2005 and 2016. The search words included were as follows: studies performed in Africa or/other developing countries or/worldwide; studies for the detection of HBoV in patients with/without diarrhea and respiratory tract infection; studies using standardized laboratory techniques for detection. Results The search yielded a total of 756 publications with 70 studies meeting the inclusion criteria. Studies included children and individuals of all age groups. HBoV prevalence in Africa was 13% in individuals suffering gastroenteritis with/without respiratory tract infection. Conclusion Reports suggest that HBoV infections are increasingly being recognized worldwide. Therefore, surveillance of individuals suffering from infections in Africa is required to monitor the prevalence of HBoV and help understand the role of HBoV in individuals suffering from gastroenteritis with/without respiratory tract infection.

Gastroenteritis in children is a major global problem. [1] In sub-Saharan Africa, children are 15 times more likely to die from diarrhoeal diseases before the age of 5 years than children living in developed countries. [2] The Vhembe District in Limpopo Province, South Africa, consists mostly of rural communities that still lack access to clean drinking water and proper sanitation. [3] Some people living in these rural communities rely mainly on open water sources such as rivers as their source of drinking water, posing a serious health risk to young children. [3][4][5] Diarrhoeal diseases are caused by various bacterial, parasitic and viral pathogens. Among these, diarrhoeagenic Escherichia coli (DEC) are frequently recognised enteric pathogens in children throughout the world. [6][7][8][9][10] DEC pathotypes co-infections with other enteric pathogens are increasingly detected in children less than 5 years of age. [11][12][13][14] Studies suggest that co-infections might result in increased clinical complications in infected children. In rural communities of the Vhembe District, few studies have been conducted on the prevalence of diarrhoeal pathogens in children. [4,5,[15][16][17][18] Consequently, data on the prevalence of co-infections have not been documented in these settings, which could be due to cost and the long waiting period for data analysis before treatment starts. The aim of the present study was to determine the prevalence of co-infections of diarrhoeacausing pathogens in children in rural communities of the Vhembe District, South Africa. Materials and methods Setting, collection of stool samples and study designThis prospective cross-sectional study was carried out in rural communities of the Vhembe District in Limpopo Province, in the northern part of South Africa. Ethical clearance was obtained from the University of Venda (Ref: SMNS/12/MBY/0212) and the Department of Health (Ref: 4/2/2). Informed and signed consent forms were obtained from participating parents and/or primary caretakers before collection of stools.Between July 2014 and June 2015, 237 diarrhoeal stool samples from children under the age of 5 years were collected from primary healthcare facilities in the Vhembe District. Diarrhoea was defined as the passage of ≥3 loose stools within 24 hours.A standard questionnaire was used to record demographic and clinical data of each study participant. Samples were collected by a qualified nurse using a sterile stool container. The specimens were then kept at -20 o C until further analysis. Bacterial analysisGenomic DNA was extracted from all stool specimens using the QIAamp Fast DNA stool mini kit according to the manufacturer's instructions (Qiagen, Germany). Three published multiplex-PCR (m-PCR) protocols were used in this study.A m-PCR protocol was used to indicate the presence of E. coli, Salmonella spp., Shigella spp., and Vibrio spp. as previously described. [19] Briefly: the polymerase chain reaction (PCR) was performed in a total volume of 20 μL containing 1 X QIAGEN multiplex PCR ...

Human bocavirus (HBoV) is an emerging virus globally associated with diarrhea in young children. This study aims to investigate the prevalence of HBoV genotypes in children (≤5 years) from rural communities in South Africa (SA) suffering from acute gastroenteritis (AGE). A total of 141 fecal samples of children ≤5 years with acute gastroenteritis (AGE) were collected from rural primary health care facilities in the Vhembe district of SA between June 2017 and July 2018. Clinical symptoms and demographic data were also recorded. A total of 102 (72%) were outpatients, and 39 (28%) were hospitalized patients. Human bocavirus (HBoV) genotypes were determined using real-time multiplex PCR. DNA extracts of positive samples were confirmed by conventional PCR targeting the NS1 gene. Co-infection with other enteric viruses were determined in HBoV-positive samples using real-time PCR. HBoV was detected in eight (5.7%) children with AGE, of which three (37.5%) were HBoV1, three (37.5%) were HBoV3, and two (25%) were HBoV2. The majority of positive cases were identified in outpatients (62%) between the ages of 1 and 24 months. Co-infection in HBoV-positive samples with other enteric viruses included rotavirus (37.5%), adenovirus (37.5%), norovirus (25%), and astrovirus (12.5%). HBoV infections could be seen as a potential emerging diarrheal pathogen in South Africa. However, more studies are needed to understand the role of HBoV infections in children with AGE.

The findings highlighted NoV genetic diversity and revealed continuous pandemic spread and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An unusual RdRp genotype GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe district/South Africa. NoV surveillance is warranted to help to inform investigations into NoV evolution and disease burden, and to support on-going vaccine development programmes.