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Article ; Online: The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population

Natasha Samsunder / Nikita Devnarain / Aida Sivro / Ayesha B. M. Kharsany

Tropical Medicine and Infectious Disease, Vol 8, Iss 12, p

A Scoping Review

2023 Volume 514

Abstract: To determine the performance and reliability of diagnostic tests for the identification of SARS-CoV-2 infection in South Africa, we conducted a scoping review to identify published studies undertaken in the English language from March 2020 to August 2022 ...

Abstract	To determine the performance and reliability of diagnostic tests for the identification of SARS-CoV-2 infection in South Africa, we conducted a scoping review to identify published studies undertaken in the English language from March 2020 to August 2022 that evaluated the performance of antigen- and antibody-based diagnostic tests for SARS-CoV-2 in South Africa. We identified 17 relevant peer-reviewed articles; six reported on SARS-CoV-2 gene and/or antigen detection whilst 11 reported on antibody detection. Of the SARS-CoV-2 gene and/or antigen-based tests, sensitivity ranged from 40% to 100%, whilst for the antibody-based tests, sensitivity ranged from 13% to 100%. All tests evaluated were highly dependent on the stage of infection and the timing of sample collection. This scoping review demonstrated that no single SARS-CoV-2 gene and/or antigen- or antibody-based assay was sufficiently sensitive and specific simultaneously. The sensitivity of the tests was highly dependent on the timing of sample collection with respect to SARS-CoV-2 infection. In the case of SARS-CoV-2 gene and/or antigen detection, the earlier the collection of samples, the greater the sensitivity, while antibody detection tests showed better sensitivity using samples from later stages of infection.
Keywords	SARS-CoV-2 ; SARS-CoV-2 gene/s ; diagnostic testing ; RT-PCR ; antigen ; antibody ; Medicine ; R
Subject code	570
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Field evaluations of four SARS-CoV-2 rapid antigen tests during SARS-CoV-2 Delta variant wave in South Africa

Natasha Samsunder / Gila Lustig / Slindile Ngubane / Thando Glory Maseko / Santhuri Rambaran / Sinaye Ngcapu / Stanley Nzuzo Magini / Lara Lewis / Cherie Cawood / Ayesha B. M. Kharsany / Quarraisha Abdool Karim / Salim Abdool Karim / Kogieleum Naidoo / Aida Sivro

Diagnostic and Prognostic Research, Vol 7, Iss 1, Pp 1-

2023 Volume 6

Abstract: Abstract Background Rapid antigen tests detecting SARS-CoV-2 were shown to be a useful tool in managing the COVID-19 pandemic. Here, we report on the results of a prospective diagnostic accuracy study of four SARS-CoV-2 rapid antigen tests in a South ... ...

Abstract	Abstract Background Rapid antigen tests detecting SARS-CoV-2 were shown to be a useful tool in managing the COVID-19 pandemic. Here, we report on the results of a prospective diagnostic accuracy study of four SARS-CoV-2 rapid antigen tests in a South African setting. Methods Rapid antigen test evaluations were performed through drive-through testing centres in Durban, South Africa, from July to December 2021. Two evaluation studies were performed: nasal Panbio COVID-19 Ag Rapid Test Device (Abbott) was evaluated in parallel with the nasopharyngeal Espline SARS-CoV-2 Ag test (Fujirebio), followed by the evaluation of nasal RightSign COVID-19 Antigen Rapid test Cassette (Hangzhou Biotest Biotech) in parallel with the nasopharyngeal STANDARD Q COVID-19 Ag test (SD Biosensor). The Abbott RealTime SARS-CoV-2 assay was used as a reference test. Results Evaluation of Panbio and Espline Ag tests was performed on 494 samples (31% positivity), while the evaluation of Standard Q and RightTest Ag tests was performed on 539 samples (13.17% positivity). The overall sensitivity for all four tests ranged between 60 and 72% with excellent specificity values (> 98%). Sensitivity increased to > 80% in all tests in samples with cycle number value < 20. All four tests performed best in samples from patients presenting within the first week of symptom onset. Conclusions All four evaluated tests detected a majority of the cases within the first week of symptom onset with high viral load.
Keywords	COVID-19 ; SARS-CoV-2 ; Antigen rapid diagnostic test ; Performance evaluation ; Medicine (General) ; R5-920
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pre-infection plasma cytokines and chemokines as predictors of HIV disease progression

Samukelisiwe Ngcobo / Refilwe P. Molatlhegi / Farzana Osman / Sinaye Ngcapu / Natasha Samsunder / Nigel J. Garrett / Salim S. Abdool Karim / Quarraisha Abdool Karim / Lyle R. McKinnon / Aida Sivro

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 8

Abstract: Abstract Previous studies have highlighted the role of pre-infection systemic inflammation on HIV acquisition risk, but the extent to which it predicts disease progression outcomes is less studied. Here we examined the relationship between pre-infection ... ...

Abstract	Abstract Previous studies have highlighted the role of pre-infection systemic inflammation on HIV acquisition risk, but the extent to which it predicts disease progression outcomes is less studied. Here we examined the relationship between pre-infection plasma cytokine expression and the rate of HIV disease progression in South African women who seroconverted during the CAPRISA 004 tenofovir gel trial. Bio-Plex 200 system was used to measure the expression of 47 cytokines/chemokines in 69 seroconvertors from the CAPRISA 004 trial. Cox proportional hazards regression analyses were used to measure associations between cytokine expression and CD4 decline prior to antiretroviral therapy initiation. Linear regression models were used to assess whether pre-infection cytokine expression were predictors of disease progression outcomes including peak and set-point viral load and CD4:CD8 ratio at less and greater than180 days post infection. Several cytokines were associated with increased peak HIV viral load (including IL-16, SCGFβ, MCP-3, IL-12p40, SCF, IFNα2 and IL-2). The strongest association with peak viral load was observed for SCGFβ, which was also inversely associated with lowest CD4:CD8 ratio < 180 days post infection and faster CD4 decline below 500 cells/µl (adjusted HR 4.537, 95% CI 1.475–13.954; p = 0.008) in multivariable analysis adjusting for age, study site, contraception, baseline HSV-2 status and trial arm allocation. Our results show that pre-infection systemic immune responses could play a role in HIV disease progression, especially in the early stages of infection.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CAPRISA 018

Cheryl Baxter / Nonhlanhla Yende Zuma / Natasha Samsunder / Salim Abdool Karim / Catherine Hankins / Quarraisha Abdool Karim / Bruno Pozzetto / Leila Mansoor / Tanuja Narayansamy Gengiah / Ishana Harkoo / Precious Radebe / B Maharaj / Marc M Baum / John A Moss

BMJ Open, Vol 12, Iss

a phase I/II clinical trial study protocol to assess the safety, acceptability, tolerability and pharmacokinetics of a sustained-release tenofovir alafenamide subdermal implant for HIV prevention in women

2022 Volume 1

Keywords	Medicine ; R
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative cost analysis of point-of-care versus laboratory-based testing to initiate and monitor HIV treatment in South Africa.

Kate Simeon / Monisha Sharma / Jienchi Dorward / Jessica Naidoo / Ntuthu Dlamini / Pravikrishnen Moodley / Natasha Samsunder / Ruanne V Barnabas / Nigel Garrett / Paul K Drain

PLoS ONE, Vol 14, Iss 10, p e

2019 Volume 0223669

Abstract: BACKGROUND:The number of people living with HIV (PLHIV) in need of treatment monitoring in low-and-middle-income countries has been rapidly expanding, placing an increasing burden on laboratories. Promising new point-of-care (POC) test have the potential ...

Abstract	BACKGROUND:The number of people living with HIV (PLHIV) in need of treatment monitoring in low-and-middle-income countries has been rapidly expanding, placing an increasing burden on laboratories. Promising new point-of-care (POC) test have the potential to reduce laboratory workloads, but the implementation cost is uncertain. We sought to estimate the costs of decentralized POC testing compared to centralized laboratory testing for PLHIV initiating treatment in South Africa. METHODS:We conducted a microcosting analyses comparing clinic-based POC testing to centralized laboratory testing for HIV viral load, creatinine, and CD4 count monitoring. We completed time-and-motion studies to assess staff time for sample collection and processing. Instrument costs were estimated assuming five-year lifespans and we applied a 3% annual discount rate. Total costs and cost per patient were estimated over a five-year period: the first year of ART initiation and four years of routine HIV monitoring, following World Health Organization ART monitoring guidelines. RESULTS:We estimated that per-patient costs of POC HIV viral load, CD4, and creatinine tests were USD $25, $11, and $9, respectively, assuming a clinic volume of 50 patients initiated per month. At centralized laboratories, per-patient costs of POC HIV viral load, CD4, and creatinine tests were USD $26, $6, $3. Total monitoring costs of all testing over a 5-year period was $45 higher for POC testing compared to centralized laboratory testing ($210 vs $166). CONCLUSIONS:POC testing for HIV care and treatment can be feasibly implemented within clinics in South Africa, particularly those with larger patient volumes. POC HIV viral load costs are similar to lab-based testing while CD4 count and creatinine testing are more costly as POC tests. Our cost estimates are useful to policymakers in planning resource allocation and can inform cost-effectiveness analyses of POC testing.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ex vivo HIV entry into blood CD4+ T cells does not predict heterosexual HIV acquisition in women.

Vineet Joag / Aida Sivro / Nonhlanhla Yende-Zuma / Hajra Imam / Natasha Samsunder / Quarraisha Abdool Karim / Salim Abdool Karim / Lyle McKinnon / Rupert Kaul

PLoS ONE, Vol 13, Iss 7, p e

2018 Volume 0200359

Abstract: BACKGROUND:A blood-based assay that could quantify HIV susceptibility would be very valuable for HIV prevention research. Previously, we developed and validated an ex vivo, flow-based, HIV entry assay to assess genital HIV susceptibility in endocervical ... ...

Abstract	BACKGROUND:A blood-based assay that could quantify HIV susceptibility would be very valuable for HIV prevention research. Previously, we developed and validated an ex vivo, flow-based, HIV entry assay to assess genital HIV susceptibility in endocervical CD4+ T cells. METHODS:Here we assessed whether this tool could be used to predict HIV risk using blood-derived CD4+ T cells in a rigorously-blinded, nested case-control study using blood samples collected from high-risk, HIV-uninfected South African women enrolled in the CAPRISA 004 clinical trial. Cases, subsequently acquiring HIV were sampled prior to HIV infection and compared with controls, who remained HIV-uninfected. The primary endpoint was ex vivo entry of a CCR5-tropic HIV founder virus into blood CD4+ T cells. Secondary endpoints included HIV entry into CD4+ central (TCM) and effector (TEM) memory T cells, and into CD4+ T cell subsets expressing CCR5, CD69, CCR6, α4β1 or α4β7. RESULTS:Compared to bulk CD4+ T cells (4.9% virus entry), CD4+ T cells expressing CCR5, CCR6 or α4β1 and TEM were highly susceptible (15.5%, 8.8%, 8.2% and 10.8% entry, respectively, all p<0.0001), while TCM, CD69+ or α4β7+ CD4+ cells were moderately susceptible (6.4%, 6.0% and 5.8% respectively, p ≤ 0.003). While the proportion of the aforementioned highly susceptible cells correlated with overall virus entry into CD4+ T cells within an individual (r = 0.68, 0.47, 0.67, and 0.60 respectively, p<0.0001), blood virus entry did not predict subsequent mucosal HIV acquisition after controlling for sexual behaviour and condom use (OR 0.92, 95% CI 0.77-1.11, p = 0.40). CONCLUSIONS:Although virus entry identified several previously known highly susceptible cellular HIV targets, blood HIV entry did not predict subsequent heterosexual HIV acquisition. Assessment of mucosal HIV susceptibility may require sampling at the site of HIV exposure.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

Khadija Khan / Farina Karim / Yashica Ganga / Mallory Bernstein / Zesuliwe Jule / Kajal Reedoy / Sandile Cele / Gila Lustig / Daniel Amoako / Nicole Wolter / Natasha Samsunder / Aida Sivro / James Emmanuel San / Jennifer Giandhari / Houriiyah Tegally / Sureshnee Pillay / Yeshnee Naidoo / Matilda Mazibuko / Yoliswa Miya /

Nokuthula Ngcobo / Nithendra Manickchund / Nombulelo Magula / Quarraisha Abdool Karim / Anne von Gottberg / Salim S. Abdool Karim / Willem Hanekom / Bernadett I. Gosnell / COMMIT-KZN Team / Richard J. Lessells / Tulio de Oliveira / Mahomed-Yunus S. Moosa / Alex Sigal

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 7

Abstract: Emerging SARS-CoV-2 Omicron sub-lineages BA.4 and BA.5 raise concerns about potential immune evasion. Here, Khan et al. show that both BA.4 and BA.5 are able to escape immune response induced by prior BA.1 infection, but that this effect is less ... ...

Abstract	Emerging SARS-CoV-2 Omicron sub-lineages BA.4 and BA.5 raise concerns about potential immune evasion. Here, Khan et al. show that both BA.4 and BA.5 are able to escape immune response induced by prior BA.1 infection, but that this effect is less pronounced in vaccinated individuals.
Keywords	Science ; Q
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: HPV infection and the genital cytokine milieu in women at high risk of HIV acquisition

Lenine J. P. Liebenberg / Lyle R. McKinnon / Nonhlanhla Yende-Zuma / Nigel Garrett / Cheryl Baxter / Ayesha B. M. Kharsany / Derseree Archary / Anne Rositch / Natasha Samsunder / Leila E. Mansoor / Jo-Ann S. Passmore / Salim S. Abdool Karim / Quarraisha Abdool Karim

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 12

Abstract: Cervicovaginal inflammation and human papillomavirus (HPV) are separately associated with increased risk of HIV acquisition. Here the authors longitudinally profile 48 cervicovaginal cytokines and HPV status in a large observational HIV high-risk cohort, ...

Abstract	Cervicovaginal inflammation and human papillomavirus (HPV) are separately associated with increased risk of HIV acquisition. Here the authors longitudinally profile 48 cervicovaginal cytokines and HPV status in a large observational HIV high-risk cohort, and show the same cytokines associate with HPV infection and HIV risk.
Keywords	Science ; Q
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: HPV infection and the genital cytokine milieu in women at high risk of HIV acquisition

Nature Communications, Vol 10, Iss 1, Pp 1-

2019 Volume 12

Abstract	Cervicovaginal inflammation and human papillomavirus (HPV) are separately associated with increased risk of HIV acquisition. Here the authors longitudinally profile 48 cervicovaginal cytokines and HPV status in a large observational HIV high-risk cohort, and show the same cytokines associate with HPV infection and HIV risk.
Keywords	Science ; Q
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessing the safety and pharmacokinetics of the anti-HIV monoclonal antibody CAP256V2LS alone and in combination with VRC07-523LS and PGT121 in South African women

BMJ Open, Vol 10, Iss

study protocol for the first-in-human CAPRISA 012B phase I clinical trial

2020 Volume 11

Abstract: Introduction New HIV prevention strategies are urgently required. The discovery of broadly neutralising antibodies (bNAbs) has provided the opportunity to evaluate passive immunisation as a potential prevention strategy and facilitate vaccine development. ...

Abstract	Introduction New HIV prevention strategies are urgently required. The discovery of broadly neutralising antibodies (bNAbs) has provided the opportunity to evaluate passive immunisation as a potential prevention strategy and facilitate vaccine development. Since 2014, several bNAbs have been isolated from a clade C-infected South African donor, CAPRISA 256. One particular bNAb, CAP256-VRC26.25, was found to be extremely potent, with good coverage against clade C viruses, the dominant HIV clade in sub-Saharan Africa. Challenge studies in non-human primates demonstrated that this antibody was fully protective even at extremely low doses. This bNAb was subsequently structurally engineered and the clinical variant is now referred to as CAP256V2LS.Methods and analysis CAPRISA 012B is the second of three trials in the CAPRISA 012 bNAb trial programme. It is a first-in-human, phase I study to assess the safety and pharmacokinetics of CAP256V2LS. The study is divided into four groups. Group 1 is a dose escalation of CAP256V2LS administered intravenously to HIV-negative and HIV-positive women. Group 2 is a dose escalation of CAP256V2LS administered subcutaneously (SC), with and without the dispersing agent recombinant human hyaluronidase (rHuPH20) as single or repeat doses in HIV-negative women. Groups 3 and 4 are randomised placebo controlled to assess two (CAP256V2LS+VRC07-523LS; CAP256V2LS+PGT121) and three (CAP256V2LS+VRC07-523LS+PGT121) bNAb combinations administered SC to HIV-negative women. Safety will be assessed by the frequency of reactogenicity and adverse events related to the study product. Pharmacokinetic disposition of CAP256V2LS alone and in combination with VRC07-523LS and PGT121 will be assessed via dose subgroups and route of administration.Ethics and dissemination The University of KwaZulu-Natal Biomedical Research Ethics Committee (BREC) and the South African Health Products Regulatory Authority (SAHPRA) have granted regulatory approval (trial reference numbers: BREC00000857/2019 and SAHPRA 20200123). ...
Keywords	Medicine ; R
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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