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The use of wastewater for SARS-CoV-2 surveillance is a useful complementary tool to clinical surveillance. The aims of this study were to characterize SARS-CoV-2 from wastewater samples, and to identify variants of concern present in samples collected from wastewater treatment plants in South African urban metros from April 2021 to January 2022. A total of 325 samples were collected from 15 wastewater treatment plants. Nucleic acids were extracted from concentrated samples, and subjected to amplicon-based whole genome sequencing. To identify variants of concerns and lineages, we used the Freyja tool (https://github.com/andersen-lab/Freyja), which assigns each sample with the prevalence of each variant present. We also used signature mutation analysis to identify variants in each wastewater treatment site. A heatmap was generated to identify patterns of emerging mutations in the spike gene using Excel conditional formatting. Using the Freyja tool, the Beta variant was detected and became predominate from April to June 2021 followed by the Delta variant and lastly the Omicron variant. Our heatmap approach was able to identify a pattern during the changes of predominate variant in wastewater with the emergence of mutations and the loss of others. In conclusion, sequencing of SARS-CoV-2 from wastewater largely corresponded with sequencing from clinical specimens. Our heatmap has the potential to detect new variants prior to emergence in clinical samples and this may be particularly useful during times of low disease incidence between waves, when few numbers of positive clinical samples are collected and submitted for testing. A limitation of wastewater sequencing is that it is not possible to identify new variants, as variants are classified based on known mutations in clinical strains.

Hepatitis B, a potentially life-threatening viral infection of the liver, remains a global public health concern despite the availability of effective vaccines for over three decades. Given that most HBsAg studies targeted distinct cohorts, we aimed to provide HBsAg data nationally in the public health sector of South Africa.We conducted a cross-sectional study on HBsAg tests obtained from the National Health Laboratory Service Central Data Warehouse for tests performed nationally during the period 2015 to 2019. Annual data were cleaned and appended prior to data interrogation to determine and analyse the total number of cases who tested positive for HBsAg and the number of chronic HBV infections.We identified 176,530 cases who tested positive for HBsAg at least once during the 5-year period, with a test positivity rate of 9%. Chronic infections were identified in 6.4% of HBsAg positive cases. Clearance of HBsAg was observed in 5,571 cases, inclusive of clearance in 135 chronic cases. Significantly more males tested positive for HBsAg and were chronically infected (p < 0.0001). Amongst individuals who were vaccine-eligible as infants (0 to 19 years old), 4,980 tested HBsAg positive, of which 22.7% (1,131) were under 5 years old, with a HBsAg population positivity rate of 0.02% and test positivity rate of 4.83%.HBsAg positivity amongst vaccine-eligible individuals is likely due to suboptimal vaccine coverage rates reported for South Africa. Without a birth dose of the HBV vaccine and lack of routine HBsAg screening at antenatal care, it is likely that the majority of HBsAg positive cases under 5 years old were vertically infected. Optimal HBV vaccine coverage, inclusive of a birth dose, is key to eliminating horizontal and vertical transmission of HBV. Early identification of HBV chronicity is fundamental in reducing the risk of liver cirrhosis and hepatocellular carcinoma.

Introduction. Global poliovirus eradication is a public health emergency of international concern. The acute flaccid paralysis (AFP) surveillance programme in South Africa has been instrumental in eliminating polioviruses and keeping the country poliovirus free. Gap statement. The sensitivity of surveillance for polioviruses by every African country is of global interest in the effort to ensure global health security from poliovirus re-emergence. Aim. To describe the epidemiology of polioviruses from AFP cases and environmental samples in South Africa and to report the performance of the AFP surveillance system for the years 2016–2019 against targets established by the World Health Organization (WHO). Methods. Stool specimens from AFP or suspected AFP cases were received and tested as per WHO guidelines. Environmental samples were gathered from sites across the Gauteng province using the grab collection method. Concentration was effected by the two-phase polyethylene glycol method approved by the WHO. Suspected polioviruses were isolated in RD and/or L20B cell cultures through identification of typical cytopathic effects. The presence of polioviruses was confirmed by intratypic differentiation PCR. All polioviruses were sequenced using the Sanger method, and their VP1 gene analysed for mutations. Results. Data from 4597 samples (2385 cases) were analysed from the years 2016–2019. Two cases of immunodeficiency-associated vaccine-derived poliovirus (iVDPV) type 3 were detected in 2017 and 2018. A further 24 Sabin type 1 or type 3 polioviruses were detected for the 4 years. The national surveillance programme detected an average of 3.1 cases of AFP/100 000 individuals under 15 years old (2.8/100 000–3.5/100 000). The stool adequacy of the samples received was 53.0 % (47.0–55.0%), well below the WHO target of 80 % adequacy. More than 90 % of results were released from the laboratory within the turnaround time (96.6 %) and non-polio enteroviruses were detected in 11.6 % of all samples. Environmental surveillance detected non-polio enterovirus in 87.5 % of sewage samples and Sabin polioviruses in 12.5 % of samples. Conclusion. The AFP surveillance programme in South Africa is sensitive to detect polioviruses in South Africa and provided no evidence of wild poliovirus or VDPV circulation in the country.

Pocapavir exhibits antiviral activity against both polio and nonpolio enteroviruses. There is limited experience of the use of this investigational drug in young children with enteroviral infection. We describe the successful clearance of prolonged immunodeficiency-associated vaccine-derived type 3 poliovirus infection by pocapavir in an infant with underlying X-linked agammaglobulinemia.

Primary B-cell immunodeficiencies are risk factors for the generation of vaccine-derived polioviruses. We report immunodeficiency-associated vaccine-derived poliovirus serotype 3 in an 11-week-old boy with X-linked agammaglobulinemia. Unique characteristics of this case include early age of presentation, high viral evolutionary rate, and the child’s perinatal exposure to human immunodeficiency virus.

IntroductionThe prevalence of HIV infection in South African pregnant women has been approximately 30% over the past decade; however, there has been a steady decline in mother-to-child transmission of HIV from 8% in 2008 to MethodsSerum polio neutralization antibody titres were evaluated to serotype-1, serotype-2 and serotype-3 at 6, 10 and 18 weeks of age. Antibody titres ≥8 were considered seropositive and sero-protective.ResultsAt 18 weeks of age, following the complete primary series of four OPV doses, no differences in GMTs, percentage of infants with sero-protective titres and median fold change in antibody titre (18 weeks vs 6 weeks) were observed in HEU infants (n = 114) and HIV+/ART+ infants (n = 162) compared to HU infants (n = 104) for the three polio serotypes. However, comparing HIV+/ART- infants (n = 70) to HU infants at 18 weeks of age, we observed significantly lower GMTs for serotype-1 (p = 0.022), serotype-2 (pConclusionDelaying initiation of ART in HIV-infected infants was associated with an attenuated immune response to OPV following a four-dose primary series of vaccines, whereas immune responses to OPV in HIV-infected children initiated on ART early in infancy and HEU children were similar to HU infants.

Introduction: Guillain-Barré Syndrome (GBS) is an autoimmune disease characterized by acute or subacute symmetrical ascending motor weakness, areflexia, and mild-to-moderate sensory abnormalities. Campylobacter jejuni is reported to be the most common bacterium associated with GBS cases. Despite the eradication of polio, the number of reported GBS cases remains considerably high in South Africa with the causative agents not being well described. Methodology: The aim of the study was to investigate the proportion of Campylobacter spp. detected in stool specimens from patients with symptoms of acute flaccid paralysis (AFP). Stool specimens from patients presenting with AFP, that were negative for polio and non-polio enteroviruses (NPENT), were processed and screened for the presence of Campylobacter spp. using quantitative PCR (qPCR). Results: Of the 512 stool specimens screened between October 2014 to December 2015, 12% (62/512) were positive for Campylobacter spp. Of these 62 Campylobacter infections: 77.4% (48/62) was C. jejuni; 19.4% (12/62) was Campylobacter coli; 3.2% (2/62) was mixed infections of C. jejuni and C. coli. Conclusions: True association of the disease with Campylobacter spp. will enable the proportion of Campylobacter-induced GBS to be better described in South Africa; this can only be done through systematic studies that include bacterial culture and serology together with molecular methodologies.