Hepatitis B infection status among South Africans attending public health facilities over a five-year period: 2015 to 2019.

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. The aim of our study was to provide national data on active hepatitis B infections in the public health sector of South Africa. We conducted retrospective analyses on national laboratory data over the period 2015 to 2019. We identified 176,530 cases who tested positive for HBsAg (active infection) with a test positivity rate of 9.02%. Of these active infections, 11,355 (6.43%) were found to be chronically infected. We linked 24,839 (14.07%) and 2,461 (21.67%) HBeAg positive results to all active HBV infections and identified chronic infections respectively. Clearance of HBsAg was observed in 5,569 cases, inclusive of clearance in 135 chronic cases. Active HBV infections were significantly higher in men than women over the five years (p < 0.0001). Among individuals who were vaccine-eligible as infants (0 to 19 years old), we observed 4,981 active HBV infections, including 1,131 infections under five years old, majority of which (65.78%) were under one year old. In the under five-year age group, the HBsAg population positivity rate was 0.02% and test positivity rate was 4.83%. Among all women with active HBV infections (78,935), 85.17% were of reproductive age and of these, 13.73% were HBeAg positive. Without a birth dose of the HBV vaccine, lack of routine HBsAg screening at antenatal care, and HBsAg and HBeAg prevalence among women of reproductive age, it is likely that the majority of cases under five 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 through real time data analysis is fundamental in reducing the risk of liver cirrhosis and hepatocellular carcinoma.

Prevalence and incidence rates of laboratory-confirmed hepatitis B infection in South Africa, 2015 to 2019.

BACKGROUND: Hepatitis B virus (HBV), a global public health threat, is targeted for elimination by 2030. As national HBV prevalence and incidence is lacking for South Africa, our study aimed to provide such data in the public health sector. METHODS: We analysed laboratory-confirmed HBV data from 2015 to 2019 to determine annual prevalence and incidence rates of HBV infection per 100,000 population, HBsAg and anti-HBc IgM test positivity rates, and HBsAg and anti-HBc IgM testing rates per 100,000 population. Time trend and statistical analyses were performed on HBsAg and anti-HBc IgM test positivity rates. RESULTS: The national prevalence rate of HBV infection per 100,000 population increased from 56.14 in 2015 to 67.76 in 2019. Over the five years, the prevalence rate was higher in males than females, highest amongst individuals 25 to 49 years old and highest in Gauteng province. The HBsAg test positivity rate dropped from 9.77% in 2015 to 8.09% in 2019. Over the five years, the HBsAg test positivity rate was higher in males than females, amongst individuals 25 to 49 years old and amongst individuals of Limpopo province. Amongst HBsAg positive children under 5 years old, the majority (65.7%) were less than a year old. HBsAg testing rates per 100,000 population were higher in females under 45 years of age and in males 45 years and above. The national incidence rate of acute HBV infection per 100,000 population dropped from 3.17 in 2015 to 1.69 in 2019. Over the five-year period, incidence rates were similar between males and females, highest amongst individuals 20 to 39 years old and highest in Mpumalanga province. Amongst individuals 20 to 24 years old, there was a substantial decline in the incidence and anti-HBc IgM test positivity rates over time. Anti-HBc IgM testing rates per 100,000 population were higher in females under 40 years of age and in males 40 years and above. CONCLUSION: Critical to hepatitis B elimination is strengthened infant vaccination coverage and interruption of vertical transmission. Transmission of HBV infection in adults may be reduced through heightened awareness of transmission routes and prevention measures.

Establishment of Outbreak Thresholds for Hepatitis A in South Africa Using Laboratory Surveillance, 2017-2020.

As South Africa transitions from endemic to intermediate endemicity, hepatitis A surveillance needs strengthening to monitor trends in disease incidence and to identify outbreaks. We used passive laboratory-based surveillance data from the National Health Laboratory Services to calculate national hepatitis A incidence and to establish thresholds for outbreaks. Incidence was calculated by age and geographic location. The static threshold used two or three standard deviations (SDs) above the mean hepatitis A incidence in 2017-2019, and a cumulative summation (CuSum2) threshold used three SDs above the mean of the preceding seven months. These thresholds were applied to hepatitis A data for 2020. From 2017 to 2020, the mean incidence of hepatitis A IgM was 4.06/100,000 and ranged from 4.23 to 4.85/100,000 per year. Hepatitis A incidence was highest in the Western Cape province (WCP) (7.00-10.92/100,000 per year). The highest incidence was in the 1-9-year-olds. The incidence of hepatitis A in 2020 exceeded the static threshold in two districts of the WCP: Cape Winelands in January and Overberg district in August. The provincial incidence did not exceed the static and CuSum2 thresholds. District-level analysis using either threshold was sensitive enough to monitor trends and to alert district health authorities, allowing early outbreak responses.

The performance of hepatitis C virus (HCV) antibody point-of-care tests on oral fluid or whole blood and dried blood spot testing for HCV serology and viral load among individuals at higher risk for HCV in South Africa.

BACKGROUND AND AIMS: To enhance screening and diagnosis in those at-risk of hepatitis C virus (HCV), efficient and improved sampling and testing is required. We investigated the performance of point-of-care (POC) tests and dried blood spots (DBS) for HCV antibody and HCV RNA quantification in individuals at higher risk for HCV (people who use and inject drugs, sex workers and men who have sex with men) in seven South African cities. METHODS: Samples were screened on the OraQuick HCV POC test (471 whole blood and 218 oral fluid); 218 whole blood and DBS paired samples were evaluated on the ARCHITECT HCV antibody (Abbott) and HCV viral load (COBAS Ampliprep/COBAS TaqMan version 2) assays. For HCV RNA quantification, 107 dB were analyzed with and without normalization coefficients. RESULTS: POC on either whole blood or oral fluid showed an overall sensitivity of 98.5% (95% CI 97.4-99.5), specificity of 98.2% (95% CI 98.8-100) and accuracy of 98.4% (95% CI 96.5-99.3). On the antibody immunoassay, DBS showed a sensitivity of 96.0% (95% CI 93.4-98.6), specificity of 97% (95% CI 94.8-99.3) and accuracy of 96.3% (95% CI 93.8-98.8). A strong correlation (R 2 = 0.90) between viral load measurements for DBS and plasma samples was observed. After normalization, DBS viral load results showed an improved bias from 0.5 to 0.16 log10 IU/mL. CONCLUSION: The POC test performed sufficiently well to be used for HCV screening in at-risk populations. DBS for diagnosis and quantification was accurate and should be considered as an alternative sample to test. POC and DBS can help scale up hepatitis services in the country, in light of our elimination goals.

Hepatitis B, hepatitis C and HIV prevalence and related sexual and substance use risk practices among key populations who access HIV prevention, treatment and related services in South Africa: findings from a seven-city cross-sectional survey (2017).

BACKGROUND: People who use drugs including people who inject drugs (PWUD/ID), sex workers (SWs) and men who have sex with men (MSM) are at increased risk of HIV and viral hepatitis infection. Limited epidemiological data on the infections exists in key populations (KPs) in South Africa. We investigated the prevalence of hepatitis B (HBV), hepatitis C (HCV) and HIV and selected risk factors among these KPs to inform effective responses. METHODS: We used convenience sampling to recruit a targeted 3500 KPs accessing HIV-related health services across Cape Town (SWs, MSM, PWUD/ID), Durban (SWs, PWUD/ID), Pietermaritzburg (SWs), Mthatha (SWs), Port Elizabeth (SWs), Johannesburg (MSM) and Pretoria (MSM and PWUD/ID) into a cross-sectional survey. An interviewer questionnaire to assess socio-demographic characteristics, drug use and sexual risk practices, was administered. HBV surface antigen (HBsAg); HCV antibody, viral load and genotype, and HIV antibody, was tested. RESULTS: Among the 3439 people included in the study (1528 SWs, 746 MSM, 1165 PWUD/ID) the median age was 29 years, most participants were black African (60%), and 24% reported homelessness. 82% reported substance use in the last month, including alcohol (46%) and heroin (33%). 75% were sexually active in the previous month, with condom use at last sex at 74%. HIV prevalence was 37% (highest among SWs at 47%), HBsAg prevalence 4% (similar across KPs) and HCV prevalence was 16% (highest among PWUD/ID at 46%). CONCLUSIONS: HBV, HCV and HIV pose a health burden for KPs in South Africa. While HIV is key for all included KPs, HCV is of particular importance to PWUD/ID. For KPs, HBV vaccination and behavioural change interventions that support consistent condom and lubricant access and use are needed. Coverage of opioid substitution therapy and needle and syringe services, and access to HCV treatment for PWUD/ID need to be expanded.

Hepatitis B sero-prevalence in children under 15 years of age in South Africa using residual samples from community-based febrile rash surveillance.

INTRODUCTION AND METHODS: Hepatitis B is a vaccine preventable disease and is notifiable in South Africa. Hepatitis B vaccination was incorporated into the Expanded Programme on Immunisation in South Africa in 1995. We used a convenience sample from community-based febrile rash surveillance in 2013 to estimate hepatitis B sero-prevalence. Of samples serologically negative for acute measles infection, 450 samples spanning nine provinces of South Africa were tested for hepatitis B surface antigen (HBsAg), hepatitis B surface antibody (anti-HBs) and hepatitis B core antibody (anti-HBc). RESULTS: Two children (2/450; 0.4%) tested positive for HBsAg. Three hundred and three children (67.3%) had evidence of vaccine induced immunity. Vaccine induced immunity was present in 80.2% of 1-5 year olds, but only 60.3% of 10-14 year olds. Natural immunity, indicating exposure to circulating hepatitis B, was present in 13/450 (2.9%) children. CONCLUSION: Chronic hepatitis B in South African has decreased in prevalence from highly endemic levels prior to vaccine introduction to approximately 0.4% in this sample, demonstrating impact of a successful vaccination programme 18 years after introduction. Decreased vaccine-induced immunity with increasing age may reflect waning antibody titres over time.

Understanding hepatitis B, hepatitis C and HIV among people who inject drugs in South Africa: findings from a three-city cross-sectional survey.

BACKGROUND: People who inject drugs (PWID) are at high risk for hepatitis C (HCV), hepatitis B (HBV) and HIV without accessible harm reduction programmes. Coverage of needle and syringe and opioid substitution therapy (OST) services in South Africa is below global recommendations and no hepatitis services exist for PWID. We assessed HCV, HBV and HIV prevalence and risk factors among PWID accessing harm reduction services in Cape Town, Durban and Pretoria to inform policy and programming. METHODS: We conducted a cross-sectional survey among PWID in these cities between August 2016 and October 2017. Participants were opportunistically sampled while accessing services. Study team members administered a questionnaire that assessed sociodemographic characteristics, drug use and sexual risk practices. We tested for HCV (antibody, viral load and genotype), HBV surface antigen (HBsAg) and HIV. Bivariate and multivariate analyses assessed associations with HCV serostatus. RESULTS: Nine hundred and forty-three PWID were included in the per protocol analysis. The majority (87%, 819/943) were male, the overall median age was 29 and most lived on the street (66%, 626/943). At last injection, 77% (722/943) reported using a new needle and syringe and 17% (163/943) shared equipment. HIV prevalence was 21% (196/926), HBsAg positivity 5% (47/936), HCV seroprevalence 55% (513/937), HCV viraemic prevalence (proportion tested with detectable HCV) 43% (404/937) and HCV viraemic rate (proportion HCV antibody positive with detectable HCV) 79% (404/513). HCV genotype 1a (73%, 270/368) was the most prevalent. In multivariate analysis, HCV infection was positively associated with residing in Pretoria (adjusted odds ratio (aOR) 1.27, 95% CI 1.21-1.34), living on the street (aOR 1.90, 95% CI 1.38-2.60), frequent injecting (aOR 1.58, 95% CI 1.15-2.16) and HIV infection (aOR 1.69, 95% CI 1.15-2.47), and negatively associated with black race (aOR 0.52, 95% CI 0.36-0.74) and sexual activity in the previous month (aOR 0.61, 95% CI 0.42-0.88). CONCLUSIONS: HCV and HIV are major health threats affecting PWID in these cities. Access to OST and needle and syringe services needs to be increased and integrated with HCV services. Social and structural factors affecting PWID who live on the street need to be addressed.

Exploring the knowledge, attitudes and practices (KAP) of health care professionals on viral hepatitis notification in Gauteng, South Africa, 2015.

BACKGROUND: Data on viral hepatitis in South Africa is scarce. Although viral hepatitis A, B and C are notifiable conditions in South Africa, discrepancies have been noted in the number of viral hepatitis cases notified by the National Department of Health (NDOH) compared with laboratory confirmed cases from the National Institute for Communicable Diseases (NICD). The aim of the study was to assess the knowledge, attitudes and practices of health care professionals on the notification of viral hepatitis A, B and C. METHODS: A descriptive, cross-sectional study on 385 health care professionals was conducted at Charlotte Maxeke Johannesburg Academic and Tshwane District hospitals in Gauteng province, South Africa, between March and May 2015. A pre-tested, structured questionnaire with 21 (6 demographic and 15 knowledge, attitudes, and practice (KAP)) questions was used to collect information from invited participants. A score was assigned to each KAP question and a mean (SD) score was calculated for each section. Data were analyzed using descriptive statistics in STATA version 13. RESULTS: Of the total 385 respondents, 65% (n = 250) were nurses and 35% (n = 135) were doctors. The overall mean knowledge score for health care professionals was 2.0 ± 1.6 (mean ± SD) out of a score of 6 regarding viral hepatitis notification. Overall mean scores of practice and attitude towards notification were higher at 2.9 ± 0.4 and 3.3 ± 0.7, out of a score of 4 and 5, respectively. Lack of training, poor knowledge, a complex process and excessive workload were some of the reasons for poor notification of viral hepatitis. CONCLUSIONS: Overall, knowledge on notification of viral hepatitis was poor among health care professionals. Adequate training on viral hepatitis, notification process, roles and responsibilities of health care professionals to notify and the implication of viral hepatitis notifications is recommended to improve reporting rate of notifiable diseases and referrals to increase linkage to care.

South African Ebola diagnostic response in Sierra Leone: A modular high biosafety field laboratory.

BACKGROUND: In August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases. METHODS AND FINDINGS: The SA FEDL operated in the Western Area of Sierra Leone, which remained a "hotspot" of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA. CONCLUSIONS: The bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens.

Hepatitis C virus genotype 5a subgenomic replicons for evaluation of direct-acting antiviral agents.

Hepatitis C virus (HCV) exists as six major genotypes that differ in geographical distribution, pathogenesis, and response to antiviral therapy. In vitro replication systems for all HCV genotypes except genotype 5 have been reported. In this study, we recovered genotype 5a full-length genomes from four infected voluntary blood donors in South Africa and established a G418-selectable subgenomic replicon system using one of these strains. The replicon derived from the wild-type sequence failed to replicate in Huh-7.5 cells. However, the inclusion of the S2205I amino acid substitution, a cell culture-adaptive change originally described for a genotype 1b replicon, resulted in a small number of G418-resistant cell colonies. HCV RNA replication in these cells was confirmed by quantification of viral RNA and detection of the nonstructural protein NS5A. Sequence analysis of the viral RNAs isolated from multiple independent cell clones revealed the presence of several nonsynonymous mutations, which were localized mainly in the NS3 protein. These mutations, when introduced back into the parental backbone, significantly increased colony formation. To facilitate convenient monitoring of HCV RNA replication levels, the mutant with the highest replication level was further modified to express a fusion protein of firefly luciferase and neomycin phosphotransferase. Using such replicons from genotypes 1a, 1b, 2a, 3a, 4a, and 5a, we compared the effects of various HCV inhibitors on their replication. In conclusion, we have established an in vitro replication system for HCV genotype 5a, which will be useful for the development of pan-genotype anti-HCV compounds.

Sequence-based in silico analysis of well studied hepatitis C virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds.

BACKGROUND: Host genetics influence the outcome of HCV disease. HCV is also highly mutable and escapes host immunity. HCV genotypes are geographically distributed and HCV subtypes have been shown to have distinct repertoires of HLA-restricted viral epitopes which explains the lack of cross protection across genotypes observed in some studies. Despite this, immune databases and putative epitope vaccines concentrate almost exclusively on HCV genotype 1 class I-epitopes restricted by the HLA-A*02 allele. While both genotype and allele predominate in developed countries, we hypothesise that HCV variation and population genetics will affect the efficacy of proposed epitope vaccines in South Africa. This in silico study investigates HCV viral variability within well-studied epitopes identified in genotype 1 and uses algorithms to predict the immunogenicity of their variants from other less studied genotypes and thus rate the most promising vaccine candidates for the South African population. Six class I- and seven class II- restricted epitope sequences within the core, NS3, NS4B and NS5B regions were compared across the six HCV genotypes using local genotype 5a sequence data together with global data. Common HLA alleles in the South African population are A30:01, A02:01, B58:02, B07:02; DRB1*13:01 and DRB1*03:01. Epitope binding to 13 class I- and 8 class -II alleles were described using web-based prediction servers, Immune Epitope Database, (IEDB) and Propred. Online population coverage tools were used to assess vaccine efficacy. RESULTS: Despite the homogeneity of genotype 1 and genotype 5 over the epitopes, there was limited promiscuity to local HLA-alleles.Host differences will make a putative vaccine less effective in South Africa. Of the 6 well-characterized class I- epitopes, only 2 class I- epitopes were promiscuous and 3 of the 7 class-II epitopes were better conserved and promiscuous. By fine tuning the putative vaccine using an optimal cocktail of genotype 1 and 5a epitopes and local HLA data, the coverage was raised from 65.85% to 91.87% in South African Blacks. CONCLUSION: While in vivo and in vitro studies are needed to confirm immunogenic epitopes, in silico HCV epitope vaccine design which takes into account HCV variation and host allele frequency will maximize population coverage in different ethnic groups.

Hepatitis C virus genotypes in two different patient cohorts in Johannesburg, South Africa.

Previous studies in South African patients have shown that hepatitis C virus (HCV) prevalence is low (2.6%) and genotype 5 is the dominant genotype. This is the first sequence-based genotype study from this country on two different patient groups (haemophiliacs (H) and liver disease (LD) patients) over two time periods (2000-2002 and 2007). Genotype 5 was found to be the dominant genotype in the LD groups, but genotype 1 dominated in the H group. Genotype 2, and a higher prevalence of genotype 3a, was present in the H group when compared to previous South African studies. Genotypes 3 and 4 have been described here in the LD groups for the first time in South Africa, with subtypes 4c and 4g being identified. A separate cluster of genotype 5 sequences were found to have only one adenine at nucleotide position 107 of the 5'UTR, as previously reported. Subtyping in the less conserved NS5B region was used to further characterize the 2000-2002 isolates and validate 5'UTR typing. The study shows that by using reliable methods of genotyping, the prevalence and frequencies of HCV genotypes can be monitored in South Africa for better diagnosis and treatment of the disease.