JCRC laboratory started operation in 1992 together with the JCRC with the main focus on HIV/AIDS testing; its test menu has since developed to a number of tests that are readily available for our clients serving the different Regional Centres of Excellency of JCRC.

Highly specialized laboratories are present in all JCRC facilities across the country to support regular clinical care, research and advanced HIV management. These laboratories are able to perform most routine medical tests as well as advanced HIV management and research processes.

A bioharzard containment level 3 (P3 level) has been completed and now fully functional at JCRC headquarters in Lubowa. It is among the only two facilities in the country with the capability at this level so far. It is housed in the new 1,250 sq. ft. modern facility, which also houses reference laboratories for Clinical Chemistry, Tuberculosis, Hematology, Immunology and Flow cytometry, Molecular biology, Virology, and Microbiology.

All laboratories are registered with external quality assurance schemes, and have consistently maintained internationally recognised standards of quality.

JCRC laboratories are CAP accredited; College of American pathologists (CAP) certification, having completed the CAP accreditation readiness assessment, taking even higher the established standard of quality.

Laboratory Information Management System (LIMS) system that manages all laboratory activities from test request and information, results to storage information.

Maintaining the rigorous quality requirements, and keeping up a culture of continuous learning makes JCRC the partner of choice to undertake Laboratory-based endeavours. At various levels within JCRC laboratories, scientists are thoroughly trained and highly experienced, including scientists at PhD level. The intellectual property of the laboratories is significant, with contributions to hundreds of publications, and influencing policy at the national level.

Members of the technical staff sit on various national advisory committees and sub-committees at the ministry of Health. JCRC Laboratory staff participated in the development of national; Laboratory Policy, Laboratory strategic Plan, Quality assurance management system, laboratory mentorship plan and the Strengthening Laboratory Management towards Accreditation (SLMTA) Training and follow up of trainees.

In addition, JCRC staff participated in the review of Laboratory Technology Training Curricula for Certificate and Diploma courses. Working with the Central Public Health Laboratories (CPHL), JCRC through Targeted HIV/AIDS and Laboratories services (THALAS) project supported and effected performance improvement of the supported public health labs through the SLMTA approach up to Star 2 level.

As members of the Laboratory equipment and Infrastructure subcommittee of the Laboratory Technical and Advisory Committee of MOH – the JCRC team participated in the standardizing of laboratory equipment, supplies and infrastructural designs for public laboratories at gazetted health delivery levels.

JCRC laboratory staff also participated in developing registration guidelines now in use by the Allied Health Professionals’ Council (AHPC) in registering and monitoring health laboratories in the country.

Products being produced by the Laboratory – De Egre De Ionized water. From 5L to 20L denominations

Laboratory Test Menu

The laboratory offers a vast test menu. Some of the common tests include: COVID Tests, HIV Rapid, HIV RNA, CBC/Diff, LFTS, RFTS, URINE HCG, HIV Resistance tests, etc. —

Laboratory Sections

Processing and Storage

Sample storage, Shipment, sample separation

Bio Repository


The main analyzer is a Roche COBAS Integra which is fully automated for performing clinical chemistry tests which include; Renal functional tests(RFTs), Liver functional tests(LFTs), Lipid profile, Elecrolytes, Creatinine kinase, Glucose (Fasting and Random), HBA1C, Haptogloblin, C reactive Protein, GGT, LDH, Lactate, Lipase, Amaylase, Uric acid, Magnesium, CSF(Glucose and Total Protein) Urine Chemistry; Albumin Total Protein in Urine Phosphate, Calcium, Creatinine,

The Lab also uses the Abbott Architect Plus i1000 SR Immuno analyzer Where the following tests are performed;

Anti HCV, Anti HBc, Anti HBe, FHS, HBsAg, HIV Ag/Ab COMBO P24, TOXO IgM, TOXO IgG, CMV IgG ,CMV IgM 

Immunology_2(Flow Cytometry)

This lab runs the CD4/CD8/CD3/45 lymphocytes subsets using two BD FACSCaliburs. The lab also has BD FACS Presto machine which runs CD4 absolutes and percentages. HIV testing is conducted using ministry of Health alogarithm.

The lab uses GEENIUS for differentiation of HIV types.

The laboratory runs P24 ELISA for detection of both Antigen and Antibodies. 


The analyzers

The lab has six analyzers that include 2 Coulter AC.T 5diff analyzes for CBC/Diff, Sysmex XN 550 for CBC /Diff and Reticulocyte, Gazelle for sickling test, ACL 9000 for Coagulation Assays, Mirasol for Pathogen reduction technique.

Test Menu

  • Peripheral and bone marrow smear examinations with the Hematologists on site.
  • ABO and Cross match testing for both emergency transfusion and Apheresis.
  • Reticulocyte counting
  • Pathogen reduction
  • Blood Transfusion: A fully functional blood transfusion section performing:

  • ABO Grouping
  • Cross matching
  • Apheresis
  • Antibody screening
  • Pathogen reduction


The Virology laboratory is one of the Joint Clinical Research Centre’s Laboratory units supporting Research and Clinical Molecular Laboratory needs (testing). The unit is equipped with modern and fully automated Molecular testing (PCR) platforms including Abbott m2000 system and COBAS Ampliprep/COBAS TaqMan 96 (Roche). The Abbott m2000 system is a PCR testing platform that is used at JCRC virology unit for quantitative detection of;

  1. HIV (RNA PCR).
  2. Hepatitis B and C.

In addition to the quantitative assays mentioned above, we have capabilities at JCRC Virology laboratory for the qualitative detection (confirmatory diagnosis) of these organisms below using Abbott m2000 system;

  1. COVID-19.
  2. Hepatitis B and C.
  3. Cytomegalovirus (CMV).
  4. Mycobacterium Tuberculosis Complex (MTBC).
  5. Human Papilloma Virus (HPV).
  6. Chlamydia trachomatis and Neisseria gonnorhoeae.
  7. Herpes Simplex Virus types 1 and 2.

We have capabilities to detect Mycobacterium Tuberculosis (MTB) resistance to rifampicin and isoniazid using Abbott m2000 system. We use COBAS Ampliprep/TaqMan 96 for the qualitative detection (confirmatory diagnosis) and quantification of HIV (RNA PCR) and Hepatitis B and C. We also isolate and store using liquid nitrogen, peripheral blood mononuclear cells (PBMC) for research needs.

Since automation is the foundation for clinical molecular laboratory to report patient results with confidence, the JCRC Virology laboratory is built to meet this need. The Abbott m2000 system and COBAS Ampliprep/TaqMan 96 that provides sample preparation and real-time amplification and detection, are the corner stone for this process (automation). To ensure our customers get the best quality service, the JCRC Laboratory generally and the virology unit specifically, participates regularly in External Quality Assurance schemes provided by the College of American Pathologists (CAP), Virology Quality Assurance Program (VQA) and Immunology Quality Assurance Program (IQA). The performance in these schemes builds confidence in our systems and assures us that our results (patient reports) meet international standards.

Molecular Biology (CFAR)

This well-established lab is supported by the Case Western Reserve University CFAR under the supervision of Dr. Immaculate Nankya, Ph.D. The laboratory plays a pivotal role in the care and monitoring of HIV patients both at the JCRC and other research institutions in the country.

The lab carries out HIV-1 drug resistance testing for collaborative research as well as for patient care. To this end, the lab is well equipped with state-of-the-art equipment including a high throughput ABI 3730xl sequencer that is capable of running 96 samples at a time. While the ABI machine is capable of detecting polymorphisms when at about 20-30%, the lab has a multiplex machine that is capable of detecting polymorphisms when present at very low frequencies as low as 1% in the population.

The lab is organized according to WHO guidelines and is VQA-certified. The tissue culture BL-2 lab is well equipped with two laminar flow hoods, refrigerated and non-refrigerated centrifuges for sample processing, as well as incubators for cell culture.

Application of the Ion Gene Studio S5 in our studies at JCRC:

Cancer Research and Diagnosis

The Ion Gene Studio S5 will be a game charger in the management of cancers in Uganda.  Cancer associated mutations within the genetic material can be monitored through NGS platforms such as the S5.  A number of patients will be benefit from this new technology which has only been available in developed countries only and even at a limited scale.  Introduction of this technology by JCRC will see improvement in management cancers as below:

Hereditary Cancer risk assessment: Early identification of individuals with such genes associated with different hereditary cancers so as to provide measures for prevention (if no cancer as yet) or provide treatment early in time.  

Identification of pathogenic cancer mutations that could later result into cancer.

Detection of Somatic mutations for disease prognosis and to predict response to treatment.

Infectious disease research and diagnosis

NGS technologies are increasingly employed to study infectious diseases and microorganisms. JCRC’s state of the art laboratories handle so many infectious diseases and this technology will be a boost in the deciphering the mechanisms of many of these diseases and diagnosis, as well as improving treatment outcome for many infectious diseases.  These include:

Diagnosis and study of microbial resistance to drugs, such as antibacterial resistance, HIV-1 drug resistance and antifungal drug resistance. Interpretation of drug resistance patterns is important in the control and management of infectious diseases as especially in the era of unregulated use of antimicrobial drugs.

NGS technologies such as ion S5 is one of the most suitable technologies to study metagenomics. Metagenomic studies of micro-organisms reveal their important relationships which may be beneficial or detrimental to the environment they live it. For instance, metagenomics studies in the human gut microbiome can identify novel functional genes, microbial pathways and how they interact with the host.  The composition and interaction of microorganisms with the host has so many implications for the health of the host and this may be exploited in the management of diseased states.

Ion S5 is also used in RNA/DNA sequencing of microorganisms to study and control outbreaks such as Sars Cov-2,


The lab uses the different equipment to perform tests that is

The BD Phoenix 100

Used for automated Microbiology system for Rapid identification and anti-microbiological Susceptibility of bacteria.

BD BACTEC 9120 for Blood culture.

The lab test menu comprises tests like:-

  • Urinalysis and Culture and Sensitivity, Urine TB LAM.
  • Blood culture and Sensitivity
  • Serology: RPR, TPHA, CRAG, Serum H.pylori
  • Body fluid analysis: CSF Analysis, Pleural fluid analysis, Ascitic  fluid Analysis

  • Stool Ova /Cyst, Permanent stain
  • Stool modified ZN
  • Stool culture and sensitivity

Turn Around Time Schedule –  TAT

All tests have TAT which are monitored by QA/QC unit on monthly basis.