Explanipedia

Novel integrase mutations linked to genotypic DTG resistance in non-B HIV-1 strains from African participants: The DTG RESIST study Open

Nuri Han, Tom Loosli, Mamatha Sauermann, İpek Çelikağ, Nanina Anderegg , et al. · 2025

Background Integrase mutations associated with dolutegravir resistance have been well characterized, but based on limited data from non-B subtypes. Objectives We aim to identify integrase mutations not currently classified as integrase str…

Drug Resistance in People With Viremia on Dolutegravir-based Antiretroviral Therapy in Sub-Saharan Africa: The DTG RESIST Study Open

Tom Loosli, Carolyn Bolton‐Moore, Lydia Buzaalirwa, Helen Byakwaga, İpek Çelikağ , et al. · 2025

Dolutegravir resistance is an increasing concern. An analysis of the DTG RESIST study found that among 227 integrase sequences from 7 African countries (all non-B subtypes), 59 (26.0%) had at least 1 major drug resistance mutation (primari…

Building Pathogen Genomic Sequencing Capacity in Africa: Centre for Epidemic Response and Innovation Fellowship Open

Eric Agboli, Molalegne Bitew, Christian Malaka, Tiangay Kallon, Alhaji Jalloh , et al. · 2025

The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epid…

The effect of COVID-19 on the non-COVID health outcomes of crisis-affected peoples: a systematic review Open

Nathan Thompson, Khine Wut Yee Kyaw, Lavanya Singh, Justin Cirhuza Cikomola, N. S. Singh , et al. · 2024

Viremia and HIV Drug Resistance Among People Receiving Dolutegravir Versus Efavirenz-Based First-Line Antiretroviral Therapy Open

Jienchi Dorward, Yukteshwar Sookrajh, Richard Lessells, Elliot Bulo, Nicola Bodley , et al. · 2024

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Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2 Open

Chantal B. F. Vogels, Mallery I. Breban, Isabel M. Ott, Tara Alpert, Mary E. Petrone , et al. · 2023

Broadly accessible and inexpensive surveillance methods are needed to track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOC) around the world. While sequencing is the gold standard to identify circulat…

Insights into SARS‐CoV‐2 in Angola during the COVID‐19 peak: Molecular epidemiology and genome surveillance Open

Ngiambudulu M. Francisco, Stephanie van Wyk, Monika Moir, James Emmanuel San, Cruz S. Sebastião , et al. · 2023

Background In Angola, COVID‐19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS‐CoV‐2 virus has been conducted i…

Insights into SARS-CoV-2 in Angola during the COVID-19 Peak: Molecular Epidemiology and Genome Surveillance Open

Ngiambudulu M. Francisco, Stephanie van Wyk, Monika Moir, James Emmanuel San, Cruz S. Sebastião , et al. · 2023

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1,900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted…

Viraemia and HIV drug resistance among people receiving dolutegravir versus efavirenz-based first-line antiretroviral therapy Open

Jienchi Dorward, Yukteshwar Sookrajh, Richard Lessells, Elliot Bulo, Nicola Bodley , et al. · 2023

SUMMARY Limited data exists to inform management of viraemia among people receiving dolutegravir-based first-line ART in low- and middle-income countries. Among South-Africans with viraemia ≥1000copies/mL receiving dolutegravir (n=43) and …

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022 Open

Abay Sisay, Derek Tshiabuila, Stephanie van Wyk, Abraham Tesfaye, Gerald Mboowa , et al. · 2023

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there i…

Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique Open

Nália Ismael, Stephanie van Wyk, Houriiyah Tegally, Jennifer Giandhari, James Emmanuel San , et al. · 2023

Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome se…

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022 Open

Abay Sisay, Derek Tshiabuila, Abraham Tesfaye, Gerald Mboowa, Samuel O. Oyola , et al. · 2023

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499 000 cases, and ∼7 500 COVID-19-related deaths as of January 2023, there …

Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018 Open

Nália Ismael, Eduan Wilkinson, Isabel Mahumane, Hernane Gemusse, Jennifer Giandhari , et al. · 2022

HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain e…

Automated Kantian Ethics: A Faithful Implementation Open

Lavanya Singh · 2022

As we grant artificial intelligence increasing power and independence in contexts like healthcare, policing, and driving, AI faces moral dilemmas but lacks the tools to solve them. Warnings from regulators, philosophers, and computer scien…

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa Open

Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers , et al. · 2022

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 …

Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages Open

Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers , et al. · 2022

South Africa’s fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern. We have now identified two new lineages, BA.4 and BA.5. The spike proteins of BA.4 and BA.5 …

Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing Open

Lavanya Singh, James Emmanuel San, Houriiyah Tegally, Pius Brzoska, Ugochukwu J. Anyaneji , et al. · 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is adaptively evolving to ensure its persistence within human hosts. It is therefore necessary to continuously monitor the emergence and prevalence of novel variants that arise. …

Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests Open

Mary A. Rodgers, Alessandro Olivo, Barbara J. Harris, Chris Lark, Xinxin Luo , et al. · 2022

SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape Open

Sandile Cele, Farina Karim, Gila Lustig, James Emmanuel San, Tandile Hermanus , et al. · 2022

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa Open

Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers , et al. · 2022

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)…

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa Open

Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers , et al. · 2021

Summary The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third wa…

HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral therapy in KwaZulu-Natal Province, South Africa Open

Benjamin Chimukangara, Richard Lessells, Benn Sartorius, Lilishia Gounder, Sontaga Manyana , et al. · 2021

One-third of people failing second-line ART had significant PI DRMs. A subgroup of these individuals had extensive HIVDR, where the predicted activity of third-line ART was suboptimal, highlighting the need for continuous evaluation of out…

Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa Open

Benjamin Chimukangara, Richard Lessells, Lavanya Singh, Indra Grigalionyte, Nonhlanhla Yende‐Zuma , et al. · 2021

Background Introduction of tenofovir (TDF) plus lamivudine (3TC) and dolutegravir (DTG) in first- and second-line HIV treatment regimens in South Africa warrants characterization of acquired HIV-1 drug resistance (ADR) mutations that could…

Rapid replacement of the Beta variant by the Delta variant in South Africa Open

Houriiyah Tegally, Eduan Wilkinson, Christian L. Althaus, Marta Giovanetti, James Emmanuel San , et al. · 2021

The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second ep…

SARS-CoV-2 evolved during advanced HIV disease immunosuppression has Beta-like escape of vaccine and Delta infection elicited immunity Open

Sandile Cele, Farina Karim, Gila Lustig, James Emmanuel San, Tandile Hermanus , et al. · 2021

Summary Characterizing SARS-CoV-2 evolution in specific geographies may help predict the properties of variants coming from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from the ancestral virus …

Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing Open

Lavanya Singh, Ugochukwu J. Anyaneji, Wilfred Ndifon, Neil Turok, Stacey A. Mattison , et al. · 2021

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages Open

Darren P. Martin, Steven Weaver, Houriiyah Tegally, James Emmanuel San, Stephen D. Shank , et al. · 2021

The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. …

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape Open

Darren P. Martin, Steven Weaver, Houryiah Tegally, Emmanuel James San, Stephen D. Shank , et al. · 2021

The emergence and rapid rise in prevalence of three independent SARS-CoV-2 “501Y lineages’’, B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to bot…

Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection Open

Farina Karim, MYS Moosa, BI Gosnell, Sandile Cele, Jennifer Giandhari , et al. · 2021

Summary While most people effectively clear SARS-CoV-2, there are several reports of prolonged infection in immunosuppressed individuals. Here we present a case of prolonged infection of greater than 6 months with shedding of high titter S…

Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing Open

Lavanya Singh, Ugochukwu J. Anyaneji, Wilfred Ndifon, Neil Turok, Stacey A. Mattison , et al. · 2021

The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be …

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