PEPFAR's annual planning process is done either at the country (COP) or regional level (ROP).
PEPFAR's programs are implemented through implementing partners who apply for funding based on PEPFAR's published Requests for Applications.
Since 2010, PEPFAR COPs have grouped implementing partners according to an organizational type. We have retroactively applied these classifications to earlier years in the database as well.
Also called "Strategic Areas", these are general areas of HIV programming. Each program area has several corresponding budget codes.
Specific areas of HIV programming. Budget Codes are the lowest level of spending data available.
Expenditure Program Areas track general areas of PEPFAR expenditure.
Expenditure Sub-Program Areas track more specific PEPFAR expenditures.
Object classes provide highly specific ways that implementing partners are spending PEPFAR funds on programming.
Cross-cutting attributions are areas of PEPFAR programming that contribute across several program areas. They contain limited indicative information related to aspects such as human resources, health infrastructure, or key populations programming. However, they represent only a small proportion of the total funds that PEPFAR allocates through the COP process. Additionally, they have changed significantly over the years. As such, analysis and interpretation of these data should be approached carefully. Learn more
Beneficiary Expenditure data identify how PEPFAR programming is targeted at reaching different populations.
Sub-Beneficiary Expenditure data highlight more specific populations targeted for HIV prevention and treatment interventions.
PEPFAR sets targets using the Monitoring, Evaluation, and Reporting (MER) System - documentation for which can be found on PEPFAR's website at https://www.pepfar.gov/reports/guidance/. As with most data on this website, the targets here have been extracted from the COP documents. Targets are for the fiscal year following each COP year, such that selecting 2016 will access targets for FY2017. This feature is currently experimental and should be used for exploratory purposes only at present.
Years of mechanism: 2008 2009
Plan to move entire TB-HIV actiities for National Health Laboratory Services from HLAB and add NHLS to
the HVTB budget category with narrative.
New/Continuing Activity: New Activity
Continuing Activity:
Table 3.3.12:
SUMMARY:
Activities will be carried out to address laboratory-specific unmet needs that impede full implementation of
national laboratory programs. Activities will increase national coverage of HIV and TB diagnostics and
treatment monitoring capabilities; ensure uniform quality assurance measures among laboratories;
strengthen laboratory reporting systems; promote efforts to synchronize infection control activities in
collaboration with the National Institute of Occupation Health (NIOH); and to expand upon the regional
support and collaboration with other PEPFAR-funded countries.
BACKGROUND:
The NHLS is accountable to the National Department of Health (NDOH) through its Executive Board and is
responsible for public sector laboratory services. The NHLS also governs activities and provides funding to
the National Institute of Communicable Diseases (NICD) to provide surveillance, research and
programmatic operations, as well as funding to the NIOH for policy development activities related to
occupational health.
ACTIVITY 1: HIV testing at point of care
HIV testing at point of care settings using HIV rapid tests is set to increase in terms of the National strategic
plan developed by the NDOH. Project Goals and Objectives: (1) Assess rapid HIV kits performance at a
laboratory level; (2) routine monitoring of new lots/batches prior to release to testing sites and (3) produce
training materials for HIV QMS, external quality assurance (PT) and internal quality controls (IQC) for
testing sites for quality assurance purposes. The target would be 200 sites in 5 provinces over a year period
to determine feasibility of the program. This will include piloting of dried plasma PT panels. Project Outputs:
The objective of HIV assessment at field level allows for rational decision making in terms of algorithm
setting and alternatives to current tests. Post marketing surveillance permits early warning systems to
become operative. IQC usage will allow for program managers to become aware of any problems that could
be site-specific or systematic. The EQA/PT program will assess overall program performance.
ACTIVITY 2: HIV Rapid kit Quality Management Training
As part of the National Strategic Plan to reduce infections by 50% by 2011 there is a need to expanded
services for counselling and testing. Project Strategy: To continue QMS training implemented in 2008 and to
provide direct support to the Provinces in terms of a train the trainer-type approach or direct training as
needed. The current time spent per training is 2-3 months per province at the trainer level. The outcome will
be that at least 5 provinces will be trained by the third quarter of 2009. The training will be integrated with
implementation of EQA and IQC programs as well as M&E programs. Project Goals and Objectives: (1)
Training of trainers in 9 Provinces in HIV rapid Test QMS and implementation of training at provincial level.
(2) Integration of QMS training with implementation of EQA and IQC programs in at least 6 provinces. (3)
Implementation of an M&E program that integrates with provincial- level monitoring of HIV rapid testing.
Project Outputs: Monitoring of numbers trained: trainers and direct technical assistance, provincial
coverage, IQC coverage and EQA scores, M&E evaluation scores in terms of numbers of sites trained and
implementation of QMS program.
ACTIVITY 3: HIV-1 NAT EQA
External Quality Assessment (EQA) and IQC will be an integral part of the laboratory quality management
system (QMS) that will detect weak spots in performance as well as improve on the reliability and
confidence when performing HIV-1 NAT. Project Strategy - Description and Methodologies: The NICD will
source local material as well as characterize materials in collaboration with QCMD for HIV viral load and
subtyping PT and IQC. NICD will make the program available to 25-30 participating laboratories for two
distributions: first and last quarters of 2009. Data will collated by an independent secretariat that includes
the NICD and QCMD for data analysis. For the IQC program software development allows for web-based
submission of data with real time analysis and trend analysis. A positive standard has been selected
(subtype C, 5000 copies/ml) and characterized for this purpose. The program will be introduced in the first
quarter of 2009. The NICD intends to introduce IQC program for HIV DNA testing on DBS in the second
quarter of 2009 to 11 participating laboratories. Project Outcomes: (1) The implementation of an EQA
program that will monitor laboratory performance related to the ART program. (2) Capacity development of
the NICD to perform as a molecular EQA provider. (3) The development of an IQC program for HIV viral
load testing and infant diagnosis that can provide real time monitoring (4) The use of locally relevant
materials to be characterized and included in panels.
ACTIVITY 4: Early Infant Diagnosis
Project Goals and Objectives: (1) To develop a clinical and laboratory infrastructure that supports early
testing and HIV diagnosis in infants. (2) To assess the most appropriate method for early and accurate
diagnosis of HIV infection in infants. The primary objective is to utilize the DBS HIV DNA PCR as a tool for
diagnostic purposes in a setting with approximately 6000 infants over a 12 month period from the second
quarter of 2009. The objectives would be the identification of processes that will ensure high throughput that
will allow for access to diagnostics, care and follow-up as required. Project Outputs: The primary outcome
will be the establishment of technologies that can be applied in the public health setting for the early
diagnosis of HIV infected infants as well as monitoring antiretroviral therapy. An algorithm of cost-effective
testing will be a primary accomplishment. The application will be at an operational level to ensure that
clinical sites that do not have easy access to diagnostic services benefit.
ACTIVITY 5: Increased access of TB culture and referral services
In light of the significant increase in MDR and XTR-TB cases within South Africa, and recognizing that there
is a significant lack of laboratory capacity to capture and report suspect TB cases, it has been determined
Activity Narrative: that an immediate expansion of TB culture and referral services are required. TB culture facilities have been
established in all provinces but to make a significant impact quickly, it has been proposed that a further 3
TB laboratories be renovated to meet current demands during this funding period, in Mpumalanga, the
Western Cape, and KZN. The selected sites would provide a responsive and regional impact in respect to
TB culture services and the overall ability to capture possible MDR and XTR-TB cases. The proposed sites
would provide relief to the existing laboratory services and improve overall performance and TB diagnostic
capacity within the entire region. Proposed funding would be used to provide equipment purchases and
renovations for the proposed sites.
ACTIVITY 6: Approaches to increase TB laboratory throughput
With the current number of sputum samples submitted for laboratory smear microscopy and culture already
at an all time high and continuing to increase, it is recognized that one of the most significant rate
determining factors directly impacting laboratory through-put is that of the NALC decontamination process,
a labor intensive processes of sputum concentration and decontamination. In order to streamline this
process and to increase overall laboratory through-put of sputum specimens to meet the increased demand
and lack of available staff to process such specimens, alternate or automated measures should be
investigated. Currently, NICD has vested time in investigating possible automated methods that could
significantly reduce and provide standardized decontamination processes. The currently proposed funds
would be used, in partnership and through co-funding with NHLS, for the development of automated NALC
decontamination instrumentation and technologies. The project with full details and project plan has been
submitted. There is strict adherence to the time lines in the project plan and budget. Completion date of
project will be January 2010.
ACTIVITY 7: National TB Quality Programs
Proficiency testing: Second line DST EQA for culture laboratories is a priority and will be developed during
this funding period, as there is NO PT for second line anti-TB drugs in the NHLS. Description and
Methodology: Simulated specimens for DTS testing will be prepared and distributed to all culture facilities
within the NHLS. The resistance profile among the organisms will vary from organism to organism and
measure the proficiency of the laboratories to correctly identify resistance to second line drugs amikacin or
kanamycin, ethionamide and ofloxacin. Capreomycin. Objectives of the program include: (1) capacity
building, (2) improvement of quality (3) institution of corrective actions where deficiencies are detected and
follow up, as well as (4) providing support to peripheral laboratories. Outputs: Second line DST is
performed by MGIT liquid culture in the following NHLS Laboratories: Green Point, Port Elizabeth, Umtata,
Albert Luthuli, Braamfontein. All these laboratories will be required to participate in the PT.
ACTIVITY 8: Rechecking program
A blind rechecking program is in the process of being rolled out in the NHLS. Goals and objective: (1)
Blanket approach of rechecking random selected slides from the laboratory register is inadequate. (2)
Selection of sample size is based on implementation and sustainability, rather than rigorous analytical
methods. (3) The recommended sample size provides relative information on the sensitivity of microscopy.
(4) Sample size is based on annual laboratory volume and the proportion of positive smears. (5) Positive
slides are included to achieve blinding, but numbers are insufficient to determine specificity. (6) Guidelines
to interpret Discrepancies.
ACTIVITY 9: Line Probes
Project Strategy: 20 NHLS regional laboratories will be identified for roll out of the line probe over the next
24 months. This entails (1) Identify additional space for PCR laboratories (2) Renovate the space for PCR
laboratories to an acceptable standard (3) Purchasing of equipment (4) Training newly employed scientists
(5) Validation of the assays (6) Institute quality systems for the ongoing monitoring of performance. A
partnership will be established with Davies Diagnostics, the local supplier of the Hain line probe, for
technical assistance in the training and roll out of the assay. Project Goals and Objectives: The overall goal
is the establishment of line probe assays in 20 regional laboratories throughout South Africa for the early
identification, isolation and treatment of new MDR-TB cases to improve outcomes in these patients. Project
Outputs: PCR Laboratory space would have been identified and renovated, capital equipment put in place
and scientists trained to perform the assay. Quality systems will be in place. These laboratories would be
confident in performing routine diagnostic PCR investigation on smear positive sputa for the identification of
MDR-TB patients.
ACTIVITY 10: National Tuberculosis Reference Laboratory
Molecular Biology: Goals and objectives: (1) With an emphasis on the MDR-TB and XDR-TB strains
isolated nationally, molecular characterization of sensitive and resistant M tuberculosis will be commenced
on the collection of MDR and XDR organisms from all provinces in South Africa. (2) Molecular investigations
into outbreaks will be performed and unique mycobacterial strains and NTM species encountered will be
identified and characterized by conventional, molecular and HPLC technology. (3) Molecular genotyping on
a sample of the isolates obtained from drug resistance survey (about 14,000 strains) to accurately reflect
the genotypic epidemiology of M tuberculosis in South Africa. Outcomes expected: (1) Characterizing
general circulating M tuberculosis strains, MDR-TB strains and longitudinal characterization of repeat
isolates from MDR-TB patients (2) Sequencing the resistance genes of M tuberculosis MDR-TB strains and
promoters,(3) Molecular investigations into outbreaks (4) Characterizing general circulating M tuberculosis
strains, MDR-TB strains and longitudinal characterization of repeat isolates from MDR-TB patients. Assays
planned to be performed in the NTBRL include RFLP, spoligotyping, sequencing of drug resistance loci.
ACTIVITY 11: ACILT - African Centre for Integrated Laboratory Training
Objective: Recent reviews of TB and HIV laboratory practices throughout Africa have affirmed the principle
Activity Narrative: that accurate laboratory results are not only based on the number of people employed in laboratories, but
on the quality of their work. This is chiefly a matter of better training, motivation and management according
to good laboratory practices. The primary objective is to train technical staff from across Africa in current
technologies and methodologies for TB and HIV. Strategy: It is proposed that a Technical Advisory
Committee be formed which would provide technical expertise to the Centre management on issues related
to management, laboratory curriculum development and training programs, review the training centre's
training priorities and strategies so that they are in line with the regional requirements and targets, and give
support to the faculty. Outputs: courses to be focused on in the short-term are: (1) TB culture/DST and
molecular diagnostics. (2) Early Infant Diagnosis PCR (3) Laboratory management (4) Quality management
systems (QMS) (5) Commodity management (quantification).
ACTIVITY 12: CDC Management & Administration
The NHLS/NICD has implemented financial and administrative processes to ensure improved focus and
oversight of the funding of this Cooperative Agreement. These processes are broadly divided into two,
being 1) processes around the budget development and the funding needs affecting the application, and 2)
financial controls for project finances. Budget development and funding needs affecting the previous
application were addressed by having a centralized budget development function. All the budgets and carry-
forward requests are consolidated in conjunction with individual PIs, the Cooperate Services Manager of the
NICD, the NHLS Cooperate Services and the PI managing the CDC grant overall. Secondly, financial
controls affecting funds have been investigated and are currently being implemented in alignment with
NHLS policies and procedures. The processes followed for committing expenditure and the treatment
thereof have been documented. This forms the basis for the implementation of financial controls, including
monthly reporting of expenditure, and the review of these expenditures by the relevant PIs.
New/Continuing Activity: Continuing Activity
Continuing Activity: 14328
Continued Associated Activity Information
Activity Activity ID USG Agency Prime Partner Mechanism Mechanism ID Mechanism Planned Funds
System ID System ID
14328 14328.08 HHS/Centers for National Health 6777 6777.08 $12,000,000
Disease Control & Laboratory
Prevention Services
Emphasis Areas
Construction/Renovation
Health-related Wraparound Programs
* TB
Human Capacity Development
Estimated amount of funding that is planned for Human Capacity Development $2,177,049
Public Health Evaluation
Food and Nutrition: Policy, Tools, and Service Delivery
Food and Nutrition: Commodities
Economic Strengthening
Education
Water
Table 3.3.16:
National Health Laboratory Services (NHLS) is accountable to the National Department of Health (NDOH)
through its Executive Board and is responsible for public sector laboratory services. The NHLS also governs
activities and provides funding to the National Institute of Communicable Diseases (NICD) to provide
surveillance, research and programmatic operations, as well as funding to the NIOH for policy development
activities related to occupational health.
ACTIVITY 1: Point of care testing
services for counseling and testing. Project Strategy: To continue QMS training implemented in 2008 and to
implementation of External Quality Assessment (EQA) and IQC programs as well as M&E programs.
Project Goals and Objectives: (1) Training of trainers in 9 Provinces in HIV rapid Test QMS and
implementation of training at provincial level. (2) Integration of QMS training with implementation of EQA
and IQC programs in at least 6 provinces. (3) Implementation of an M&E program that integrates with
provincial- level monitoring of HIV rapid testing. Project Outputs: Monitoring of numbers trained: trainers and
direct technical assistance, provincial coverage, IQC coverage and EQA scores, M&E evaluation scores in
terms of numbers of sites trained and implementation of QMS program.
ACTIVITY 3: HIV-1 NAT EQA and IQC
HIV-1 NAT EQA and IQC will be an integral part of the laboratory quality management system (QMS) that
will detect weak spots in performance as well as improve on the reliability and confidence when performing
HIV-1 NAT. Project Strategy - Description and Methodologies: The NICD will source local material as well
as characterize materials in collaboration with QCMD for HIV viral load and subtyping PT and IQC. NICD
will make the program available to 25-30 participating laboratories for two distributions: first and last
quarters of 2009. Data will collated by an independent secretariat that includes the NICD and QCMD for
data analysis. For the IQC program software development allows for web-based submission of data with
real time analysis and trend analysis. A positive standard has been selected (subtype C, 5000 copies/ml)
and characterized for this purpose. The program will be introduced in the first quarter of 2009. The NICD
intends to introduce IQC program for HIV DNA testing on DBS in the second quarter of 2009 to 11
participating laboratories. Project Outcomes: (1) The implementation of an EQA program that will monitor
laboratory performance related to the ART program. (2) Capacity development of the NICD to perform as a
molecular EQA provider. (3) The development of an IQC program for HIV viral load testing and infant
diagnosis that can provide real time monitoring (4) The use of locally relevant materials to be characterized
and included in panels.
established in all provinces but to make a significant impact quickly, it has been proposed that a further
three TB laboratories be renovated to meet current demands during this funding period, in Mpumalanga, the
20 NHLS regional laboratories will be identified for rollout of the line probe over the next 24 months. This
entails (1) Identify additional space for PCR laboratories (2) Renovate the space for PCR laboratories to an
acceptable standard (3) Purchasing of equipment (4) Training newly employed scientists (5) Validation of
the assays (6) Institute quality systems for the ongoing monitoring of performance. A partnership will be
established with Davies Diagnostics, the local supplier of the Hain line probe, for technical assistance in the
training and roll out of the assay. The overall goal is the establishment of line probe assays in 20 regional
laboratories throughout South Africa for the early identification, isolation and treatment of new MDR-TB
cases to improve outcomes in these patients. PCR Laboratory space would have been identified and
renovated, capital equipment put in place and scientists trained to perform the assay. Quality systems will
be in place. These laboratories would be confident in performing routine diagnostic PCR investigation on
smear positive sputa for the identification of MDR-TB patients.
that accurate laboratory results are not only based on the number of people employed in laboratories, but
Activity Narrative: on the quality of their work. This is chiefly a matter of better training, motivation and management according
technologies and methodologies for TB and HIV. It is proposed that a Technical Advisory Committee be
formed which would provide technical expertise to the Centre management on issues related to
management, laboratory curriculum development and training programs, review the training centre's training
priorities and strategies so that they are in line with the regional requirements and targets, and give support
to the faculty. Courses to be focused on in the short-term are: (1) TB culture/DST and molecular
diagnostics. (2) Early Infant Diagnosis PCR (3) Laboratory management (4) Quality management systems
(QMS) (5) Commodity management (quantification).
NHLS policies and procedures. The processes followed for committing expenditure have been documented.
This forms the basis for the implementation of financial controls, including monthly reporting of expenditure,
and the review of these expenditures.
Estimated amount of funding that is planned for Human Capacity Development $1,260,192
Estimated amount of funding that is planned for Public Health Evaluation $0
Table 3.3.17: