National HIV Reference Laboratory (NHRL)

About Us

The National HIV Reference Laboratory (NHRL) was established by the Ministry of Health in 2003 to provide oversight of Laboratory HIV Quality Assurance services for the National HIV Program – NASCOP.   NHRL monitors the impact of the growing HIV epidemic in the country and coordinates specialized HIV testing services, monitors viral load trends and early infant diagnosis (EID). NHRL operates under the administrative jurisdiction of National Public Health Laboratory (NPHL) within the Department of Preventive and Promotive Health (DPPH). The NHRL was in 2012 the first ISO 15189:2012 accredited public health laboratory in the country.

The laboratory ensures high-quality HIV testing at all public health facilities offering HIV laboratory services in Kenya. It  plays a key role in the fight against HIV/AIDS and addresses the UNAIDS 90 – 90 – 90 – an ambitious treatment target to help end the AIDS epidemic; the aim being to diagnose 90% of all HIV-positive persons, provide antiretroviral therapy (ART) for 90% of those diagnosed, and achieve viral suppression for 90% of those treated by 2020.

Additionally, NHRL is involved in the formulation of HIV policies and guidelines and is involved in conducting HIV population-based surveys as well as other proxy group surveys and surveillance in HIV.

Key Functions

The key functions include;

  • Developing Laboratory HIV National policies and guidelines for use in Health facilities in the country.
  • Evaluation and validation of new Laboratory HIV Equipment and reagents for fitness and use in the country.
  • Providing National HIV Proficiency testing schemes and quality laboratory interventions for HIV service providers in the country.
  • Conducts national laboratory-based HIV surveillance for projection of country HIV prevalence and incidence.
  • HIV drug resistance monitoring and special population-based surveys.
  • Strengthening of laboratory systems in HIV prevention, care, treatment and surveillance.
  • To coordinate national partner activities in scaling up of quality HIV laboratory services in the country.
  • Plan and implement national HIV laboratory-based surveillance for projection and determination of HIV prevalence and incidence, HIV drug resistance and special population surveys in Kenya including ( KAIS I 2007, KAIS II 2012, KENPHIA 2018).
  • Provide and coordinate external quality assessments in HIV Laboratory services
  • Develops national training curricula for HIV Laboratory services and conduct training/or and mentorship of HIV Service providers in the country.
  • Fosters national and international collaborations with other national and international reference laboratories and centres of excellence worldwide for continuous quality improvements.
  • Strengthening of Laboratory networks through designing and capacity enabling of county and peripheral facilities to share diagnostic resources and improve equity and access to quality Laboratory HIV Services.

HIV ART Monitoring Sites by Year


The laboratory is divided into sections namely;

  1.  Sample and data management section which is responsible for receiving all the samples coming to the laboratory by sorting and logging them into the Laboratory Information Management System (LIMS) and ensures that quality samples are received in the laboratory through screening them by use of the established rejection criteria.
  2.  Diagnostic and monitoring section which is also responsible for rapid kits validation and verification with other related reagents. It is also for CD4 enumerations, external quality assurance (EQA), coordination and monitoring through quality assurance (QA) tests using the sample split and QASI.
  3. Molecular section for viral load testing and monitoring of trends of ART patients, EID testing of all HIV exposed infants through the HIV molecular Deoxyribonucleic Acid (DNA) Polymerase Chain Reaction (PCR). It also monitors the molecular Point of Care (POC) equipment and viral load across the country through POC QA monitoring and feedbacks to facilities.
  4. Molecular HIV Drug Resistance monitoring section which has a platform that is equipped with 96-capillary 3730xl Genetic Analyzer which is the Gold Standard for high throughput genetic analysis. This instrument is very significant in HIV-1 genotyping assays for the growing number of patients with therapy failure and acquired HIV drug-resistance. The section helps inform policy to maximize the durability and rational use of available HIV drug regimens. The section is also well equipped with a series of other equipment for downstream processes.
  5. Quality Assurance section which comprises of the all-section heads and some appointed officer to help the QA to execute its mandates. The section also ensures that there is scheduled training /capacity building of testing personnel by the manufacturers. The section also plans and implements the quarterly QA VL TWG meetings for testing laboratories and stakeholders and plans regular data audit between systems and registers to inform program and other interested parties. All the viral load and EID DNA PCR testing laboratories 10 (100%) are enrolled to VL/EID Proficiency Testing in the following External Quality Assurance schemes (EQAs)
  • CDC –GAP Atlanta Scheme
  • VL/EID PT Inter-lab  -peer comparisons
  • QASI Canada for CD4 T- lymphocytes enumerations

HIV monitoring tools in use are standardized, harmonized across the country and are coordinated by QA section such as:

  • VL /EID request form
  • VL/EID Tracking Log

Progress towards 90-90-90 UNAIDS targets

Sample Type

Sample types that are accepted in the NHRL include: whole blood for CD4 enumerations, plasma for viral load testing, and Dry Blood Spot (DBS) for DNA PCR discrepancy determination and Early Infant Diagnosis (EID).

Tests Done

The tests that are done are viral load, DNAPCR, CD4 enumerations, ELISA testing and other related HIV testing methods. NHRL monitors a total 2196 facilities that refer viral load-specific samples to the 10 testing referral laboratories.

Viral load capacity by sample type include 66% plasma (facilities close to testing labs); and 34 % DBS (hard to reach areas).

Testing capacity

The laboratory has capacity to handle high volumes of viral load tests received. Currently there are 38 conventional platforms in 10 VL/EID testing laboratories. The total capacity per year is: 1,801,440; functional capacity per year is 1,441,152; total utilization per year 2017 is: 1,088,753. The total percent utilization is at 76%.

Number of EID/VL HIV Molecular Platforms in the country

No of EID/VL HIV Molecular Platforms in the country
LaboratoryNo. of Cobas 8800No. of CAP/CTM V2.0No. of m2000sp
WRP 23

Frequency of Viral Load Monitoring

Population on ARTFrequency
PCR positive HEIsBaseline at the time of ART initiation
Age 0-24 years oldEvery 6 months
Age ≥ 25 years oldMonth 6, 12, and then annually in the subsequent years
Pregnant or breastfeeding mothersAt confirmation of the pregnancy (if already on ART) or 3 months after ART initiation (if ART initiated during pregnancy/breastfeeding), and then every 6 months until complete cessation of breastfeeding
Regimen modification (including single substitution)Regimen modification can be done if no VL result available prior 6 monthsThree months after any regimen modification

Achievements/ Milestones

  1. NHRL was the first public health laboratory to go full digital in their service delivery.
  2. Eight out of ten laboratories countrywide conducting viral load EID testing are ISO 15189:2012 accredited, and the remaining two are in the process of accreditation.
  3. The laboratory is implementing remote log-in to improve data quality and  sample and results tracking by clinicians which has helped to improve on TAT leading to prompt interventions
  4. The use of viral load champions in ART monitoring has helped to increase the interventions.
  5. Increased universal access to viral load testing and monitoring through support sample referral networks and result tracking at facilities.
  6. Increase sources of results access to facilities by adopting various methods such as Online access from laboratories websites; National dashboards; facility emails; SMS on facility phones and to designated staff with rights
  7. Set up a Viral Load Technical Working Group (TWG) that conducts laboratory reviews on quality indicators and share best practices to standardize and optimize service delivery and performs

Role of the laboratory in the devolved system

The testing laboratories have been placed strategically in high burden zones across the country in order to help the population that lives with HIV to access the service.

Future Plans

NHRL plans to decentralize the molecular HIV viral load and EID services to more than 15 laboratories located in various counties in the country.

  • Scale up of the HIV point of care (POC) for both viral load and EID testing.
  • Scale up the drug resistance testing in NHRL in order to put all clients who have tested HIV positive on ART
  • To develop a database of the genomics for HIV treatment failures.