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1. 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).

Author

Scheibe A, Young K, Versfeld A, Spearman CW, Sonderup MW, Prabdial-Sing N, Puren A, and Hausler H

Subjects
Adult, Cross-Sectional Studies, Female, Genotype, HIV Antibodies blood, HIV Infections drug therapy, HIV Infections etiology, HIV Infections prevention & control, Hepatitis B etiology, Hepatitis B Surface Antigens blood, Hepatitis C etiology, Hepatitis C Antibodies blood, Homosexuality, Male, Humans, Male, Prevalence, Prospective Studies, Risk Factors, Sex Workers, Sexual and Gender Minorities, South Africa epidemiology, Substance Abuse, Intravenous complications, Viral Load, Young Adult, HIV immunology, HIV Infections epidemiology, Hepacivirus genetics, Hepacivirus immunology, Hepatitis B epidemiology, Hepatitis B virus immunology, Hepatitis C epidemiology
Abstract

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.

Published
2020
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2. Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012.

Author

Prabdial-Sing N, Chirwa T, Thaver J, Smuts H, Vermeulen M, Suchard M, and Puren AJ

Subjects
Adolescent, Adult, Aged, Child, Female, Genotyping Techniques, Hepacivirus isolation & purification, Hepatitis C epidemiology, Humans, Male, Middle Aged, Molecular Epidemiology, RNA, Viral blood, Real-Time Polymerase Chain Reaction, Retrospective Studies, South Africa epidemiology, Young Adult, Blood virology, Blood Donors, Genotype, Hepacivirus classification, Hepacivirus genetics, Hepatitis C virology
Abstract

There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease., (© 2016 John Wiley & Sons Ltd.)

Published
2016
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3. Naturally occurring resistance mutations within the core and NS5B regions in hepatitis C genotypes, particularly genotype 5a, in South Africa.

Author

Prabdial-Sing, N., Blackard, J.T., Puren, A.J., Mahomed, A., Abuelhassan, W., Mahlangu, J., Vermeulen, M., and Bowyer, S.M.

Subjects
*GENETIC mutation, *HEPATITIS C, *INTERFERONS, *RIBAVIRIN, *EPITOPES
Abstract

Approximately 1 million South Africans are infected with Hepatitis C virus (HCV). The standard of care (SOC) in South Africa is combination therapy (pegylated interferon and ribavirin). HCV genotypes and/or mutations in the core/non-structural regions have been associated with response to therapy and/or disease progression. This study examines mutations in the core (29–280 amino acids, including ∼90 E1 amino acids) and NS5B (241–306 amino acids) regions on pre-treatment isolates from patients attending Johannesburg hospitals or asymptomatic South African blood donors. Diversity within known CD4+ and CD8+ T-cell epitopes was also explored. Samples grouped into subtypes 1a(N = 10) 1b(N = 12), 3a(N = 5), 4a(N = 3) and 5a(N = 61). Two mutations, associated with interferon resistance–R70Q and T110N–were present in 29 genotype 5a core sequences. No resistance mutation to NS5B nucleotide inhibitors, sofosbuvir was found. Six putative CD8+ and one CD4+ T-cell epitope sequence in the core region showed binding scores of <300 IC 50 nM to HLA alleles frequently observed in the South African population. No known CD8+ and CD4+ T-cell epitopes were mapped in the NS5B region. The analysis begs the question whether those infected with genotype 5a will benefit better on interferon-free combination therapies. This study provides new insight into one of the lesser studied HCV genotypes and compares the diversity seen in a large pre-treatment cohort with other subtypes. [ABSTRACT FROM AUTHOR]

Published
2016
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4. Palindromic-nucleotide substitutions (PNS) of hepatitis C virus genotypes 1 and 5a from South Africa

Author

Prabdial-Sing, N., Giangaspero, M., Puren, A.J., Mahlangu, J., Barrow, P., and Bowyer, S.M.

Subjects
*NUCLEOTIDE sequence, *HEPATITIS C virus, *DISEASE prevalence, *HEPATITIS C, *PHYLOGENY, *GENETIC mutation
Abstract

Abstract: The HCV stem–loop subdomains III-a, -b and -c have been shown to reflect the characteristics of the virus and identify isolates by genus, genotype and subtype. The aim of this study was to investigate the genotype-specific PNS within the 5′UTR of prevalent HCV genotypes (1 and 5a) found in South Africa. The genotype 5a (N =35) and genotype 1 sequences (N =20) were from patients presenting with liver disease or haemophilia, respectively. PNS HCV typing characteristics, defined previously, were observed. The PNS method differentiated subtypes 1a and 1c from subtype 1b by the base change at nucleotide position 243. A lack of structural data from the variable loci V1 of the 5′UTR did not allow us to further differentiate the subtypes of 1. A nucleotide change from a thymine (T) to a cytosine (C) at position 183 was found among genotype 5a sequences. This mutation changed the stable U–AA bond to a Y AA bulge at base-pair position 32. There was an insertion of a single adenine (A) at position 207. At present PNS analysis is labour intensive but, with development of further software to aid the computer analysis, it has the potential to provide a rapid, reliable alternative to phylogenetic analysis. [Copyright &y& Elsevier]

Published
2011
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5. Global prevalence and genotype distribution of hepatitis C virus infection in 2015:a modelling study

Author

Hans Van Vlierberghe, Soo Aleman, Naveed Z. Janjua, Henry Lik-Yuen Chan, Olufunmilayo A. Lesi, Irena Hrstić, Abdullah M. Assiri, William Rosenberg, Moon sing Lai, Vladimir Chulanov, Jan Sperl, Beat Müllhaupt, Michael Manns, William Sievert, Sabahattin Kaymakoglu, Cesar Yaghi, Evy Yunihastuti, Pierre Van Damme, Jon G. Jonasson, Antonio Javier Blasco, Young Sik Kim, S. Olafsson, Rohani Jahis, Christoph Sarrazin, Manik Sharma, Aasim Yusuf, Omer Hajelssedig, Javier García-Samaniego, Boris Lukšić, Peter Stärkel, Stefan Zeuzem, Stephen Oguche, E. A. Croes, Abdullah S. Alghamdi, Richard Njouom, CE Omuemu, Carlos E Brandão Mello, Adam Mahomed, Behzad Hajarizadeh, Ogu Omede, Said A. Al-Busafi, Sarah Robbins, Peer Brehm Christensen, Ammal M. Metwally, Béla Hunyady, Gamal Esmat, Ivane Gamkrelidze, Maheeba Abdulla, Suzanne Norris, Sarah Blach, Harald Hofer, Maria C Mendes Correa, Devin Razavi-Shearer, Matti Maimets, Chien-Jen Chen, Peter Jarcuska, Marian Oltman, Francesco Negro, Ilias Gountas, Ayman Yosry, Sona Frankova, Adrian Goldis, Laurentius A. Lesmana, Ivan Schréter, Danute Speiciene, Kevork M. Peltekian, Berhane Redae, Stuart K. Roberts, Valentina Liakina, Seyed M Alavian, Wai-cheung C Lao, Ziv Ben-Ari, Imad Al Ghazzawi, Cheryl Brunton, Rudolf E. Stauber, Akram Khan, Tung-Hung Su, Manal H El-Sayed, Kimberly Murphy, Kyriakos Souliotis, Adriana Vince, Ramazan Idilman, Christophe Moreno, Angelos Hatzakis, Lewis R. Roberts, Richard Phillips, Jason Grebely, Michael Gschwantler, Hugo Cheinquer, Vana Sypsa, Samir Shah, Wolfgang Vogel, M. Blachier, Abate Bane, Henri Leleu, Saeed Hamid, Ohene Opare-Sem, Hamad Al-Romaihi, Wan-Long Chuang, Alexander J. Thompson, Agita Jeruma, Robert Flisiak, Catherine A.M. Stedman, Ingo van Thiel, Carole Seguin-Devaux, Jonathan Schmelzer, Juan F.Sanchez Avila, Rui Tato Marinho, Muhammad S. Memon, Nina Weis, Rosmawati Mohamed, Florian Bihl, Moon Seok Choi, David Kershenobich, Vic Arendt, Yee Tak Hui, Mei Hsuan Lee, N. N. Pimenov, Saad Al Kaabi, Ken Pasini, Henrik Krarup, Stefan Mauss, Shahin Merat, Khalid Al Namaani, Rong-Nan Chien, Perttu Arkkila, Henk W. Reesink, Françoise Roudot-Thoraval, Paul Marotta, Shirley Owusu-Ofori, Fadi H. Mourad, Abdul Rahman Bizri, Chris Estes, Heiner Wedemeyer, Faisal M. Sanai, Mihály Makara, Stephen D. Ryder, Mel Krajden, Laura Cisneros, Adriaan J. van der Meer, Eli Zuckerman, Matthew E. Cramp, Rui Sarmento-Castro, Magnus Gottfredsson, Gregory J. Dore, Huma Qureshi, Yasser Kamel, Olga Sagalova, Rifaat Safadi, Wim Laleman, Solomon Obekpa, Karolin Falconer, Edward Gane, Philip Bruggmann, Fernando Bessone, Jia-Horng Kao, Daniel Lavanchy, Riina Salupere, Anne Øvrehus, Ulus Salih Akarca, Monique Andersson, Man-Fung Yuen, Ala I. Sharara, Olav Dalgard, Homie Razavi, Gamal Shiha, Paulo R. Ferreira, George V. Papatheodoridis, Anatoly Shevaldin, Jawad Khamis, Waseem Hamoudi, Kathryn Razavi-Shearer, Vincent Ws Wong, Loreta A. Kondili, Maria Lucia Gomes Ferraz, Wasim Jafri, Pablo Lázaro, Faisal Abaalkhail, David H. Muljono, Youssif Al Serkal, Imam Waked, Zaher Koutoubi, Oidov Baatarkhuu, Nahum Méndez-Sánchez, Abraham O. Malu, Daniel Struck, Helen Nde, Alnoor Ramji, Ahmed Abdou, Antoine Abou Rached, Michael Li, Diana Nonković, Jorge Daruich, Ezequiel Ridruejo, Gül Ergör, Ann-Sofi Duberg, Krzysztof Tomasiewicz, Filipe Calinas, Hossein Poustchi, Layla Al-Dabal, Jessie Gunter, Mark W. Sonderup, Colm Bergin, Mario G. Pessoa, Jonas Valantinas, Asad Chaudhry, Junko Tanaka, Tsendsuren S. Oyunsuren, Soek Siam Tan, Vivek A. Saraswat, Young-Suk Lim, Ibrahim Altraif, Victor de Ledinghen, Faryal Al Lawati, Mette Rye Clausen, Ieva Tolmane, Antonio Craxì, Abdulrahman Aljumah, Elmoubashar Farag, Inka Aho, Sayed Himatt, Nishi Prabdial-Sing, Blach S., Zeuzem S., Manns M., Altraif I., Duberg A.-S., Muljono D.H., Waked I., Alavian S.M., Lee M.-H., Negro F., Abaalkhail F., Abdou A., Abdulla M., Abou Rached A., Aho I., Akarca U., Al Ghazzawi I., Al Kaabi S., Al Lawati F., Al Namaani K., Al Serkal Y., Al-Busafi S.A., Al-Dabal L., Aleman S., Alghamdi A.S., Aljumah A.A., Al-Romaihi H.E., Andersson M.I., Arendt V., Arkkila P., Assiri A.M., Baatarkhuu O., Bane A., Ben-Ari Z., Bergin C., Bessone F., Bihl F., Bizri A.R., Blachier M., Blasco A.J., Brandao Mello C.E., Bruggmann P., Brunton C.R., Calinas F., Chan H.L.Y., Chaudhry A., Cheinquer H., Chen C.-J., Chien R.-N., Choi M.S., Christensen P.B., Chuang W.-L., Chulanov V., Cisneros L., Clausen M.R., Cramp M.E., Craxi A., Croes E.A., Dalgard O., Daruich J.R., De Ledinghen V., Dore G.J., El-Sayed M.H., Ergor G., Esmat G., Estes C., Falconer K., Farag E., Ferraz M.L.G., Ferreira P.R., Flisiak R., Frankova S., Gamkrelidze I., Gane E., Garcia-Samaniego J., Khan A.G., Gountas I., Goldis A., Gottfredsson M., Grebely J., Gschwantler M., Guimaraes Pessoa M., Gunter J., Hajarizadeh B., Hajelssedig O., Hamid S., Hamoudi W., Hatzakis A., Himatt S.M., Hofer H., Hrstic I., Hui Y.-T., Hunyady B., Idilman R., Jafri W., Jahis R., Janjua N.Z., Jarcuska P., Jeruma A., Jonasson J.G., Kamel Y., Kao J.-H., Kaymakoglu S., Kershenobich D., Khamis J., Kim Y.S., Kondili L., Koutoubi Z., Krajden M., Krarup H., Lai M.-S., Laleman W., Lao W.-C., Lavanchy D., Lazaro P., Leleu H., Lesi O., Lesmana L.A., Li M., Liakina V., Lim Y.-S., Luksic B., Mahomed A., Maimets M., Makara M., Malu A.O., Marinho R.T., Marotta P., Mauss S., Memon M.S., Mendes Correa M.C., Mendez-Sanchez N., Merat S., Metwally A.M., Mohamed R., Moreno C., Mourad F.H., Mullhaupt B., Murphy K., Nde H., Njouom R., Nonkovic D., Norris S., Obekpa S., Oguche S., Olafsson S., Oltman M., Omede O., Omuemu C., Opare-Sem O., Ovrehus A.L.H., Owusu-Ofori S., Oyunsuren T.S., Papatheodoridis G., Pasini K., Peltekian K.M., Phillips R.O., Pimenov N., Poustchi H., Prabdial-Sing N., Qureshi H., Ramji A., Razavi-Shearer D., Razavi-Shearer K., Redae B., Reesink H.W., Ridruejo E., Robbins S., Roberts L.R., Roberts S.K., Rosenberg W.M., Roudot-Thoraval F., Ryder S.D., Safadi R., Sagalova O., Salupere R., Sanai F.M., Sanchez Avila J.F., Saraswat V., Sarmento-Castro R., Sarrazin C., Schmelzer J.D., Schreter I., Seguin-Devaux C., Shah S.R., Sharara A.I., Sharma M., Shevaldin A., Shiha G.E., Sievert W., Sonderup M., Souliotis K., Speiciene D., Sperl J., Starkel P., Stauber R.E., Stedman C., Struck D., Su T.-H., Sypsa V., Tan S.-S., Tanaka J., Thompson A.J., Tolmane I., Tomasiewicz K., Valantinas J., Van Damme P., Van Der Meer A.J., Van Thiel I., Van Vlierberghe H., Vince A., Vogel W., Wedemeyer H., Weis N., Wong V.W.S., Yaghi C., Yosry A., Yuen M.-F., Yunihastuti E., Yusuf A., Zuckerman E., Razavi H., Polaris Observ HCV Collaborators, Negro, Francesco, and Ege Üniversitesi

Subjects
Viremia/epidemiology, Population ageing, medicine.medical_specialty, CIENCIAS MÉDICAS Y DE LA SALUD, Delphi Technique, Genotype, Voxilaprevir, Genotype, Global Health, Hepatitis C, Eradication, Modelling study, Medicina Clínica, ddc:616.07, Global Health, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, Cost of Illness, Epidemiology, Journal Article, medicine, Global health, Prevalence, Humans, Viremia, 030212 general & internal medicine, Disease Eradication, Disease burden, ddc:616, Hepatology, Hepatitis C, Chronic/epidemiology, business.industry, Gastroenterology, Hepatitis C, Glecaprevir, Hepatitis C, Chronic, medicine.disease, Viremia/epidemiology/genetics, Pibrentasvir, Global Health/statistics & numerical data, HCV, HEPATITIS C, 030211 gastroenterology & hepatology, Medicina Critica y de Emergencia, Human medicine, business, Chronic/epidemiology/genetics/prevention & control, Demography
Abstract

WOS: 000426979400014, PubMed ID: 28404132, Background The 69th World Health Assembly approved the Global Health Sector Strategy to eliminate hepatitis C virus (HCV) infection by 2030, which can become a reality with the recent launch of direct acting antiviral therapies. Reliable disease burden estimates are required for national strategies. This analysis estimates the global prevalence of viraemic HCV at the end of 2015, an update of-and expansion on-the 2014 analysis, which reported 80 million (95% CI 64-103) viraemic infections in 2013. Methods We developed country-level disease burden models following a systematic review of HCV prevalence (number of studies, n=6754) and genotype (n=11 342) studies published after 2013. A Delphi process was used to gain country expert consensus and validate inputs. Published estimates alone were used for countries where expert panel meetings could not be scheduled. Global prevalence was estimated using regional averages for countries without data. Findings Models were built for 100 countries, 59 of which were approved by country experts, with the remaining 41 estimated using published data alone. The remaining countries had insufficient data to create a model. The global prevalence of viraemic HCV is estimated to be 1.0% (95% uncertainty interval 0.8-1.1) in 2015, corresponding to 71.1 million (62.5-79.4) viraemic infections. Genotypes 1 and 3 were the most common cause of infections (44% and 25%, respectively). Interpretation The global estimate of viraemic infections is lower than previous estimates, largely due to more recent (lower) prevalence estimates in Africa. Additionally, increased mortality due to liver-related causes and an ageing population may have contributed to a reduction in infections., John C Martin Foundation, John C Martin Foundation.

Published
2017

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