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Minier N, Guingané AN, Okeke E, Sinkala E, Johannessen A, Andersson MI, Davwar P, Desalegn H, Duguru M, Fall F, Mboup S, Maponga T, Matthews PC, Ramírez Mena A, Ndow G, Orlien SMS, Riches N, Seydi M, Sonderup M, Spearman CW, Stockdale AJ, Taljaard J, Vinikoor M, Wandeler G, Lemoine M, Shimakawa Y, Sombié R. Development and evaluation of a simple treatment eligibility score (HEPSANET) to decentralise hepatitis B care in Africa: a cross-sectional study. Lancet Gastroenterol Hepatol 2024; 9:323-332. [PMID: 38367633 DOI: 10.1016/s2468-1253(23)00449-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/19/2024]
Abstract
BACKGROUND Hepatitis B virus (HBV) elimination requires expanding and decentralising HBV care services. However, peripheral health facilities lack access to diagnostic tools to assess eligibility for antiviral therapy. Through the Hepatitis B in Africa Collaborative Network (HEPSANET), we aimed to develop and evaluate a score using tests generally available at lower-level facilities, to simplify the evaluation of antiviral therapy eligibility in people living with HBV. METHODS We surveyed the availability of clinical and laboratory parameters across different health-care levels in sub-Saharan Africa. We used data from the HEPSANET dataset, the largest cross-sectional dataset of treatment-naive people living with HBV in sub-Saharan Africa, to derive and validate the score. Participants from this dataset were included in the analysis if they were aged 18 years or older and had liver fibrosis stages determined by a liver stiffness measurement or liver histopathology. Participants with co-infections or metabolic disorders were excluded. We allocated participants to the derivation and validation sets by geographical site. In the derivation set, we used stepwise logistic regression to identify the best performing parameters for identifying participants that met the 2017 European Association for the Study of the Liver (EASL) criteria. Regression coefficients were converted into integer points to construct simplified algorithms for different health-care levels. In the validation set, we estimated the area under the receiver operating characteristic, sensitivity, and specificity of the simplified algorithm for identifying antiviral therapy eligibility defined by the 2017 EASL criteria. FINDINGS At 11 sites from eight countries that returned surveys, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and platelet count were generally available at district hospital levels, and hepatitis B e antigen and point-of-care HBV DNA tests were available only at regional and provincial hospital levels or above. Among 2895 participants included from the HEPSANET database (1740 [60·1%] male, 1155 [39·9%] female), 409 (14·1%) met EASL antiviral therapy eligibility criteria. In the derivation set, the optimal district-level hospital score was: ALT (IU/L), less than 40 (0 points), 40-79 (+1), 80 or greater (+2); AST (IU/L), less than 40 (0), 40-79 (+1), 80 or greater (+2); and platelet counts (109/L), less than 100 (+2), 100-149 (+1), 150 or greater (0). When combined with family history and clinical data for decompensated cirrhosis that do not require any biological tests, a cut-off of 2 points or more had a sensitivity and specificity of 82% (95% CI 76-86) and 95% (93-96) to identify treatment-eligible individuals in the derivation set, and 78% (71-85) and 87% (86-89) in the validation set, respectively. INTERPRETATION Using a score incorporating platelet counts, AST, and ALT, the majority of people living with HBV requiring antiviral therapy can be identified. Our findings suggest that clinical staging can be decentralised down to district hospital level in sub-Saharan Africa. FUNDING European Association for the Study of the Liver Foundation, John C Martin Foundation. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Nicolas Minier
- Insitut Pasteur, Université Paris Cité, Unité d'Épidémiologie des Maladies Émergentes, Paris, France
| | - Alice Nanelin Guingané
- Hepato-Gastroenterology Department, Bogodogo University Hospital Center, Ouagadougou, Burkina Faso
| | - Edith Okeke
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Edford Sinkala
- Department of Internal Medicine, University of Zambia, Lusaka, Zambia
| | - Asgeir Johannessen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Infectious Diseases, Vestfold Hospital, Tønsberg, Norway
| | - Monique I Andersson
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences & National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Pantong Davwar
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Hailemichael Desalegn
- Department of Infectious Diseases, Vestfold Hospital, Tønsberg, Norway; Medical Department, St Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Mary Duguru
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Fatou Fall
- Department of Hepatology and Gastroenterology, Hopital Principal de Dakar, Dakar, Senegal
| | - Souleyman Mboup
- L'Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Dakar, Senegal
| | - Tongai Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences & National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Philippa C Matthews
- The Francis Crick Institute, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - Adrià Ramírez Mena
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Gibril Ndow
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; MRC Unit The Gambia, London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Stian M S Orlien
- Department of Infectious Diseases, Vestfold Hospital, Tønsberg, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Nicholas Riches
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Moussa Seydi
- Service de Maladies Infectieuses et Tropicales, Centre Regional de Recherche et de Formation, Centre Hospitalier National Universitaire de Fann, Dakar, Senegal
| | - Mark Sonderup
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - C Wendy Spearman
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alexander J Stockdale
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Program, Blantyre, Malawi
| | - Jantjie Taljaard
- Division of Infectious Diseases, Department of Medicine, Tygerberg Hospital and Stellenbosch University, Cape Town, South Africa
| | - Michael Vinikoor
- Department of Internal Medicine, University of Zambia, Lusaka, Zambia; University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Maud Lemoine
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Yusuke Shimakawa
- Insitut Pasteur, Université Paris Cité, Unité d'Épidémiologie des Maladies Émergentes, Paris, France.
| | - Roger Sombié
- Hepato-Gastroenterology Department, Yalgado Ouédraogo University Hospital Center, Ouagadougou, Burkina Faso
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Delphin M, Mohammed KS, Downs LO, Lumley SF, Waddilove E, Okanda D, Aliyan N, Van Schalkwyk M, Anderson M, Ocama P, Maponga T, Torimiro J, Iwuji C, Ndung'u T, Matthews PC, Taljaard J. Under-representation of the WHO African region in clinical trials of interventions against hepatitis B virus infection. Lancet Gastroenterol Hepatol 2024; 9:383-392. [PMID: 38367632 DOI: 10.1016/s2468-1253(23)00315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 02/19/2024]
Abstract
The WHO African region bears a disproportionate burden of morbidity and mortality related to chronic hepatitis B virus (HBV) infection and accounts for an estimated 70% of new HBV infections worldwide. We investigated the extent to which HBV clinical trials represented populations in this region by searching the WHO International Clinical Trials Registry Platform and ClinicalTrials.gov for interventional clinical trials published in English between database inception and May 29, 2023, using the search term "Hepatitis B". We identified 1804 unique clinical trials, of which 18 (1·0%) recorded involvement of the WHO African region. There is no evidence that the number of HBV clinical trials in this region has improved over time. The diversity of new interventions and industry sponsorship in the WHO African region were low, with trials of HBV comparing poorly with those of other endemic infectious diseases (eg, malaria, HIV, and SARS-CoV-2). HBV research and clinical trial investigations have neglected the WHO African region, leading to profound health inequities. HBV clinical trials are urgently needed to evaluate the efficacy of newly discovered therapeutics and to ensure that interventions can be equitably distributed and deployed as they become available.
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Affiliation(s)
| | - Khadija Said Mohammed
- The Francis Crick Institute, London, UK; Division of Biosciences, Faculty of Life Sciences, University College London, London, UK
| | - Louise O Downs
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK; Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sheila F Lumley
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK
| | | | - Dorcas Okanda
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Marije Van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University-Tygerberg Academic Hospital, Cape Town, South Africa
| | - Motswedi Anderson
- The Francis Crick Institute, London, UK; Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana; Africa Health Research Institute, Durban, South Africa
| | - Ponsiano Ocama
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Tongai Maponga
- Division of Medical Virology, Stellenbosch University-National Health Laboratory Service Tygerberg Business Unit, Cape Town, South Africa
| | - Judith Torimiro
- Molecular Biology Laboratory, Chantal Biya International Reference Centre for AIDS Research, Yaounde, Cameroon
| | - Collins Iwuji
- Africa Health Research Institute, Durban, South Africa; Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Thumbi Ndung'u
- Division of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, Durban, South Africa
| | - Philippa C Matthews
- The Francis Crick Institute, London, UK; Division of Infection and Immunity, University College London, London, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Department of Infectious Diseases, University College London Hospital, London, London, UK.
| | - Jantjie Taljaard
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University-Tygerberg Academic Hospital, Cape Town, South Africa
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Van Zyl GU, Maponga T, Rabie H, Taljaard J. The role of new hepatitis B vaccines in South Africa. S Afr Med J 2024; 114:e1473. [PMID: 38525577 DOI: 10.7196/samj.2024.v114i2.1473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/20/2023] [Indexed: 03/26/2024] Open
Abstract
Vaccination is key to eliminating hepatitis B virus infection in South Africa (SA). Despite introducing immunisation in 1995, as part of the expanded programme of immunisation (EPI), hepatitis B virus infection remains endemic, and EPI vaccine coverage is incomplete. In addition to infants, non-immune adults at risk of infection through their occupation or with behavioural risk factors should receive vaccination. SA has many individuals with diabetes mellitus (a prevalence of almost 13%), obesity, HIV (8.45 million) or older age (5 million >60 years old), associated with a poorer vaccine response. Recently two new hepatitis B vaccines have been licensed: HEPLISAV-B includes an adjuvant that improves immunogenicity and has shown improved vaccine response in individuals with HIV, old age or diabetes mellitus. PreHevbrio, which includes three hepatitis B surface protein domains, instead of one, may also be more immunogenic, although clinical study data are still limited. These two novel vaccines have not yet been investigated in children and licensed in SA. Should HEPLISAV-B become available in SA, it may be particularly valuable to target high-risk groups in the country, such as people living with HIV, who show a poor response to the currently licensed vaccine.
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Affiliation(s)
- G U Van Zyl
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa.
| | - T Maponga
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa.
| | - H Rabie
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Tygerberg Children's Hospital, Cape Town, South Africa.
| | - J Taljaard
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Tygerberg Academic Hospital, Cape Town, South Africa.
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Tshiabuila D, Choga W, James SE, Maponga T, Preiser W, van Zyl G, Moir M, van Wyk S, Giandhari J, Pillay S, Anyaneji UJ, Lessells RJ, Naidoo Y, Sanko TJ, Wilkinson E, Tegally H, Baxter C, Martin DP, de Oliveira T. An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings. medRxiv 2024:2024.01.19.24301519. [PMID: 38293032 PMCID: PMC10827254 DOI: 10.1101/2024.01.19.24301519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Chronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A - J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
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Affiliation(s)
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Wonderful Choga
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - San E. James
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa & National Health Laboratory Service
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Stephanie van Wyk
- Collaborating Centre for Optimizing Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, South Africa
| | - Jennifer Giandhari
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Darren P. Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu Natal, Durban, South Africa
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5
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Riches N, Vinikoor M, Guingane A, Johannessen A, Lemoine M, Matthews P, Okeke E, Shimakawa Y, Sombie R, Stockdale A, Wandeler G, Andersson M, Davwar P, Desalegn H, Duguru M, Fall F, Maponga T, Nyampaul D, Seydi M, Sinkala E, Taljaard J, Sonderup M, Spearman CW. Hepatitis B in Africa collaborative Network (HEPSANET): Cohort profile and analysis of baseline data. Epidemiol Infect 2023; 151:e65. [PMID: 37009881 DOI: 10.1017/s095026882300050x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Approximately 80 million people live with chronic hepatitis B virus (HBV) infection in the WHO Africa Region. The natural history of HBV infection in this population is poorly characterised, and may differ from patterns observed elsewhere due to differences in prevailing genotypes, environmental exposures, co-infections, and host genetics. Existing research is largely drawn from small, single-centre cohorts, with limited follow-up time. The Hepatitis B in Africa Collaborative Network (HEPSANET) was established in 2022 to harmonise the process of ongoing data collection, analysis, and dissemination from 13 collaborating HBV cohorts in eight African countries. Research priorities for the next 5 years were agreed upon through a modified Delphi survey prior to baseline data analysis being conducted. Baseline data on 4,173 participants with chronic HBV mono-infection were collected, of whom 38.3% were women and the median age was 34 years (interquartile range 28-42). In total, 81.3% of cases were identified through testing of asymptomatic individuals. HBeAg-positivity was seen in 9.6% of participants. Follow-up of HEPSANET participants will generate evidence to improve the diagnosis and management of HBV in this region.
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Preiser W, Maponga T. So far, no novel SARS-CoV-2 variants from Beijing-and hopefully better scientific cooperation going forward. Lancet 2023; 401:621-622. [PMID: 36773617 PMCID: PMC9908086 DOI: 10.1016/s0140-6736(23)00268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/11/2023]
Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service Tygerberg Campus, Cape Town 7505, South Africa.
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service Tygerberg Campus, Cape Town 7505, South Africa
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7
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Johannessen A, Stockdale AJ, Henrion MYR, Okeke E, Seydi M, Wandeler G, Sonderup M, Spearman CW, Vinikoor M, Sinkala E, Desalegn H, Fall F, Riches N, Davwar P, Duguru M, Maponga T, Taljaard J, Matthews PC, Andersson M, Mboup S, Sombie R, Shimakawa Y, Lemoine M. Systematic review and individual-patient-data meta-analysis of non-invasive fibrosis markers for chronic hepatitis B in Africa. Nat Commun 2023; 14:45. [PMID: 36596805 PMCID: PMC9810658 DOI: 10.1038/s41467-022-35729-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
In sub-Saharan Africa, simple biomarkers of liver fibrosis are needed to scale-up hepatitis B treatment. We conducted an individual participant data meta-analysis of 3,548 chronic hepatitis B patients living in eight sub-Saharan African countries to assess the World Health Organization-recommended aspartate aminotransferase-to-platelet ratio index and two other fibrosis biomarkers using a Bayesian bivariate model. Transient elastography was used as a reference test with liver stiffness measurement thresholds at 7.9 and 12.2kPa indicating significant fibrosis and cirrhosis, respectively. At the World Health Organization-recommended cirrhosis threshold (>2.0), aspartate aminotransferase-to-platelet ratio index had sensitivity (95% credible interval) of only 16.5% (12.5-20.5). We identified an optimised aspartate aminotransferase-to-platelet ratio index rule-in threshold (>0.65) for liver stiffness measurement >12.2kPa with sensitivity and specificity of 56.2% (50.5-62.2) and 90.0% (89.0-91.0), and an optimised rule-out threshold (<0.36) with sensitivity and specificity of 80.6% (76.1-85.1) and 64.3% (62.8-65.8). Here we show that the World Health Organization-recommended aspartate aminotransferase-to-platelet ratio index threshold is inappropriately high in sub-Saharan Africa; improved rule-in and rule-out thresholds can optimise treatment recommendations in this setting.
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Affiliation(s)
- Asgeir Johannessen
- Department of Infectious Diseases, Vestfold Hospital, Tønsberg, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Alexander J Stockdale
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marc Y R Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Edith Okeke
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Moussa Seydi
- Service de Maladies Infectieuses et Tropicales, Centre Regional de Recherche et de Formation, Centre Hospitalier National Universitaire de Fann, Dakar, Senegal
| | - Gilles Wandeler
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Mark Sonderup
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - C Wendy Spearman
- Division of Hepatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michael Vinikoor
- Department of Internal Medicine, University of Zambia, Lusaka, Zambia
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Edford Sinkala
- Department of Internal Medicine, University of Zambia, Lusaka, Zambia
| | - Hailemichael Desalegn
- Department of Infectious Diseases, Vestfold Hospital, Tønsberg, Norway
- Medical Department, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Fatou Fall
- Department of Hepatology and Gastroenterology, Hopital Principal de Dakar, Dakar, Senegal
| | - Nicholas Riches
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Pantong Davwar
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Mary Duguru
- Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Tongai Maponga
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
| | - Jantjie Taljaard
- Division of Infectious Diseases, Department of Medicine, Tygerberg Hospital and Stellenbosch University, Cape Town, South Africa
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
- University College London, London, UK
| | - Monique Andersson
- Division of Medical Virology, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Souleyman Mboup
- L'Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formations (IRESSEF), Dakar, Senegal
| | - Roger Sombie
- Yalgado Ouédraogo University Hospital Center, Ouagadougou, Burkina Faso
| | - Yusuke Shimakawa
- Unité d'Epidémiologie des Maladies Emergentes, Institut Pasteur, Paris, France
| | - Maud Lemoine
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Hepatology section, Imperial College London, London, UK
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8
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Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Makatini Z, Moyo S, Amoako DG, Baxter C, Althaus CL, Anyaneji UJ, Kekana D, Viana R, Giandhari J, Lessells RJ, Maponga T, Maruapula D, Choga W, Matshaba M, Mbulawa MB, Msomi N, Naidoo Y, Pillay S, Sanko TJ, San JE, Scott L, Singh L, Magini NA, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht FK, Venter M, Chiloane G, McIntyre C, O'Toole A, Ruis C, Peacock TP, Roemer C, Kosakovsky Pond SL, Williamson C, Pybus OG, Bhiman JN, Glass A, Martin DP, Jackson B, Rambaut A, Laguda-Akingba O, Gaseitsiwe S, von Gottberg A, de Oliveira T. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med 2022; 28:1785-1790. [PMID: 35760080 PMCID: PMC9499863 DOI: 10.1038/s41591-022-01911-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dikeledi Kekana
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Wonderful Choga
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nonkululeko A Magini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Graeme Dor
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florette K Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Georginah Chiloane
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Caitlyn McIntyre
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal N Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Lancet Laboratories, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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9
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Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Engelbrecht S, Wasserman S, Schrueder N, Boloko L, Symons G, Raubenheimer P, Viljoen A, Parker A, Cohen C, Jasat W, Lessells R, Wilkinson RJ, Boulle A, Hsiao M. Higher mortality associated with the SARS-CoV-2 Delta variant in the Western Cape, South Africa, using RdRp target delay as a proxy: a cross-sectional study. Gates Open Res 2022; 6:117. [PMID: 37994361 PMCID: PMC10663174 DOI: 10.12688/gatesopenres.13654.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 11/24/2023] Open
Abstract
Background: The SARS-CoV-2 Delta variant (B.1.617.2) has been associated with more severe disease, particularly when compared to the Alpha variant. Most of this data, however, is from high income countries and less is understood about the variant's disease severity in other settings, particularly in an African context, and when compared to the Beta variant. Methods: A novel proxy marker, RNA-dependent RNA polymerase (RdRp) target delay in the Seegene Allplex TM 2019-nCoV (polymerase chain reaction) PCR assay, was used to identify suspected Delta variant infection in routine laboratory data. All cases diagnosed on this assay in the public sector in the Western Cape, South Africa, from 1 April to 31 July 2021, were included in the dataset provided by the Western Cape Provincial Health Data Centre (PHDC). The PHDC collates information on all COVID-19 related laboratory tests, hospital admissions and deaths for the province. Odds ratios for the association between the proxy marker and death were calculated, adjusted for prior diagnosed infection and vaccination status. Results: A total of 11,355 cases with 700 deaths were included in this study. RdRp target delay (suspected Delta variant) was associated with higher mortality (adjusted odds ratio [aOR] 1.45; 95% confidence interval [CI]: 1.13-1.86), compared to presumptive Beta infection. Prior diagnosed infection during the previous COVID-19 wave, which was driven by the Beta variant, was protective (aOR 0.32; 95%CI: 0.11-0.92) as was vaccination (aOR [95%CI] 0.15 [0.03-0.62] for complete vaccination [≥28 days post a single dose of Ad26.COV2.S or ≥14 days post second BNT162b2 dose]). Conclusion: RdRp target delay, a proxy for infection with the Delta variant, is associated with an increased risk of mortality amongst those who were tested for COVID-19 in our setting.
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Affiliation(s)
- Hannah Hussey
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Wofgang Preiser
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Tongai Maponga
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | | | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Linda Boloko
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Greg Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Abraham Viljoen
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Arifa Parker
- Department of Medicine, Tygerberg Hospital,, Stellenbosch University, Cape Town, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jasat
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu Natal, Durban, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Francis Crick Institute, London, UK
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, Cape Town, South Africa
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Marvin Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
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10
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Hussey H, Davies MA, Heekes A, Williamson C, Valley-Omar Z, Hardie D, Korsman S, Doolabh D, Preiser W, Maponga T, Iranzadeh A, Wasserman S, Boloko L, Symons G, Raubenheimer P, Parker A, Schrueder N, Solomon W, Rousseau P, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Boulle A, Hsiao NY. Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis. Int J Infect Dis 2022; 118:150-154. [PMID: 35235826 PMCID: PMC8882068 DOI: 10.1016/j.ijid.2022.02.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/23/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity. METHODS RdRp target delay (RTD) in the Seegene AllplexTM 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene AllplexTM assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection. RESULTS A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77). CONCLUSION Omicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.
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Affiliation(s)
- Hannah Hussey
- Health Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa.
| | - Mary-Ann Davies
- Health Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Alexa Heekes
- Health Intelligence, Western Cape Government: Health, South Africa; Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Ziyaad Valley-Omar
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Diana Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Stephen Korsman
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Deelan Doolabh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
| | - Tongai Maponga
- National Health Laboratory Service, South Africa; Division of Medical Virology, University of Stellenbosch, South Africa
| | - Arash Iranzadeh
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, South Africa
| | - Linda Boloko
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Greg Symons
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Peter Raubenheimer
- Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Arifa Parker
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
| | - Neshaad Schrueder
- Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
| | | | | | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Waasila Jassat
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research, Innovation & Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; The Francis Crick Institute, Midland Road, London, NW1 1AT, UK; Department of Infectious Diseases, Imperial College London, W12 0NN, UK
| | - Andrew Boulle
- Health Intelligence, Western Cape Government: Health, South Africa; Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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11
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Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, National Health Laboratory Service (NHLS) Tygerberg, Cape Town 8000, South Africa
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12
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Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022; 603:679-686. [PMID: 35042229 PMCID: PMC8942855 DOI: 10.1038/s41586-022-04411-y] [Citation(s) in RCA: 918] [Impact Index Per Article: 459.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/02/2023]
Abstract
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Affiliation(s)
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Phillip A Bester
- Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michaela Davids
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Deelan Doolabh
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diana Hardie
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Rageema Joseph
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Legodile Koopile
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Lesego Kuate-Lere
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Onalethatha Lesetedi-Mafoko
- Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Boitshoko Mahlangu
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Kamela Mahlakwane
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Gert Marais
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Kereng Masupu
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, USA
| | - Simnikiwe Mayaphi
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Nokuzola Mbhele
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Adriano Mendes
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Anele Mnguni
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kgomotso Moruisi
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Mosepele Mosepele
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Gerald Motsatsi
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Modisa S Motswaledi
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Thongbotho Mphoyakgosi
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Peter N Mwangi
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Noxolo Ntuli
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Martin Nyaga
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Lucier Olubayo
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Botshelo Radibe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Strydom
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Naume Tebeila
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Joseph Tsui
- Department of Zoology, University of Oxford, Oxford, UK
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Constantinos K Wibmer
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- PathCare Vermaak, Pretoria, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Florette Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Marietje Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- Lancet Laboratories, Johannesburg, South Africa
- Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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13
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Kuhlmann C, Mayer CK, Claassen M, Maponga T, Burgers WA, Keeton R, Riou C, Sutherland AD, Suliman T, Shaw ML, Preiser W. Breakthrough infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose. Lancet 2022; 399:625-626. [PMID: 35063123 PMCID: PMC8765759 DOI: 10.1016/s0140-6736(22)00090-3] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Constanze Kuhlmann
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Carla Konstanze Mayer
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch Tygerberg Campus, Cape Town ZA-7505, South Africa
| | - Mathilda Claassen
- Medical Virology, National Health Laboratory Service Tygerberg, Parow, Cape Town, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch Tygerberg Campus, Cape Town ZA-7505, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Roanne Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, Cape Town, South Africa
| | - Andrew D Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch Tygerberg Campus, Cape Town ZA-7505, South Africa
| | - Tasnim Suliman
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Megan L Shaw
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch Tygerberg Campus, Cape Town ZA-7505, South Africa; Medical Virology, National Health Laboratory Service Tygerberg, Parow, Cape Town, South Africa.
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14
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Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies MA, Boulle A, Doolabh D, Laubscher M, Wojno J, Deetlefs JD, Maritz J, Scott L, Msomi N, Naicker C, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao NY. Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. J Virol Methods 2022; 302:114471. [PMID: 35051442 PMCID: PMC8763409 DOI: 10.1016/j.jviromet.2022.114471] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
Abstract
Routine SARS-CoV-2 surveillance in the Western Cape region of South Africa (January-August 2021) found a reduced RT-PCR amplification efficiency of the RdRp-gene target of the Seegene, Allplex 2019-nCoV diagnostic assay from June 2021 when detecting the Delta variant. We investigated whether the reduced amplification efficiency denoted by an increased RT-PCR cycle threshold value (RΔE) can be used as an indirect measure of SARS-CoV-2 Delta variant prevalence. We found a significant increase in the median RΔE for patient samples tested from June 2021, which coincided with the emergence of the SARS-CoV-2 Delta variant within our sample set. Whole genome sequencing on a subset of patient samples identified a highly conserved G15451A, non-synonymous mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. While whole genome sequencing plays an important in identifying novel SARS-CoV-2 variants, monitoring RΔE value can serve as a useful surrogate for rapid tracking of Delta variant prevalence.
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Affiliation(s)
- Ziyaad Valley-Omar
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa.
| | - Gert Marais
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Arash Iranzadeh
- University of Cape Town, Cape Town, Western Cape, South Africa
| | - Michelle Naidoo
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Stephen Korsman
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Tongai Maponga
- Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Hannah Hussey
- University of Cape Town, Cape Town, Western Cape, South Africa; Centre Health Intelligence, Western Cape Government: Health, South Africa
| | - Mary-Ann Davies
- University of Cape Town, Cape Town, Western Cape, South Africa
| | - Andrew Boulle
- University of Cape Town, Cape Town, Western Cape, South Africa
| | - Deelan Doolabh
- University of Cape Town, Cape Town, Western Cape, South Africa
| | | | | | | | | | - Lesley Scott
- University of the Witwatersrand, Johannesburg, Gauteng, South Africa
| | - Nokukhanya Msomi
- National Health Laboratory Service, South Africa; University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | - Cherise Naicker
- National Health Laboratory Service, South Africa; University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | | | - Jinal Bhiman
- National institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, Gauteng, South Africa
| | - Carolyn Williamson
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Wolfgang Preiser
- National Health Laboratory Service, South Africa; Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Diana Hardie
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
| | - Nei-Yuan Hsiao
- University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa
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15
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Matthews PC, Maponga T, Ghosh I, Lemoine M, Ocama P, Abubakar I, Story A, Flanagan S. Hepatitis B Virus: Infection, liver disease, carcinogen or syndemic threat? Remodelling the clinical and public health response. PLOS Glob Public Health 2022; 2:e0001359. [PMID: 36962907 PMCID: PMC10022007 DOI: 10.1371/journal.pgph.0001359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Philippa C Matthews
- The Francis Crick Institute, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Infectious Diseases, University College London Hospitals, London, United Kingdom
| | - Tongai Maponga
- Division of Virology, Tygerberg Hospital, University of Stellenbosch, Stellenbosch, South Africa
| | - Indrajit Ghosh
- Mortimer Market Centre, Central North West London NHS Foundation Trust, London, United Kingdom
- Find & Treat, Inclusion Health, University College London, London, United Kingdom
| | - Maud Lemoine
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Hepatology, Imperial College London, London, United Kingdom
| | - Ponsiano Ocama
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Ibrahim Abubakar
- Faculty of Population Health Sciences, University College London, Mortimer Market Centre, London, United Kingdom
| | - Alistair Story
- Find & Treat, Inclusion Health, University College London, London, United Kingdom
| | - Stuart Flanagan
- Department of Infectious Diseases, University College London Hospitals, London, United Kingdom
- Mortimer Market Centre, Central North West London NHS Foundation Trust, London, United Kingdom
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16
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Downs LO, Vawda S, Bester PA, Lythgoe KA, Wang T, McNaughton AL, Smith DA, Maponga T, Freeman O, Várnai KA, Davies J, Woods K, Fraser C, Barnes E, Goedhals D, Matthews PC. Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa. Wellcome Open Res 2020; 5:113. [PMID: 33274299 PMCID: PMC7682492 DOI: 10.12688/wellcomeopenres.15941.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
Hepatitis B virus (HBV) viral load (VL) is used as a biomarker to assess risk of disease progression, and to determine eligibility for treatment. While there is a well recognised association between VL and the expression of the viral e-antigen protein, the distributions of VL at a population level are not well described. We here present cross-sectional, observational HBV VL data from two large population cohorts in the UK and in South Africa, demonstrating a consistent bimodal distribution. The right skewed distribution and low median viral loads are different from the left-skew and higher viraemia in seen in HIV and hepatitis C virus (HCV) cohorts in the same settings. Using longitudinal data, we present evidence for a stable 'set-point' VL in peripheral blood during chronic HBV infection. These results are important to underpin improved understanding of HBV biology, to inform approaches to viral sequencing, and to plan public health interventions.
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Affiliation(s)
- Louise O. Downs
- Department of Infectious Diseases and Microbiology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabeehah Vawda
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | | | - Katrina A. Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
- Department of Zoology, University Of Oxford, Oxford, UK
| | - Tingyan Wang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - David A. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tongai Maponga
- Department of Virology, University of Stellenbosch, Cape Town, South Africa
| | - Oliver Freeman
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kinga A. Várnai
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim Davies
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Kerrie Woods
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Hepatology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Philippa C. Matthews
- Department of Infectious Diseases and Microbiology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
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17
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Downs LO, Vawda S, Bester PA, Lythgoe KA, Wang T, McNaughton AL, Smith DA, Maponga T, Freeman O, Várnai KA, Davies J, Woods K, Fraser C, Barnes E, Goedhals D, Matthews PC. Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa. Wellcome Open Res 2020; 5:113. [PMID: 33274299 PMCID: PMC7682492 DOI: 10.12688/wellcomeopenres.15941.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 03/31/2024] Open
Abstract
Hepatitis B virus (HBV) viral load (VL) is used as a biomarker to assess risk of disease progression, and to determine eligibility for treatment. While there is a well recognised association between VL and the expression of the viral e-antigen (HBeAg) protein, the precise determinants and distribution of VL at a population level are not well described. We here report the distribution of HBV VL in two large cross-sectional population cohorts in the UK and in South Africa, demonstrating a consistent bimodal distribution. The right skewed distribution and low median viral loads are significantly different from the left-skew and higher viraemia in seen in comparable HIV and hepatitis C virus (HCV) cohorts. Using longitudinal data, we present evidence for a stable 'set-point' VL in peripheral blood during chronic HBV infection. These results are important to underpin improved understanding of HBV biology and to plan public health interventions.
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Affiliation(s)
- Louise O. Downs
- Department of Infectious Diseases and Microbiology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabeehah Vawda
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | | | - Katrina A. Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
- Department of Zoology, University Of Oxford, Oxford, UK
| | - Tingyan Wang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - David A. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tongai Maponga
- Department of Virology, University of Stellenbosch, Cape Town, South Africa
| | - Oliver Freeman
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kinga A. Várnai
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jim Davies
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Kerrie Woods
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Hepatology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Philippa C. Matthews
- Department of Infectious Diseases and Microbiology, Oxford Radcliffe Hospital NHS Trust, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Health Informatics Collaborative, NIHR Oxford Biomedical Research Centre, Oxford, UK
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18
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Mokaya J, McNaughton AL, Burbridge L, Maponga T, O'Hara G, Andersson M, Seeley J, Matthews PC. A blind spot? Confronting the stigma of hepatitis B virus (HBV) infection - A systematic review. Wellcome Open Res 2018; 3:29. [PMID: 30483598 PMCID: PMC6234740 DOI: 10.12688/wellcomeopenres.14273.2] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Stigma, poverty, and lack of knowledge present barriers to the diagnosis and treatment of chronic infection, especially in resource-limited settings. Chronic Hepatitis B virus (HBV) infection is frequently asymptomatic, but accounts for a substantial long-term burden of morbidity and mortality. In order to improve the success of diagnostic, treatment and preventive strategies, it is important to recognise, investigate and tackle stigma. We set out to assimilate evidence for the nature and impact of stigma associated with HBV infection, and to suggest ways to tackle this challenge. Methods: We carried out a literature search in PubMed using the search terms ‘hepatitis B’, ‘stigma’ to identify relevant papers published between 2007 and 2017 (inclusive), with a particular focus on Africa. Results: We identified a total of 32 articles, of which only two studies were conducted in Africa. Lack of knowledge of HBV was consistently identified, and in some settings there was no local word to describe HBV infection. There were misconceptions about HBV infection, transmission and treatment. Healthcare workers provided inaccurate information to individuals diagnosed with HBV, and poor understanding resulted in lack of preventive measures. Stigma negatively impacted on help-seeking, screening, disclosure, prevention of transmission, and adherence to treatment, and had potential negative impacts on mental health, wellbeing, employment and relationships. Conclusion: Stigma is a potentially major barrier to the successful implementation of preventive, diagnostic and treatment strategies for HBV infection, and yet we highlight a ‘blind spot’, representing a lack of data and limited recognition of this challenge. There is a need for more research in this area, to identify and evaluate interventions that can be used effectively to tackle stigma, and to inform collaborative efforts between patients, clinical services, policy makers, traditional healers, religious leaders, charity organisations and support groups.
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Affiliation(s)
- Jolynne Mokaya
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK
| | - Anna L McNaughton
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK
| | - Lela Burbridge
- Department of Gastroenterology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tongai Maponga
- Department of Virology, University of Stellenbosch, Tygerberg Hospital, Bellville, Cape Town , 7500, South Africa
| | - Geraldine O'Hara
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX1 3SY, UK
| | - Janet Seeley
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, 51/59 Nakiwogo Rd, Entebbe, Uganda
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX1 3SY, UK
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19
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Mokaya J, McNaughton AL, Burbridge L, Maponga T, O'Hara G, Andersson M, Seeley J, Matthews PC. A blind spot? Confronting the stigma of hepatitis B virus (HBV) infection - A systematic review. Wellcome Open Res 2018; 3:29. [PMID: 30483598 DOI: 10.12688/wellcomeopenres.14273.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Stigma, poverty, and lack of knowledge present barriers to the diagnosis and treatment of chronic infection, especially in resource-limited settings. Chronic Hepatitis B virus (HBV) infection is frequently asymptomatic, but accounts for a substantial long-term burden of morbidity and mortality. In order to improve the success of diagnostic, treatment and preventive strategies, it is important to recognise, investigate and tackle stigma. We set out to assimilate evidence for the nature and impact of stigma associated with HBV infection, and to suggest ways to tackle this challenge. Methods: We carried out a literature search in PubMed using the search terms 'hepatitis B', 'stigma' to identify relevant papers published between 2007 and 2017 (inclusive), with a particular focus on Africa. Results: We identified a total of 32 articles, of which only two studies were conducted in Africa. Lack of knowledge of HBV was consistently identified, and in some settings there was no local word to describe HBV infection. There were misconceptions about HBV infection, transmission and treatment. Healthcare workers provided inaccurate information to individuals diagnosed with HBV, and poor understanding resulted in lack of preventive measures. Stigma negatively impacted on help-seeking, screening, disclosure, prevention of transmission, and adherence to treatment, and had potential negative impacts on mental health, wellbeing, employment and relationships. Conclusion: Stigma is a potentially major barrier to the successful implementation of preventive, diagnostic and treatment strategies for HBV infection, and yet we highlight a 'blind spot', representing a lack of data and limited recognition of this challenge. There is a need for more research in this area, to identify and evaluate interventions that can be used effectively to tackle stigma, and to inform collaborative efforts between patients, clinical services, policy makers, traditional healers, religious leaders, charity organisations and support groups.
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Affiliation(s)
- Jolynne Mokaya
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK
| | - Anna L McNaughton
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK
| | - Lela Burbridge
- Department of Gastroenterology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tongai Maponga
- Department of Virology, University of Stellenbosch, Tygerberg Hospital, Bellville, Cape Town , 7500, South Africa
| | - Geraldine O'Hara
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX1 3SY, UK
| | - Janet Seeley
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine, Uganda Research Unit, 51/59 Nakiwogo Rd, Entebbe, Uganda
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford, OX1 3SY, UK.,Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford, OX1 3SY, UK
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20
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O’Hara GA, McNaughton AL, Maponga T, Jooste P, Ocama P, Chilengi R, Mokaya J, Liyayi MI, Wachira T, Gikungi DM, Burbridge L, O’Donnell D, Akiror CS, Sloan D, Torimiro J, Yindom LM, Walton R, Andersson M, Marsh K, Newton R, Matthews PC. Hepatitis B virus infection as a neglected tropical disease. PLoS Negl Trop Dis 2017; 11:e0005842. [PMID: 28981505 PMCID: PMC5628785 DOI: 10.1371/journal.pntd.0005842] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Geraldine A. O’Hara
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Co-infection Studies Programme, MRC/UVRI Uganda Research Unit, Entebbe, Uganda
| | - Anna L. McNaughton
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Tongai Maponga
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Tygerberg, Cape Town, South Africa
| | - Pieter Jooste
- Department of Paediatrics, Kimberley Hospital, Kimberley, South Africa
| | - Ponsiano Ocama
- Co-infection Studies Programme, MRC/UVRI Uganda Research Unit, Entebbe, Uganda
| | - Roma Chilengi
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Jolynne Mokaya
- Health System Research Ethics Department, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mitchell I. Liyayi
- Mother and Child Health Department, Baringo County Referral Hospital, Baringo, Kenya
| | - Tabitha Wachira
- Medical-Surgical Department, Machakos Level 5 Hospital, Machakos, Kenya
| | | | - Lela Burbridge
- Patient and Public Involvement Committee, Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Denise O’Donnell
- Patient and Public Involvement Committee, Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | | | - Derek Sloan
- School of Medicine, Medical & Biological Sciences, University of St Andrews, St Andrews, Scotland, United Kingdom
| | - Judith Torimiro
- Chantal Biya International Reference Centre for Research on HIV/AIDS, Yaounde, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaounde I, Yaounde, Cameroon
| | - Louis Marie Yindom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Robert Walton
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Monique Andersson
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Tygerberg, Cape Town, South Africa
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trusts, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kevin Marsh
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Africa-Oxford (AfOx) Initiative, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
| | - Robert Newton
- Co-infection Studies Programme, MRC/UVRI Uganda Research Unit, Entebbe, Uganda
- Department of Health Sciences, University of York, York, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trusts, John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail:
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21
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Horn A, Scheller C, du Plessis S, Arendt G, Nolting T, Joska J, Sopper S, Maschke M, Obermann M, Husstedt IW, Hain J, Maponga T, Riederer P, Koutsilieri E. Increases in CSF dopamine in HIV patients are due to the dopamine transporter 10/10-repeat allele which is more frequent in HIV-infected individuals. J Neural Transm (Vienna) 2013; 120:1411-9. [PMID: 24057505 PMCID: PMC3779317 DOI: 10.1007/s00702-013-1086-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 08/23/2013] [Indexed: 11/30/2022]
Abstract
Dysfunction of dopaminergic neurotransmission has been implicated in HIV infection. We showed previously increased dopamine (DA) levels in CSF of therapy-naïve HIV patients and an inverse correlation between CSF DA and CD4 counts in the periphery, suggesting adverse effects of high levels of DA on HIV infection. In the current study including a total of 167 HIV-positive and negative donors from Germany and South Africa (SA), we investigated the mechanistic background for the increase of CSF DA in HIV individuals. Interestingly, we found that the DAT 10/10-repeat allele is present more frequently within HIV individuals than in uninfected subjects. Logistic regression analysis adjusted for gender and ethnicity showed an odds ratio for HIV infection in DAT 10/10 allele carriers of 3.93 (95% CI 1.72-8.96; p = 0.001, Fishers exact test). 42.6% HIV-infected patients harbored the DAT 10/10 allele compared to only 10.5% uninfected DAT 10/10 carriers in SA (odds ratio 6.31), whereas 68.1 versus 40.9%, respectively, in Germany (odds ratio 3.08). Subjects homozygous for the 10-repeat allele had higher amounts of CSF DA and reduced DAT mRNA expression but similar disease severity compared with those carrying other DAT genotypes. These intriguing and novel findings show the mutual interaction between DA and HIV, suggesting caution in the interpretation of CNS DA alterations in HIV infection solely as a secondary phenomenon to the virus and open the door for larger studies investigating consequences of the DAT functional polymorphism on HIV epidemiology and progression of disease.
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Affiliation(s)
- Anne Horn
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Carsten Scheller
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Stefan du Plessis
- Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - Gabriele Arendt
- Department of Neurology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Thorsten Nolting
- Department of Neurology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - John Joska
- Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | | | - Matthias Maschke
- Department of Neurology, University Hospital of Duisburg-Essen, Essen, Germany
| | - Mark Obermann
- Department of Neurology, University Hospital of Duisburg-Essen, Essen, Germany
| | - Ingo W. Husstedt
- Department of Neurology, University Hospital of Münster, Münster, Germany
| | - Johannes Hain
- Institute of Mathematics and Informatics, Chair of Mathematics VIII (Statistics), University of Würzburg, Würzburg, Germany
| | - Tongai Maponga
- Department of Virology, Stellenbosch University, Stellenbosch, South Africa
| | - Peter Riederer
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Eleni Koutsilieri
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
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