Start main page content

National Priority Programme (NPP)

Operations Manager: Dr. Leigh Berrie

In 2010, the NHLS established the National Priority Programmes (NPP) division to address the National Department of Health's need to provide increased access to patient testing and treatment. The division is led by Professor Wendy Stevens; with a mission to provide affordable, accessible HIV and TB diagnostic services that yield accurate, reliable, relevant and timely results aligned with the NDoH strategy and are based on current scientific knowledge and international norms. 

The group has expanded its original mandate and now employs 20 individuals to ensure that multi-disciplinary approaches and widespread consultations are used to facilitate and in many cases assist in implementation of National Programmes. The division is divided into various units, which include HIV viral load, CD4, early infant diagnosis, HIV drug resistance and TB GeneXpert. Additional expertise lies with Point-of-Care Testing (POCT) and more recently, greater involvement with contributing towards Global fund and other grants that support activities such as the Department of Correctional Services (DCS), mining and peri-mining communities, and HIV and TB drug resistance testing. The team is assisted by scientist and pathologist expert committees to provide technical expertise, biomedical engineers, a health economist, clinicians, and a research and development unit. This group conducts consultative work for the WHO, CDC, Gates foundation, Clinton foundation, among others. Additional projects based on health priorities are in the pipeline. The division has made significant contributions to laboratory medicine through research and development and implementation science.

Teaching and Training

The CD4 unit training initiatives include six training workshops per year as well as on-site training following new installations/upgrades of instruments. All training initiatives serve to consolidate knowledge and skills of staff across the NHLS and to address skills required for day-to-day testing, use of standardised PLG/CD4 protocols, sample-to-sample and daily instrument quality control and review of external quality assessment, as well as instrument maintenance and extensive trouble-shooting.

For HIV viral load, training needs are identified and discussed on a monthly basis with suppliers who provide on-site training for both new staff as well as refresher trainings. Two successful advanced training courses (Roche and Abbott) are held per year for selected HIV viral load testing staff from each site.

Activities of the TB GeneXpert molecular testing unit include training of approximately 400 laboratory staff and 3,500 health care workers per year since inception in 2011. This will be an on-going process to support both NDoH training on the clinical algorithm as well as laboratory staff on technical and quality aspects of the test. In addition, three Advanced GeneXpert Training courses have been conducted by the NPP in collaboration with Cepheid (supplier) at which 20-30 participants were trained at each course. The NPP team has also been working together with the Foundation for Innovative New Diagnostics (FIND) to develop on-line web-based GeneXpert clinical training material for healthcare workers. This technology has revolutionised the diagnosis of both drug susceptible and drug resistant TB. This group was responsible for the implementation of 289 analysers in 207 centres across South Africa.

E-Learning Training Initiatives- The NPP unit is working hand-in-hand with the NHLS Learning Academy to develop on-line training material to be available for laboratory staff with regards to HIV and TB diagnostic tests. This training material will include aspects of Good Laboratory Practice (GLP) and will be accredited for continuous professional development (CPD) points. This training initiative will assist greatly in the improvement of training coverage and frequency as well as adding value to the programme.

Service and support

The NPP CD4 unit is involved with service and support to ~62 labs through coordination and integration of functions to cover all aspects of CD4 servicing across the NHLS. This support includes site evaluation, equipment validation, audits, SANAS accreditation support, equipment implementation and set-up, data management and full technical support. To assist laboratories, the CD4 unit monitors testing volumes and turn-around-times daily to ensure minimum instrument downtime and impact of quality of results. A monthly dashboard with CD4 test result data from national and provincial down to district level is distributed to both internal and external stakeholders in terms of test volumes and ranges. Approximately 4 million CD4s were conducted annually across the 62 sites.

Approximately 2.4 million HIV viral load tests were performed across the country in 2013. On-going monthly meetings are held between the HIV viral load NPP team and suppliers to identify any problem areas. All sites are responsible for submitting a monthly indicator report, which is reviewed and acted upon accordingly. Site visits have been conducted in order to assist and prepare the labs for accreditation.

All GeneXpert labs are monitored in terms of test volumes, positivity rates, rifampicin (RIF) resistant rates, error rates and in-lab turnaround time on a monthly basis, through data extracted from the CDW and the development of a monthly operational dashboard. Reports for each NHLS region as to lab’s performance are now being prepared and distributed on a monthly basis to the Business and Area Managers to assist with continuous monitoring of the programme. The programme is now being further expanded to a quarter of a million people in special risk populations such as the Correctional Services and peri-mining communities.


The NPP collaborates on research projects with the CD4 laboratory, the EID unit and the HIV drug resistance laboratory. In addition, the NPP contains a research and development (R&D) group comprising a multidisciplinary team specialising in clinical microbiology, HIV and TB research and development, as well as engineering. The group’s focus under the leadership of Professor Lesley Scott is on applied science for problem-solving using molecular diagnostic tools. In 2012, the NPP R&D team developed a novel programme for verification of the GeneXpert modules. Every newly placed GeneXpert instrument requires verification in order to prove that the instrument is “fit for purpose” before clinical results can be reported. Protocols for testing extra-pulmonary specimen types such as fine needle aspiration (FNA), pleural fluids, cerebrospinal fluid, ascites fluid, urine, gastric aspirates and tissue have been developed in collaboration with the TB referral laboratory in Braamfontein. An Xpert MTB-RIF paediatric protocol in collaboration with FIND is also being setup, to evaluate the Xpert MTB-RIF assay on paediatric stool specimens.

A remote monitoring project and operational dashboard, specific for GeneXpert instruments, has been designed by the NPP group. This monitor allows for real-time analysis of the national performance of the GeneXpert instruments and laboratories. The NPP is also involved in a collaborative NIH-funded Xpert impact study with the University of North Carolina (Professor Annelies van Rie), which aims to test patients diagnosed with MTB-RIF resistance by culture and patients diagnosed with MTB-RIF resistance by Xpert.

An initial validation of the high throughput Abbott NearMedic Plus (NMTB) assay (Abbott Molecular Diagnostics) was conducted in 2012 and the R&D group will now be performing a clinical validation of the improved version of this assay. In addition, the EasyNAT™ TB Diagnostic kit (USTAR Biotechnologies) has been validated on EQA Dried culture spots. The R&D unit also investigated various blood specimen storage, collection and transport options for HIV viral load testing.

The role of Point-of-Care (POC) testing for HIV/TB diagnosis and monitoring is being investigated. The first multiple assay POC implementation site was established at the Helen Joseph Themba Lethu clinic in collaboration with Professor Ian Sanne’s clinical team to address nurse operation of POC testing versus routine laboratory testing. The second phase, involved a randomized controlled trial at three clinic sites in North West Province to compare POC versus Standard of Care (SOC) for antiretroviral therapy (ART) initiation. This study has had important outputs and findings with regards to the development of standard operating procedures (SOPs) for POC testing, insights into challenges faced by clinics, clinical workflow and development of protocols for appropriate sample collection for POCT. A recent publication by this group reported that multiple POC testing could accurately and feasibly be performed by a dedicated nurse at the clinic on single or multiple finger sticks. The final data analysis should be completed by November 2014.


The NPP collaborates with various partners and funders for research as well as implementation programmes:

  • Department of Correctional Services (DCS): In order to improve TB control in all 242 correctional facilities in South Africa, the NHLS is working in partnership with the DCS, NDoH and NGOs such as Aurum Institute, TB/HIV Care Association and Right to Care to ensure access to regular HIV- and TB-related screening, testing and treatment of up to 150,000 offenders through various funding mechanisms including the CDC and Global Fund. Xpert MTB-Rif testing is being provided either on-site, or at the nearest referral laboratory. During 2014, Xpert MTB-RIF testing facilities have been established on-site at the following correctional facilities:
  • Kgoši Mampuru Management Area II
  • Barberton Management Area
  • Johannesburg Management Area
  • Groenpunt Management Area
  • Pollsmoor Management Area
  • St Albans Management Area
  • Durban-Westville Management Area

In order to improve linkages to treatment, both within the correctional facilities and once the patient has been released, NHLS is in the process of implementing its system of SMS printers, providing immediate results reporting from the NHLS.

  • Peri-mining Communities: NHLS, together with the Aurum Institute, has been appointed by NDoH (under the Global Fund grant) to provide services to implement interventions aimed at improving TB and HIV/AIDS management for vulnerable peri-mining communities (estimated at around 600,000 people) in 6 main mining districts. Six staffed and GeneXpert-equipped mobile TB units will be provided within the communities to undertake Xpert MTB/RIF testing for TB.
  • Multi-Drug Resistant Tuberculosis (MDR-TB) and Linkage-to-Care: Through funding provided by CDC and Global Fund, a “Linkage-to-Care” initiative is being developed for all MDR-TB cases. This initiative involves the integration of current NDoH electronic TB registers with the NHLS data warehouse as well as to be linked as part of an integrated MDR-TB contact and defaulter tracing system through a mobile health (mHealth) mechanism. It is envisioned that at the initiation of treatment for a new MDR-TB case, an SMS will be triggered and sent to the cell-phone of the appropriate nurse led ward-based team for follow-up.

Other collaborations include:

  • Gates Grand Challenges (GGC) for POC research
  • CDC for GeneXpert EQA development
  • HE2RO group and Boston University
  • Centre for TB Excellence
  • NHLS Microbiology and Virology expert Committees
  • FIND for EQA and R&D projects
  • Bill and Melinda Gates Foundation
  • Clinton Health Access Initiative