Diversity of enteroviruses in cerebrospinal fluid specimens collected from hospitalised patients in the private and public sector in South Africa.

Enteroviruses cause a wide range of neurological illnesses such as encephalitis, meningitis, and acute flaccid paralysis. Two types of enteroviruses, echovirus E4 and E9, have recently been detected in South Africa and are known to be associated with meningitis and encephalitis. The objective of this study was to characterize enterovirus strains detected in cerebrospinal fluid specimens of hospitalized patients in the private and public sector to identify genotypes associated with meningitis and encephalitis. From January 2019 to June 2021 enterovirus positive nucleic acid samples were obtained from a private (n = 116) and a public sector (n = 101) laboratory. These enteroviruses were typed using a nested set of primers targeting the VP1 region of the enterovirus genome, followed by Sanger sequencing and BLASTn analysis. Forty-two percent (91/217) of the strains could be genotyped. Enterovirus B species was the major species detected in 95% (86/91) of the specimens, followed by species C in 3% (3/91) and species A in 2% (2/91) of the specimens. Echovirus E4 and E9 were the two major types identified in this study and were detected in 70% (64/91) and in 10% (9/91) of specimens, respectively. Echovirus E11 has previously been identified in sewage samples from South Africa, but this study is the first to report Echovirus E11 in cerebrospinal fluid specimens from South African patients. The genotypes identified during this study are known to be associated with encephalitis and meningitis. The predominant detection of echovirus E4 followed by E9 corresponds with other studies conducted in South Africa.

Feasibility of the Bag-Mediated Filtration System for Environmental Surveillance of Poliovirus in Kenya.

The bag-mediated filtration system (BMFS) was developed to facilitate poliovirus (PV) environmental surveillance, a supplement to acute flaccid paralysis surveillance in PV eradication efforts. From April to September 2015, environmental samples were collected from four sites in Nairobi, Kenya, and processed using two collection/concentration methodologies: BMFS (> 3 L filtered) and grab sample (1 L collected; 0.5 L concentrated) with two-phase separation. BMFS and two-phase samples were analyzed for PV by the standard World Health Organization poliovirus isolation algorithm followed by intratypic differentiation. BMFS samples were also analyzed by a cell culture independent real-time reverse transcription polymerase chain reaction (rRT-PCR) and an alternative cell culture method (integrated cell culture-rRT-PCR with PLC/PRF/5, L20B, and BGM cell lines). Sabin polioviruses were detected in a majority of samples using BMFS (37/42) and two-phase separation (32/42). There was statistically more frequent detection of Sabin-like PV type 3 in samples concentrated with BMFS (22/42) than by two-phase separation (14/42, p = 0.035), possibly due to greater effective volume assayed (870 mL vs. 150 mL). Despite this effective volume assayed, there was no statistical difference in Sabin-like PV type 1 and Sabin-like PV type 2 detection between these methods (9/42 vs. 8/42, p = 0.80 and 27/42 vs. 32/42, p = 0.18, respectively). This study demonstrated that BMFS can be used for PV environmental surveillance and established a feasible study design for future research.

Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system.

Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.

Rotavirus G and P types circulating in the eastern region of Kenya: predominance of G9 and emergence of G12 genotypes.

BACKGROUND: The World Health Organization has recommended that rotavirus (RV) vaccines be included in all national immunization programs as part of a strategy to control RV-associated diarrheal diseases. Hospital-based surveillance of RV infection is therefore crucial in monitoring the impact pre- and post-vaccine introduction and also to document changes in genotype distribution. This study sought to determine the RV genotypes circulating in the eastern region of Kenya before introduction of the RV vaccine. METHODS: During September 2009 to August 2011, 500 stool samples were collected from children <5 years of age admitted for acute diarrhea in hospitals in the eastern region of Kenya and analyzed for the presence of group A RV using an enzyme immunoassay. G and P genotypes were determined using hemi-nested reverse transcriptase polymerase chain reaction. RESULTS: One hundred and eighty nine out of 500 (38%) samples analyzed were positive for rotavirus. The following G types were detected: G9 (50.9%), G1 (26.8%), G8 (12.1%), G12 (3.1%), G2 (0.6%), mixed G (1.3%) and 5.1% were G nontypeable. P types detected included: P[8] (63.7%), P[4] (12.1%), P[6] (4.5%), mixed P (7.6%) and 12.1% were P nontypeable. The most dominant strain was G9P[8] (35%), followed by G1P[8] (26.8%), G8P[4] (9.6%), G12P[6] (2.5%), G9P[6] (1.9%), G9P[4] (1.3%), G8P[8] (1.3%), and G2P[4] (0.6%). CONCLUSIONS: The present study demonstrates the recurring changing genotypes of RV circulating in Kenya, with genotypes G9, G1 and G8 being the dominant strains circulating in the eastern region of Kenya between 2009 and 2011. Additionally, G12 genotype was detected for the first time in Kenya.

Application of a competitive internal amplification control for the detection of sapoviruses in wastewater.

In this study, a competitive internal amplification control (IAC) was constructed for application in the real-time reverse transcription-polymerase chain reaction detection of sapoviruses (SaVs). A SaV RNA standard was also created for quantification of the virus. The IAC was included in the screening of environmental samples for SaVs. From August 2010 to December 2011, 51 wastewater samples were collected from five provinces in South Africa. SaVs were found in 72.5 % (37/51) of samples, including four samples where detection was initially inhibited. SaV concentrations ranged from 4.24 × 10(3) to 1.31 × 10(6) copies/ml. The IAC successfully identified samples which contained inhibitors and inclusion of an IAC is necessary to ensure the prevalence of SaVs is accurately determined. SaVs are present at high concentrations in wastewater in several provinces of South Africa. This widespread occurrence indicates that SaV circulation in the South African population may be underestimated.

High prevalence of species D human adenoviruses in fecal specimens from Urban Kenyan children with diarrhea.

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 < or =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.

Absence of Helicobacter pylori within the oral cavities of members of a healthy South African community.

Our study aimed to evaluate the oral cavity as a reservoir from where Helicobacter pylori may be transmitted. Histology and PCR amplification were performed. Eighty-four percent of the stomach biopsies tested positive; however, H. pylori was not detected in dental samples, indicating the absence of H. pylori within the oral cavity.

Poliovirus vaccine strains detected in stool specimens of immunodeficient children in South Africa.

After exposure to the oral poliovirus vaccine (OPV), immunocompetent persons excrete poliovirus (PV) vaccine strains for a limited period. In contrast, immunodeficient individuals remain sometimes chronically infected, and in some cases, PV excretion times as long as 10 years have been reported. During prolonged replication in the human intestine, the PV vaccine strain almost invariably reverts its attenuated character and acquires neurovirulent properties (vaccine-derived PVs, or VDPVs), which resemble wild-type PV strains. The aim of this study was to determine the occurrence of OPV strains in stools of immunodeficient children from a selected area in South Africa, as a first step toward future research on the prevalence and potential health impact of VDPVs. In a period of 1 year, a total of 164 stool samples of HIV-positive children aged 4 months to 8 years were studied for the excretion of OPV strains. In addition, 23 stool samples from healthy immunocompetent children were analyzed after receiving their OPV immunization. By applying a reverse transcription-polymerase chain reaction in combination with a nested PCR, a total of 54 enteroviruses (EVs) were detected in the stool specimens of the immunodeficient children. Using restriction enzyme analysis, 13 PVs were distinguished from 41 nonpolio EVs (NPEVs). A Sabin-specific RT-triplex PCR confirmed the presence of 7 Sabin PV type 1, 4 Sabin PV type 3, and 2 Sabin PV type 2 isolates. The majority of the NPEV group was made up of 7 coxsackievirus B3 (CBV3), 6 echovirus 11 (ECV11), 5 ECV9, and 3 coxsackievirus A6 (CAV6) isolates. According to the results, two of the immunodeficient patients (P023 and P140) who had received their last OPV immunization more than 15 months before (vaccinated at 14 weeks of age) tested positive for Sabin PVs types 3 and 1, respectively. A 5-year-old immunodeficient patient (P052) who had received her last OPV immunization more than 42 months before (vaccinated at 18 months of age) tested positive for Sabin PV type 1. These results suggested that immunodeficient patients vaccinated with OPV might excrete potentially pathogenic VDPVs for a prolonged period. These VDPVs may circulate in the community, resulting in possible infections in the unvaccinated population. Therefore, the information obtained in this study would be essential for strategies aimed at the protection of both immunodeficient as well as immunocompetent individuals against complications of vaccination with OPV.

Incidence of adenoviruses in raw and treated water.

Adenoviruses are of major public health importance and are associated with a variety of clinical manifestations, i.e. gastroenteritis, eye infections and respiratory infections. The importance of water in the epidemiology of adenoviruses and the potential health risks constituted by adenoviruses in water sources and supplies are widely recognised. This study was conducted to assess the incidence of human adenoviruses in raw and treated water systems. Various raw and treated water were routinely monitored for the presence of adenoviruses, over a 1-year period (July 2000-June 2001). The supplies were derived from acceptable quality surface water sources using treatment processes, which conform to international standards for the production of safe drinking water. Adenoviruses were detected by firstly amplifying the viruses in cell cultures and then amplifying the extracted nucleic acids of these viruses using molecular techniques (nested PCR). The results indicated human adenoviruses present in 13 (12.75%) of the raw and 9 (4.41%) of the treated water samples tested. The combination of cell culture and nested PCR has proved to be a quick and reliable method for the detection of adenoviruses in water environments.