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Diagnostics
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Highlights of Molecular Laboratory Diagnostics in South Africa
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Highlights of Molecular Laboratory Diagnostics in South Africa

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Clinical Laboratory Medicine".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 7320

Special Issue Editors

Dr. Lesley Erica Scott

E-Mail Website
Guest Editor
Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2193, South Africa
Interests: molecular diagnostics; infectious diseases; method comparison statistics; assay evaluations; diagnostics implementation; HIV; tuberculosis and COVID19; GIS mapping; quality programs
Prof. Dr. Wendy Stevens

E-Mail Website
Guest Editor
Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2193, South Africa
Interests: molecular diagnostics; infectious diseases; haematological pathologies; HIV; POCT and centralized diagnosis; EID, HIV DR, national program implementation, policy and guidelines; tuberculosis; drug resistance; infectious disease epidemiology; quality systems; digital health

Special Issue Information

Dear Colleagues,

The backbone to South Africa’s HIV, TB and COVID-19 prevention and treatment programs is a national laboratory network of connected diagnostics. Through a single laboratory information system (LIS), test quality, program operations and surveillance monitoring are centrally enabled, with data algorithms driving national policy and research agendas. Molecular diagnostics is central to this network, with capacity for 10 million tests per year, mostly established for HIV viral load, EID and TB molecular tests. In April 2020, the country felt the pressure of diagnostic needs for COVID-19 and leveraged its national molecular diagnostic platform for SARS-CoV-2 testing. Limited supply, however, catapulted the country’s innovative thinkers to strengthen public–private partnerships to expand molecular testing and develop protocols, reference materials and regulatory frameworks to rapidly evaluate new molecular technologies, often before global emergency use listing. Complementing South Africa’s molecular diagnostic program is the integration of digital health innovations with the LIS that automates specimen tracking, monitors specimen and service quality and enables rapid priority disease test result return for linkage to care.

The purpose of this Special Issue is to highlight the role molecular diagnostics and companion innovations have played in South Africa’s healthcare programs, as well as their impact. We invite authors to share their lessons learned, scaled implementation successes and innovative molecular diagnostic approaches to improve patient care. 

Dr. Lesley Erica Scott
Prof. Dr. Wendy Stevens
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular diagnostics
  • HIV, TB, HPV, COVID19 diagnostics and monitoring
  • scaled implementation
  • molecular POCT
  • method validation
  • cost effective molecular diagnostics
  • scaled laboratory services
  • molecular sequencing
  • alternative specimens
  • multi-purpose molecular platforms
  • reference materials
  • quality management
  • regulatory frameworks
  • connected diagnostics
  • digital health
  • laboratory data mining
  • molecular surveillance
  • GIS mapping

Published Papers (6 papers)

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Research

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18 pages, 1810 KiB  
Article
More Than a Decade of GeneXpert® Mycobacterium tuberculosis/Rifampicin (Ultra) Testing in South Africa: Laboratory Insights from Twenty-Three Million Tests
by Manuel Pedro da Silva, Naseem Cassim, Silence Ndlovu, Puleng Shiela Marokane, Mbuti Radebe, Anne Shapiro, Lesley Erica Scott and Wendy Susan Stevens
Diagnostics 2023, 13(20), 3253; https://doi.org/10.3390/diagnostics13203253 - 19 Oct 2023
Viewed by 975
Abstract
This study seeks to describe the rollout and current state of South Africa’s GeneXpert molecular diagnostic program for tuberculosis (TB). Xpert MTB/RIF was introduced in 2011 with a subsequent expansion to include extra-pulmonary and paediatric testing, followed by Xpert MTB/RIF Ultra in 2017. [...] Read more.
This study seeks to describe the rollout and current state of South Africa’s GeneXpert molecular diagnostic program for tuberculosis (TB). Xpert MTB/RIF was introduced in 2011 with a subsequent expansion to include extra-pulmonary and paediatric testing, followed by Xpert MTB/RIF Ultra in 2017. Through a centralised laboratory information system and the use of a standardised platform for more than a decade, over 23 million tests were analysed, describing the numbers tested, Mycobacterium tuberculosis complex detection, rifampin resistance, and the unsuccessful test rates. The stratification by province, specimen type, age, and sex identified significant heterogeneity across the program and highlighted testing gaps for men, low detection yield for paediatric pulmonary TB, and the effects of inadequate specimen quality on the detection rate. The insights gained from these data can aid in the monitoring of interventions in support of the national TB program beyond laboratory operational aspects. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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15 pages, 4402 KiB  
Article
Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF
by Lesley Erica Scott, Anne Nicole Shapiro, Manuel Pedro Da Silva, Jonathan Tsoka, Karen Rita Jacobson, Michael Emch, Harry Moultrie, Helen Elizabeth Jenkins, David Moore, Annelies Van Rie and Wendy Susan Stevens
Diagnostics 2023, 13(20), 3163; https://doi.org/10.3390/diagnostics13203163 - 10 Oct 2023
Viewed by 1026
Abstract
An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013–2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables [...] Read more.
An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013–2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables analysed include Mycobacterium tuberculosis (Mtb) positivity, the mycobacterial proportion of rifampicin-resistant Mtb (RIF), and probe frequency. The summary statistics of these variables were generated and aggregated at the facility and municipal level. The spatial distribution patterns of the indicators across municipalities were determined using the Moran’s I and Getis Ord (Gi) statistics. A case-control study was conducted to investigate factors associated with a high mycobacterial load. Logistic regression was used to analyse this study’s results. There was striking spatial heterogeneity in the distribution of Mtb and RIF across South Africa. The median patient age, urban setting classification, and number of health care workers were found to be associated with the mycobacterial load. This study illustrates the potential of using data generated from molecular diagnostics in combination with GIS technology for Mtb surveillance in South Africa. Spatially targeted interventions can be implemented in areas where high-burden Mtb persists. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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11 pages, 1746 KiB  
Article
HIV Viral Load Testing in the South African Public Health Setting in the Context of Evolving ART Guidelines and Advances in Technology, 2013–2022
by Lucia Hans, Naseem Cassim, Somayya Sarang, Diana Hardie, Silence Ndlovu, W.D. Francois Venter, Pedro Da Silva and Wendy Stevens
Diagnostics 2023, 13(17), 2731; https://doi.org/10.3390/diagnostics13172731 - 22 Aug 2023
Viewed by 1240
Abstract
HIV viral load (VL) testing plays a key role in the clinical management of HIV as a marker of adherence and antiretroviral efficacy. To date, national and international antiretroviral treatment recommendations have evolved to endorse routine VL testing. South Africa (SA) has recommended [...] Read more.
HIV viral load (VL) testing plays a key role in the clinical management of HIV as a marker of adherence and antiretroviral efficacy. To date, national and international antiretroviral treatment recommendations have evolved to endorse routine VL testing. South Africa (SA) has recommended routine VL testing since 2004. Progressively, the centralised HIV VL program managed by its National Health Laboratory Service (NHLS) has undergone expansive growth. Retrospective de-identified VL data from 2013 to 2022 were evaluated to review program performance. Test volumes increased from 1,961,720 performed in 2013 to 45,334,864 in 2022. The median total in-laboratory turnaround time (TAT) ranged from 94 h (2015) to 51 h (2022). Implementation of two new assays improved median TATs in all laboratories. Samples of VL greater than 1000 copies/mL declined steadily. Despite initial increases, samples of fewer than 50 copies/mL stagnated at about 70% from 2019 and declined to 68% in 2022. Some variations between assays were observed. Overall, the SA VL program is successful. The scale of the VL program, the largest of its kind in the world by some margin, provides lessons for future public health programs dependent on laboratories for patient outcome and program performance monitoring. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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12 pages, 1040 KiB  
Article
Eliminating Vertical Transmission of HIV in South Africa: Establishing a Baseline for the Global Alliance to End AIDS in Children
by Ahmad F. Haeri Mazanderani, Tanya Y. Murray, Leigh F. Johnson, Mathilda Ntloana, Tabisa Silere-Maqetseba, Sufang Guo and Gayle G. Sherman
Diagnostics 2023, 13(15), 2563; https://doi.org/10.3390/diagnostics13152563 - 1 Aug 2023
Cited by 1 | Viewed by 1076
Abstract
To gain a detailed overview of vertical transmission in South Africa, we describe insights from the triangulation of data sources used to monitor the national HIV program. HIV PCR results from the National Health Laboratory Service (NHLS) were analysed from the National Institute [...] Read more.
To gain a detailed overview of vertical transmission in South Africa, we describe insights from the triangulation of data sources used to monitor the national HIV program. HIV PCR results from the National Health Laboratory Service (NHLS) were analysed from the National Institute of Communicable Diseases (NICD) data warehouse to describe HIV testing coverage and positivity among children <2 years old from 2017–2021. NICD data were compared and triangulated with the District Health Information System (DHIS) and the Thembisa 4.6 model. For 2021, Thembisa estimates a third of children living with HIV go undiagnosed, with NICD and DHIS data indicating low HIV testing coverage at 6 months (49%) and 18 months (33%) of age, respectively. As immunisation coverage is reported at 84% and 66% at these time points, better integration of HIV testing services within the Expanded Programme for Immunization is likely to yield improved case findings. Thembisa projects a gradual decrease in vertical transmission to 450 cases per 100,000 live births by 2030. Unless major advances and strengthening of maternal and child health services, including HIV prevention, diagnosis, and care, can be achieved, the goal to end AIDS in children by 2030 in South Africa is unlikely to be realised. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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13 pages, 3193 KiB  
Article
How South Africa Used National Cycle Threshold (Ct) Values to Continuously Monitor SARS-CoV-2 Laboratory Test Quality
by Lesley Erica Scott, Nei-yuan Hsiao, Graeme Dor, Lucia Hans, Puleng Marokane, Manuel Pedro da Silva, Wolfgang Preiser, Helena Vreede, Jonathan Tsoka, Koleka Mlisana and Wendy Susan Stevens
Diagnostics 2023, 13(15), 2554; https://doi.org/10.3390/diagnostics13152554 - 1 Aug 2023
Cited by 2 | Viewed by 951
Abstract
The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied [...] Read more.
The high demand for SARS-CoV-2 tests but limited supply to South African laboratories early in the COVID-19 pandemic resulted in a heterogenous diagnostic footprint of open and closed molecular testing platforms being implemented. Ongoing monitoring of the performance of these multiple and varied systems required novel approaches, especially during the circulation of variants. The National Health Laboratory Service centrally collected cycle threshold (Ct) values from 1,497,669 test results reported from 6 commonly used PCR assays in 36 months, and visually monitored changes in their median Ct within a 28-day centered moving average for each assays’ gene targets. This continuous quality monitoring rapidly identified delayed hybridization of RdRp in the Allplex™ SARS-CoV-2 assay due to the Delta (B.1.617.2) variant; S-gene target failure in the TaqPath™ COVID-19 assay due to B.1.1.7 (Alpha) and the B.1.1.529 (Omicron); and recently E-gene delayed hybridization in the Xpert® Xpress SARS-CoV-2 due to XBB.1.5. This near “real-time” monitoring helped inform the need for sequencing and the importance of multiplex molecular nucleic acid amplification technology designs used in diagnostics for patient care. This continuous quality monitoring approach at the granularity of Ct values should be included in ongoing surveillance and with application to other disease use cases that rely on molecular diagnostics. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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Review

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11 pages, 269 KiB  
Review
Advancing HIV Drug Resistance Technologies and Strategies: Insights from South Africa’s Experience and Future Directions for Resource-Limited Settings
by Kim Steegen, Gert U. van Zyl, Mathilda Claassen, Aabida Khan, Melendhran Pillay, Subitha Govender, Phillip A. Bester, Johanna M. van Straaten, Vibha Kana, Ewaldé Cutler, Monalisa N. Kalimashe, Ramokone L. Lebelo, Mokopi B. H. Moloi and Lucia Hans
Diagnostics 2023, 13(13), 2209; https://doi.org/10.3390/diagnostics13132209 - 29 Jun 2023
Cited by 1 | Viewed by 1462
Abstract
Monitoring of HIV drug resistance (HIVDR) remains critical for ensuring countries attain and sustain the global goals for ending HIV as a public health threat by 2030. On an individual patient level, drug resistance results assist in ensuring unnecessary treatment switches are avoided [...] Read more.
Monitoring of HIV drug resistance (HIVDR) remains critical for ensuring countries attain and sustain the global goals for ending HIV as a public health threat by 2030. On an individual patient level, drug resistance results assist in ensuring unnecessary treatment switches are avoided and subsequent regimens are tailored on a case-by-case basis, should resistance be detected. Although there is a disparity in access to HIVDR testing in high-income countries compared to low- and middle-income countries (LMICS), more LMICs have now included HIVDR testing for individual patient management in some groups of patients. In this review, we describe different strategies for surveillance as well as where HIVDR testing can be implemented for individual patient management. In addition, we briefly review available technologies for HIVDR testing in LMICs, including Sanger sequencing, next-generation sequencing, and some point-of-care options. Finally, we describe how South Africa has implemented HIVDR testing in the public sector. Full article
(This article belongs to the Special Issue Highlights of Molecular Laboratory Diagnostics in South Africa)
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