Adetayo Obasa - Academia.edu (original) (raw)

Papers by Adetayo Obasa

Research paper thumbnail of Isolation and quarantine in South Africa during COVID-19: Draconian measures or proportional response?

South African Medical Journal, Apr 23, 2020

South Africa (SA) is currently in the midst of an unprecedented public health crisis. The transmi... more South Africa (SA) is currently in the midst of an unprecedented public health crisis. The transmission dynamics of COVID-19 mean that person-to-person spread is a serious public health risk. As such, the SA National Department of Health has invoked the Disaster Management Act, [1] and several extraordinary containment measures have been implemented as part of a national lockdown to limit the spread of infection. A recent report in the Daily Maverick refers to a move from 'self-isolation' to enforced isolation in 'government approved isolation sites for treatment' in a phase described as 'concomitant punishment' in Durban, KwaZulu-Natal (KZN). The change in strategy appears to have been triggered by the high proportion of cases in eThekweni District (383/587) and the high mortality in KZN, with the province accounting for 22 of the 54 deaths in SA as of

Research paper thumbnail of Electronic consent in a COVID-19 vaccine implementation trial in South Africa: Participant perspectives

South African Journal of Science, May 31, 2022

of the manuscript. S.M.K. designed the online survey instrument and was responsible for data capt... more of the manuscript. S.M.K. designed the online survey instrument and was responsible for data capturing. M.M.M.J.A. undertook the data cleaning and analysis. A.E.A.O. contributed to the literature review. M.G.M.C. provided expert advice on statistical analysis. All authors read and approved the final manuscript.

Research paper thumbnail of Electronic consent in a COVID-19 vaccine implementation trial in South Africa: Participant perspectives

South African Journal of Science

The COVID-19 pandemic has warranted modifications to clinical research implementation to ensure a... more The COVID-19 pandemic has warranted modifications to clinical research implementation to ensure adherence to public health and safety measures. Often, this modification has necessitated a deviation from the traditional face-to-face approach to an electronic or hybrid consent process. We assessed the acceptability and preference for electronic consent and explored understanding of the electronic consent information – an outcome which is vital in providing reassurance that consent is provided with full appreciation of the risks and benefits of study participation. In this descriptive study, healthcare professionals (HCPs) were invited, through a database of HCP contacts, snowball sampling and advertisement, to participate in an online survey between 14 July 2021 and 17 September 2021, to explore their experiences of providing electronic consent for enrolment into the largest implementation trial of a COVID vaccine in South Africa (SISONKE Trial). Descriptive analysis was used to chara...

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

Research paper thumbnail of 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

Research Square (Research Square), Jun 2, 2020

Background: HIV-1C has been shown to have a greater risk of virological failure and reduced susce... more 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 resistanceassociated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients suspected of failing on the South African national second-line cART regimen with bPIs. Methods: During 2017 and 2018, 67 patient samples were selected, of which 56 samples were successfully analyzed. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were ampli ed and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database. Results: Statistically signi cantly (p<0.001) higher PI RAMs were observed in minor viral quasispecies (25%; 14/56) compared to nucleoside reverse transcriptase inhibitors (11%; 6/56), non-nucleoside reverse transcriptase inhibitors (9%; 5/56) and integrase inhibitor RAM (4%; 2/56). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (n=13) in protease and K65R (n=5), K103N (n=7) and M184V (n=5) in reverse transcriptase. Conclusions: HTS-GRT improved the identi cation of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identi ed in <20% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.

Research paper thumbnail of Revisiting community engagement methods in the context of data science research and big data use in South Africa

South African Journal of Science

Effective community engagement for the use of large data sets in health research is faced with ch... more Effective community engagement for the use of large data sets in health research is faced with challenges similar to those in investigator-driven research. The scope of community engagement has evolved in highincome countries to embrace citizen science by communities and regulators to build trust in data science research. In South Africa and other low-and middle-income countries, with varying levels of literacy and the influence of pre-existing beliefs and past negative experiences with research, advisory committees of diverse stakeholder composition still have a role to play in protecting the rights of researched communities.

Research paper thumbnail of Additional file 2 of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

Additional file 2: Interview guide for Importance of clinical ethics committees or consultations ... more Additional file 2: Interview guide for Importance of clinical ethics committees or consultations during public health emergency over the COVID-19 outbreak.

Research paper thumbnail of Additional file 1 of 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

Additional file 1 Table S1. Individual patient wise mutation profiling.

Research paper thumbnail of Comparative strategic approaches to COVID-19 in Africa: Balancing public interest with civil liberties

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde, 2020

As COVID-19 spreads rapidly across Africa, causing havoc to economies and disruption to already f... more As COVID-19 spreads rapidly across Africa, causing havoc to economies and disruption to already fragile healthcare systems, it is becoming clear that despite standardised global health strategies, national and local government responses must be tailored to their individual settings. Some African countries have adopted stringent measures such as national lockdown, quarantine or isolation, in combination with good hand hygiene, mandatory wearing of masks and physical distancing, to prevent an impending healthcare crisis. The impact of stringent measures in low- to middle-income African countries has bought time for healthcare facilities to prepare for the onslaught of COVID-19 cases, but some measures have been challenging to implement. In some settings, public health measures have been associated with serious violations of individual rights owing to abuse of power and gaps in implementation of well-intentioned policy. Collateral damage with regard to non-COVID-19 diseases that were s...

Research paper thumbnail of 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

Research paper thumbnail of Mutations in LTR kB transcription factor binding sites in plasma virus among South African people living with HIV-1 (PLHIV)

AIDS Research and Human Retroviruses, 2019

HIV-1 subtype C (HIV-1C) is responsible for the majority of infections in sub-Saharan Africa. We ... more 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-jB plays an important role in regulating the viral gene expression from the viral promoter and controlling viral latency. LTR amplicons were sequenced and phylogenetically analyzed. In our data set, we identified F-jB sites (n = 4; 6%) at position II and (n = 1; 1%) at position I among 63 sequences analyzed. The majority of the sequences identified with H-jB at position II (n = 50; 79%) and position I (n = 55; 87%). Forty-nine (n = 49; 78%) sequences were found to exhibit C-jB site. ZA_LTR052 was identified with a single point mutation. We identified all three NF-jB-binding sites in (n = 44; 70%) the viral promoter-enhancer regions in South African patients.

Research paper thumbnail of Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes

Frontiers in microbiology, 2018

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host gen... more 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. As INSTIs are becoming increasingly accessible worldwide, it is important to understand the mechanism(s) of INSTI susceptibility. There is strong evidence suggesting differences in the patterns and mechanisms of drug resistance between HIV-1 subtype B, which dominates in United States, Western Europe and Australia, and non-B infections that are most prevalent in countries of Africa and Asia. IN polymorphisms and other genetic differences among diverse subtypes are likely responsible for these different patterns...

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

Scientific reports, Jan 16, 2018

HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed t... more 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. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furt...

Research paper thumbnail of 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

Scientific reports, Jan 16, 2018

A correction to this article has been published and is linked from the HTML and PDF versions of t... more 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.

Research paper thumbnail of Proceedings of the Frontiers of Retrovirology Conference 2016

Research paper thumbnail of Preinvasive cervical lesions and high prevalence of human papilloma virus among pregnant women in Cameroon

Research paper thumbnail of Characterization of HIV-1 subtype B near full-length genome sequences identified at the start of HIV epidemic in South Africa

By submitting this thesis electronically, I declare that the entirety of the work contained there... more By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own original work, that I am the sole owner thereof (save to the extent explicitly otherwise stated), that reproduction and publication thereof by Stellenbosch University will not infringe any third party rights and that this work has not been submitted before in its entirety or in part for any degree or examination at this or any other University.

Research paper thumbnail of Additional file 1 of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

Additional file 1: Interview guide for Promoting the establishment of Clinical Ethics Committees ... more Additional file 1: Interview guide for Promoting the establishment of Clinical Ethics Committees (CECs) in Africa.

Research paper thumbnail of 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 suscep... more 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. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Dr...

Research paper thumbnail of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

BMC Medical Ethics

Background The COVID-19 pandemic has magnified pre-existing challenges in healthcare in Africa. L... more 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. The views of African healthcare professionals or bioethicists on the role of CECs in Africa have not been explored or documented previously. In this study, we aim to explore such perspectives, as well as the challenges preventing the establishment of CECs in Africa. Methods Twenty healthcare professionals and bioethicists from Africa participated in this qualitative study that utilized in-depth semi-structured interviews with open-ended questions. Themes were identified through thematic analysis of interviews and open-ended responses. Results Kenya and South Africa are the only countries on the continen...

Research paper thumbnail of Isolation and quarantine in South Africa during COVID-19: Draconian measures or proportional response?

South African Medical Journal, Apr 23, 2020

South Africa (SA) is currently in the midst of an unprecedented public health crisis. The transmi... more South Africa (SA) is currently in the midst of an unprecedented public health crisis. The transmission dynamics of COVID-19 mean that person-to-person spread is a serious public health risk. As such, the SA National Department of Health has invoked the Disaster Management Act, [1] and several extraordinary containment measures have been implemented as part of a national lockdown to limit the spread of infection. A recent report in the Daily Maverick refers to a move from 'self-isolation' to enforced isolation in 'government approved isolation sites for treatment' in a phase described as 'concomitant punishment' in Durban, KwaZulu-Natal (KZN). The change in strategy appears to have been triggered by the high proportion of cases in eThekweni District (383/587) and the high mortality in KZN, with the province accounting for 22 of the 54 deaths in SA as of

Research paper thumbnail of Electronic consent in a COVID-19 vaccine implementation trial in South Africa: Participant perspectives

South African Journal of Science, May 31, 2022

of the manuscript. S.M.K. designed the online survey instrument and was responsible for data capt... more of the manuscript. S.M.K. designed the online survey instrument and was responsible for data capturing. M.M.M.J.A. undertook the data cleaning and analysis. A.E.A.O. contributed to the literature review. M.G.M.C. provided expert advice on statistical analysis. All authors read and approved the final manuscript.

Research paper thumbnail of Electronic consent in a COVID-19 vaccine implementation trial in South Africa: Participant perspectives

South African Journal of Science

The COVID-19 pandemic has warranted modifications to clinical research implementation to ensure a... more The COVID-19 pandemic has warranted modifications to clinical research implementation to ensure adherence to public health and safety measures. Often, this modification has necessitated a deviation from the traditional face-to-face approach to an electronic or hybrid consent process. We assessed the acceptability and preference for electronic consent and explored understanding of the electronic consent information – an outcome which is vital in providing reassurance that consent is provided with full appreciation of the risks and benefits of study participation. In this descriptive study, healthcare professionals (HCPs) were invited, through a database of HCP contacts, snowball sampling and advertisement, to participate in an online survey between 14 July 2021 and 17 September 2021, to explore their experiences of providing electronic consent for enrolment into the largest implementation trial of a COVID vaccine in South Africa (SISONKE Trial). Descriptive analysis was used to chara...

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

Research paper thumbnail of 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

Research Square (Research Square), Jun 2, 2020

Background: HIV-1C has been shown to have a greater risk of virological failure and reduced susce... more 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 resistanceassociated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients suspected of failing on the South African national second-line cART regimen with bPIs. Methods: During 2017 and 2018, 67 patient samples were selected, of which 56 samples were successfully analyzed. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were ampli ed and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database. Results: Statistically signi cantly (p<0.001) higher PI RAMs were observed in minor viral quasispecies (25%; 14/56) compared to nucleoside reverse transcriptase inhibitors (11%; 6/56), non-nucleoside reverse transcriptase inhibitors (9%; 5/56) and integrase inhibitor RAM (4%; 2/56). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (n=13) in protease and K65R (n=5), K103N (n=7) and M184V (n=5) in reverse transcriptase. Conclusions: HTS-GRT improved the identi cation of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identi ed in <20% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.

Research paper thumbnail of Revisiting community engagement methods in the context of data science research and big data use in South Africa

South African Journal of Science

Effective community engagement for the use of large data sets in health research is faced with ch... more Effective community engagement for the use of large data sets in health research is faced with challenges similar to those in investigator-driven research. The scope of community engagement has evolved in highincome countries to embrace citizen science by communities and regulators to build trust in data science research. In South Africa and other low-and middle-income countries, with varying levels of literacy and the influence of pre-existing beliefs and past negative experiences with research, advisory committees of diverse stakeholder composition still have a role to play in protecting the rights of researched communities.

Research paper thumbnail of Additional file 2 of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

Additional file 2: Interview guide for Importance of clinical ethics committees or consultations ... more Additional file 2: Interview guide for Importance of clinical ethics committees or consultations during public health emergency over the COVID-19 outbreak.

Research paper thumbnail of Additional file 1 of 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

Additional file 1 Table S1. Individual patient wise mutation profiling.

Research paper thumbnail of Comparative strategic approaches to COVID-19 in Africa: Balancing public interest with civil liberties

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde, 2020

As COVID-19 spreads rapidly across Africa, causing havoc to economies and disruption to already f... more As COVID-19 spreads rapidly across Africa, causing havoc to economies and disruption to already fragile healthcare systems, it is becoming clear that despite standardised global health strategies, national and local government responses must be tailored to their individual settings. Some African countries have adopted stringent measures such as national lockdown, quarantine or isolation, in combination with good hand hygiene, mandatory wearing of masks and physical distancing, to prevent an impending healthcare crisis. The impact of stringent measures in low- to middle-income African countries has bought time for healthcare facilities to prepare for the onslaught of COVID-19 cases, but some measures have been challenging to implement. In some settings, public health measures have been associated with serious violations of individual rights owing to abuse of power and gaps in implementation of well-intentioned policy. Collateral damage with regard to non-COVID-19 diseases that were s...

Research paper thumbnail of 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

Research paper thumbnail of Mutations in LTR kB transcription factor binding sites in plasma virus among South African people living with HIV-1 (PLHIV)

AIDS Research and Human Retroviruses, 2019

HIV-1 subtype C (HIV-1C) is responsible for the majority of infections in sub-Saharan Africa. We ... more 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-jB plays an important role in regulating the viral gene expression from the viral promoter and controlling viral latency. LTR amplicons were sequenced and phylogenetically analyzed. In our data set, we identified F-jB sites (n = 4; 6%) at position II and (n = 1; 1%) at position I among 63 sequences analyzed. The majority of the sequences identified with H-jB at position II (n = 50; 79%) and position I (n = 55; 87%). Forty-nine (n = 49; 78%) sequences were found to exhibit C-jB site. ZA_LTR052 was identified with a single point mutation. We identified all three NF-jB-binding sites in (n = 44; 70%) the viral promoter-enhancer regions in South African patients.

Research paper thumbnail of Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes

Frontiers in microbiology, 2018

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host gen... more 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. As INSTIs are becoming increasingly accessible worldwide, it is important to understand the mechanism(s) of INSTI susceptibility. There is strong evidence suggesting differences in the patterns and mechanisms of drug resistance between HIV-1 subtype B, which dominates in United States, Western Europe and Australia, and non-B infections that are most prevalent in countries of Africa and Asia. IN polymorphisms and other genetic differences among diverse subtypes are likely responsible for these different patterns...

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

Scientific reports, Jan 16, 2018

HIV-Integrase (IN) has proven to be a viable target for highly specific HIV-1 therapy. We aimed t... more 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. Genotypic analyses revealed the absence of major RAMs in the cohort collected before the broad availability of combination antiretroviral therapy (cART) and INSTI in South Africa, however, occurred at a rate of 2.85% (9/314) in database derived sequences. RAMs were present at IN-positions 66, 92, 143, 147 and 148, all of which may confer resistance to Raltegravir (RAL) and Elvitegravir (EVG), but are unlikely to affect second-generation Dolutegravir (DTG), except mutations in the Q148 pathway. Furt...

Research paper thumbnail of 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

Scientific reports, Jan 16, 2018

A correction to this article has been published and is linked from the HTML and PDF versions of t... more 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.

Research paper thumbnail of Proceedings of the Frontiers of Retrovirology Conference 2016

Research paper thumbnail of Preinvasive cervical lesions and high prevalence of human papilloma virus among pregnant women in Cameroon

Research paper thumbnail of Characterization of HIV-1 subtype B near full-length genome sequences identified at the start of HIV epidemic in South Africa

By submitting this thesis electronically, I declare that the entirety of the work contained there... more By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own original work, that I am the sole owner thereof (save to the extent explicitly otherwise stated), that reproduction and publication thereof by Stellenbosch University will not infringe any third party rights and that this work has not been submitted before in its entirety or in part for any degree or examination at this or any other University.

Research paper thumbnail of Additional file 1 of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

Additional file 1: Interview guide for Promoting the establishment of Clinical Ethics Committees ... more Additional file 1: Interview guide for Promoting the establishment of Clinical Ethics Committees (CECs) in Africa.

Research paper thumbnail of 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 suscep... more 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. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Dr...

Research paper thumbnail of COVID-19 underscores the important role of Clinical Ethics Committees in Africa

BMC Medical Ethics

Background The COVID-19 pandemic has magnified pre-existing challenges in healthcare in Africa. L... more 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. The views of African healthcare professionals or bioethicists on the role of CECs in Africa have not been explored or documented previously. In this study, we aim to explore such perspectives, as well as the challenges preventing the establishment of CECs in Africa. Methods Twenty healthcare professionals and bioethicists from Africa participated in this qualitative study that utilized in-depth semi-structured interviews with open-ended questions. Themes were identified through thematic analysis of interviews and open-ended responses. Results Kenya and South Africa are the only countries on the continen...