Public Health Institute of Malawi

The National Public Health Laboratory Service (NPHLS).

The Public Health Laboratory Service (PHLS) is a cluster of laboratory sections that has a function to develop an effective, fit-for-purpose public health laboratory system.  It is a specialized laboratory system that offers advanced essential public health laboratory leadership through science and services. It has a vision to be a centre of excellence in public health that contributes towards the high quality and productive life of all people in Malawi. Its mission is to provide strategic leadership and coordination through multi–disciplinary and multi-sectoral responses to public health emergencies and threats, disease detection and control, and generate information that informs policy and practice to achieve public health security.

The PHRL’s main goal is to develop a robust and sustainable public health reference laboratory capacity to address national public health concerns through the performance of specific activities that ensure one health laboratory testing functions are successfully implemented. In fulfilling its referral services, the laboratory comprises the following sections: HIV/, Tuberculosis (TB), Parasitology, Microbiology, Biochemistry Nutrition Influenza Haematology, and Genomic Sequencing.

In line with the mandate of promoting scientific/technological solutions and capacity building, PHRL has a quality assurance section responsible for the implementation of a Quality Management System, Coordination of Proficiency Testing Schemes and championing accreditation services, across the entire laboratory network. PHRL strengthens the performance of the national public health laboratory network by mapping all laboratories in Malawi (including laboratories from human and animal health), aligning them with one health requirement. PHRL also aims to establish an efficient integrated sample transportation system by strengthening biosecurity, biosafety and bio-risk management systems.

Sections under NPHL's


The National Genomics Sequencing Laboratory is a section that deals with understanding the genetic composition of living things. Genomic sequencing plays a pivotal role in analysing variations in an individual’s genome, identifying inherited disorders, and specific mutations driving tumour progression. This knowledge informs targeted therapies and personalized treatment plans. This section also tracks disease outbreaks by monitoring the spread of microorganisms, monitoring how they evolve, and assessing their impact on public health. The section is equipped with different technologies such as capillary electrophoresis sequencing technology (Sanger technology), Oxford Nanopore, Illumina Miseq and NextSeq 1000 to support its analysis. The section has the capacity for pathogen genomic detection and surveillance, tumour markers and paternity testing.


Microbiology is one section that performs convectional and automated culture techniques for pathogen identification and Antibiotic Sensitivity Testing (AST) of public concern. It receives samples referred from all health laboratories in the country and serves to respond to disease outbreaks and coordinate surveillance programs. This section is mainly responsible for providing a reference service for core organism/antimicrobial combinations as a minimum, for borderline isolates with unexpected or unusual resistance profiles. It is responsible for the Systematic collection of priority pathogens and communicable pathogens for analysis and reporting to MOH. It also provides guidance and technical support on AST to surveillance network laboratory, data collection, analysis, and data reporting to the Global Antimicrobial Surveillance System (GLASS).


This is a section capable of diagnosing parasitic infections, routine surveillance for various parasites and offering supportive supervision and mentorships to all laboratories doing parasitology. The tests in this section are in the form of rapid tests for the detection of malaria and other haemoparasite, wet Mount for wet examination of parasites in samples e.g., Stool, urine, blood smear, for malaria examination and other haemoparasite and filariasis examination. The section also evaluates the malaria rapid test, reagent and equipment. It checks the quality of staining materials such as the Malaria rapid test e.g. Giemsa stain, and Malaria Rapid Diagnostic Test (mRDT) microbiology, etc. and some information on sample collection, transportation, and submission procedures.


This section provides HIV viral load and HIV Early Infant diagnosis services. It acts as a referral laboratory for the HIV testing discordant that happens in all testing sites in Malawi. The section guides treatment choices, monitors the response to ART in HIV-infected patients and monitors the AIDs progression in those infected by HIV. An HIV Early infant diagnosis is done specifically to check whether a child born to a mother who is HIV positive is also infected with the condition. NHRL is a centre of excellence where students and qualified lab technicians and technologists gain experience and learn new technologies in terms of HIV diagnosis and monitoring.


The National Public Health Laboratory provides a coordinated and holistic system for surveillance, prevention and control of public health threats and the conduct of research by providing timely results. NPHL strengthen laboratory systems and networks to support emergency response to public health threats. It has also maintained a biorepository for the collection, curation, storage, preservation and containment of specimens and materials from disease outbreaks, public health events, and other situations of public health interest.


The Public Health Institute of Malawi has a mandate for sample referral networks to improve the efficiency of laboratory networks for disease surveillance and outbreak response. Currently, the institute is strengthening specimen referral networks to serve the entire healthcare delivery system. The specimen referral network comprises a tiered laboratory structure that reflects the varying complexity of tests performed in each tier. Its coordinated approach involves the safe transfer of a patient specimen from a resource-scare health facility to a facility with the capability to conduct the needed test(s). PHIM also refers specimens outside the country for further diagnostic tests. The current modes of transport are by courier, health worker, R4H, and any other Ministry of Health vehicle.


This section has a goal to ensure that every person in Malawi has access to quality TB diagnostic services and with a mission to provide quality laboratory services to strengthen the diagnostic network through leadership and expert guidance and reduce the burden of TB in Malawi. The section has an active email address where the public can reach it: The section as a facility achieved accreditation on 05 September 2022 with SADCAS and the accreditation number is MED 111. The Scope of accreditation was GeneXpert, FT Microscopy, First line DST, MPT 64, and MGIT Culture. The section offers the following services: TB diagnosis using Molecular technologies (GeneXpert), microscopy (ZN and FT), Phenotypic culture on liquid (MGIT) and solid (LJ), and first- and second-line Drug susceptibility testing.


This is a section that offers referral support for clinical chemistry services from laboratories throughout the country. Clinical Chemistry at NPHL serves referral to all hospital laboratories carrying Clinical Chemistry discrepancy results have occurred. It also supports the verification of micronutrient contents for different food substances produced by industries in Malawi. The department is also mandated to carry out influenza surveillance by using sentinel sites established in different corners of Malawi. The National Biochemistry, Nutrition, Influenza and Haematology Reference Laboratories (NBNIHRL) is among the six laboratory departments of the Public Health Institute of Malawi (PHIM).


NPHRL has the mandate of overseeing the implementation of the National Laboratory Quality Assurance Implementation Plan (NLQAIP). It coordinates and guides implementing partners and stakeholders on all EQA programs. NPHRL is also responsible for the supervision of the laboratory quality management system (QMS), guided by a quality assurance framework, monitoring the quality-of-service provision in the health facilities.