Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2.

Data sharing in research is fraught with controversy. Academic success is premised on competitive advantage, with research teams protecting their research findings until publication. Research funders, by contrast, often require data sharing.

COVID-19 underscores the important role of Clinical Ethics Committees in Africa.

Background: The COVID-19 pandemic has magnified pre-existing challenges in healthcare in Africa. Long-standing health inequities, embedded in the continent over centuries, have been laid bare and have raised complex ethical dilemmas. While there are very few clinical ethics committees (CECs) in Africa, the demand for such services exists and has increased during the COVID-19 pandemic.

Preinvasive cervical lesions and high prevalence of human papilloma virus among pregnant women in Cameroon.

Introduction: With the exception of breast cancer, gynecologic neoplasms constitute the most common cancers that complicate pregnancy. Pregnancy therefore presents a window of opportunity for all pregnant women who do not take part in routine free cervical cancer screening program to undergo a free voluntary cytological test and human papillomavirus (HPV) DNA testing. This study aimed to determine prevalent HPV genotypes among pregnant women using exfoliated cells from cervical swabs and determine risk factors responsible for the upsurge of cervical precancerous lesions.

Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa.

Background: HIV-1C has been shown to have a greater risk of virological failure and reduced susceptibility towards boosted protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study entailed an evaluation of HIV-1 drug resistance-associated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients on the South African national second-line cART regimen receiving bPIs.

Methods: During 2017 and 2018, 67 patient samples were sequenced using high-throughput sequencing (HTS), of which 56 samples were included in the final analysis because the patient's treatment regimen was available at the time of sampling.

Clinical Ethics Committees in Africa: lost in the shadow of RECs/IRBs?

Background: Clinical Ethics Committees (CECs) are well established at healthcare institutions in resource-rich countries. However, there is limited information on established CECs in resource poor countries, especially in Africa. This study aimed to establish baseline data regarding existing formal CECs in Africa to raise awareness of and to encourage the establishment of CECs or Clinical Ethics Consultation Services (CESs) on the continent.

Structural Comparison of Diverse HIV-1 Subtypes using Molecular Modelling and Docking Analyses of Integrase Inhibitors.

The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA).

Allocation of scarce resources in Africa during COVID-19: Utility and justice for the bottom of the pyramid?

The COVID-19 pandemic has raised important universal public health challenges. Conceiving ethical responses to these challenges is a public health imperative but must take context into account. This is particularly important in sub-Saharan Africa (SSA).

What Could "Fair Allocation" during the Covid-19 Crisis Possibly Mean in Sub-Saharan Africa?

The Covid-19 pandemic has sparked rapid and voluminous production of bioethics commentary in popular media and academic publications. Many of the discussions are new twists on an old theme: how to fairly allocate scarce medical resources, such as ventilators and intensive care unit beds. In this essay, we do not add another allocation scheme to the growing pile, partly out of appreciation that such schemes should be products of inclusive and transparent community engagement and partly out of recognition of their limited utility for physicians working in the field.

Correction: Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding.

[This corrects the article DOI: 10.1371/journal.pone.

Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding.

Resistance associated mutations (RAMs) threaten the long-term success of combination antiretroviral therapy (cART) outcomes for HIV-1 treatment. HIV-1 Integrase (IN) strand transfer inhibitors (INSTIs) have proven to be a viable option for highly specific HIV-1 therapy. The INSTI, Dolutegravir is recommended by the World Health Organization for use as first-line cART.

Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa.

The South African national combination antiretroviral therapy (cART) roll-out program started in 2006, with over 4.4 million people accessing treatment since it was first introduced. HIV-1 drug resistance can hamper the success of cART.

HIV-1 Integrase Diversity and Resistance-Associated Mutations and Polymorphisms Among Integrase Strand Transfer Inhibitor-Naive HIV-1 Patients from Cameroon.

The World Health Organization (WHO) has put forth recommendations for the use of integrase (IN) strand transfer inhibitors (INSTIs) to be part of the first-line combination antiretroviral therapy regimen to treat HIV infections. The knowledge of pretreatment drug resistance against INSTIs is still scarce in resource-limited settings (RLS). We characterized the gene to identify resistance-associated mutations (RAMs) in 56 INSTI-naive patient viral sequences from Cameroon.

Near full-length HIV-1 subtype B sequences from the early South African epidemic, detecting a BD unique recombinant form (URF) from a sample in 1985.

HIV-1 subtype C is the most prevalent subtype in South Africa. Although subtype B was previously detected in South Africa, there is limited sequence information available. We characterized near full-length HIV-1 subtype B sequences from samples collected at the start of the South African HIV-1 epidemic, in the 1980s.

Mutations in Long Terminal Repeats κB Transcription Factor Binding Sites in Plasma Virus Among South African People Living with HIV-1.

HIV-1 subtype C (HIV-1C) is responsible for the majority of infections in sub-Saharan Africa. We selected 63 plasma-derived samples and generated long terminal repeats (LTRs) amplicons from people living with HIV in South Africa to identify transcription factor binding sites. NF-κB plays an important role in regulating the viral gene expression from the viral promoter and controlling viral latency.

Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes.

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host genome using its 3'-end processing and strand-transfer activities. Due to the importance of HIV-1 IN, it is targeted by the newest class of approved drugs known as integrase strand transfer inhibitors (INSTIs). INSTIs are efficient in maintaining low viral load; however, as with other approved antivirals, resistance mutations emerge in patients receiving INSTI-containing therapy.

Author Correction: Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and availability of integrase inhibitors in Cape Town, South Africa.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa.

HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed to characterize the HIV-1 IN gene in a South African context and identify resistance-associated mutations (RAMs) against available first and second generation Integrase strand-transfer inhibitors (InSTIs). We performed genetic analyses on 91 treatment-naïve HIV-1 infected patients, as well as 314 treatment-naive South African HIV-1 IN-sequences, downloaded from Los Alamos HIV Sequence Database.