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Apart from providing routine and specialised test, this department is also involved in various   surveillance activities. Microbiology, Vaccine Preventable disease laboratory, National Influenza Centre (NIC) & Respiratory Disease Laboratory and HIV reference Laboratory are various subunits of Infectious Disease Laboratory.



HIV/Hepatitis Reference Laboratory is situated at Infectious Disease Block in National Public Health Laboratory and is mainly focused on the Testing and monitoring of HIV and Hepatitis related activities and program. It consists of Molecular Unit and Immuno-Serology Unit where routine and molecular level tests are performed and reported. NCASC, Global fund, EPIC Nepal (FHI360), WHO and other supporting partners are supporting for several HIV related tests and programs. Laboratory Integration System (LIS) for HIV viral load and EID reporting have been started with the support of Save the Children/Global Fund.

To assure the Quality of itself, NPHL has been participating in various international EQA program. For example: for HIV Viral Load and EID to Centres for Global Health CDC- USA, for HBV and HCV viral load to NRL Australia, for CD4 test to Siriraj Hospital- Bangkok and for Serology and molecular EQAS to CMC Vellore and NRL, Australia. 



National Influenza Centre was established on 19th April 2010. It has been recognized as 132nd IC at global level and 9th IC in the WHO south East Asia region by WHO since 2010 AD. It has been performing molecular diagnostic assay based influenza surveillance in Nepal since its establishment. It is guided by National Influenza Surveillance Network (NISN) which is Influenza surveillance network at national level and includes both animal and human component. It has been performing Integrated Influenza & SARS CoV-2 surveillance from 16 hospital-based sentinel sites for ILI and SARI cases. This dual surveillance has been implemented successfully in five province public health laboratories and 12 Sentinel Hospitals. 

National Influenza Centre (NIC) has been performing CDC Multiplex testing for respiratory pathogens such as Influenza A, Influenza B and SARS CoV-2. Besides Flu and SARS CoV-2, PCR of Respiratory syncytial virus in children of age group < 2 years, Adeno Virus, Monkey pox virus, Dengue, Zika, Chikungunya virus & Rabies Virus has been started for free of cost.

In fy 078/079 National Influenza Center performed Influenza & SARS CoV-2 Multiplex testing in 7891 samples from sentinel sites in which 39 Influenza A (H1N1 pdm 09), 570 Influenza A/H3 and 550 SARS CoV-2 samples tested positive. The Summary of the Influenza test done in 2078/79 is as shown in the figure below (ISO week wise).

New Initiatives of NIC in fiscal year 2078/079

Test Added at National Influenza Center
• Respiratory syncytial virus RT PCR
• Chicken pox (Varicella zoster virus) RT PCR
• Monkey pox RT PCR
• Dengue Virus RT PCR
• Zika Virus RT PCR
• Chikungunaya Virus RT PCR
• Rabies Virus PCR.

2. Expansion of Integrated Influenza & SARS CoV-2 Sentinel Surveillance National Public Health Laboratory has restructured the sentinel sites and has initiated sub national testing sites for Integrated Influenza & SARS CoV-2 testing. The National Influenza Centre has implemented surveillance of Influenza and SARS CoV-2 in five provinces. The five provinces are testing Influenza and SARS CoV-2 from their sentinel sites on regular basis. The five province public health laboratory are sending reports of dual surveillance weekly and ship the positive samples to NPHL for further subtyping of influenza and genome sequencing of SARS CoV-2. 

3. Initiation of Genomic Surveillance of SARS CoV-2 National Public Health Laboratory has been performing whole genome sequencing of SARS CoV-2 since September 2021. WHO Nepal played an important role for the initiation of whole genome sequencing. In the last fiscal year 541 whole genome sequencing of SARS CoV-2 was done on its own platform. Among them 415 were Omicron variant and 126 were Delta variant.

4. Establishment of Bioinformatics Unit For the analysis of data generated from whole genome sequencing, National Public Laboratory has established Bioinformatics unit since 2021. It was established with help of FHI 360. Analysis of the sequenced data of SARS CoV-2 has been performed routinely and is reported to EDCD director and other concerned officials. After 48 hours, the sequenced data are uploaded into GISAID global platform according to the protocol.

5. Activities of Pathogen Genome Sequencing Consortium Pathogen Genome Sequencing Consortium was established on March 17, 2021 after the approval of Proposal from Ministry of Health & Population. The consortium has chairperson from National Public Health Laboratory. Remaining members are from different government and non-government organizations. NPHL conducts meeting with the members of consortium on regular basis. The consortium members are benefited by Joint training, mentoring, workshops etc. The training on Bioinformatics has enabled the consortium members to analyse the data within country even without Bioinformatician. 




Infectious and communicable diseases are of growing concern and continue to be a major public health problem worldwide. Among them, vaccine preventable diseases still have the top most mortality rate worldwide among the children of below 15 years’ age. In order to reduce and control the mortality and morbidity of such vaccine preventable disease (Japanese Encephalitis, Measles, Rubella, etc.) World Health Organization and Government of Nepal are working in close collaboration. In this regard National Centre for Infectious Diseases (NCID) was established at NPHL.

The centre is performing lab based surveillance of various vaccine preventable diseases. WHO-IPD also supported with training for one Medical Microbiologist and one Laboratory Technologist for the effective and smooth performance of the centre. JE/Measles lab of was accredited by WHO on October 2018 which is still continued. 


Environmental Surveillance for Poliovirus in Nepal

Environmental surveillance is a highly sensitive and effective method for detecting Polio virus (PV) in environmental samples. This practice has been adopted by many countries and region worldwide. Environmental surveillance can provide valuable supplementary information, particularly in high density urban populations where AFP surveillance is absent or questionable, where persistent virus circulation is suspected and in area where frequent virus re-introduction is perceived.

No WPV have been reported from Nepal since 2010. National Public Health Laboratory (NPHL) in collaboration with WHO, has been conducting environmental surveillance of polio virus since November 2017 and no poliovirus (wild/VDPV/Sabin type 2) has been isolated from sewage samples.

In the past environmental Surveillance was confined only to Kathmandu valley. Now NPHL has expanded the surveillance activities to some provinces. Sewage treatment plant at Biratnagar and campus area at Janakpur are the selected sites for Koshi Province and Madhesh Province respectively. Laboratory personnel of provinces have been oriented on sample collection and processing procedures. 

National Malaria Reference Laboratory

As per National Malaria Lab Plan 2019, NPHL is recognized as National Malaria Reference Laboratory. To achieve the national goal of malaria elimination by 2025, and malaria-free status by 2026, national steering committee for malaria has been formed. NPHL works in close coordination with EDCD and has successfully conducted Malaria QA/QC workshop in all the 7 provinces. NPHL has passed the external quality assessment of 1st lot of malaria PCR. 


Rotavirus Surveillance

NPHL, with technical support from WHO, is conducting rotavirus surveillance. Stool specimens are collected from Kanti Children Hospital Kathmandu, Nepalgung Medical College Nepalgunj and B P Koirala Institute of Health Sciences, Dharan. ELISA is performed and then samples are sent to WHO regional reference laboratory. 



Microbiology laboratory at NPHL constitutes of Routine Bacteriology, Mycology and Parasitology laboratory. AMR surveillance and routine microbiology activities go hand in hand in the Microbiology Department. NPHL is the focal point for AMR surveillance. It has been designated by Ministry of Health & Population as the National Reference Laboratory and National Coordinating Centre for Antimicrobial resistance (AMR) Surveillance. AMR surveillance in Nepal started in 1999. A total of 10 organisms are monitored at present. The Director is the chairperson and The Microbiology Head is the Member Secretary of Human Health Technical Working Group (HH-TWG) for AMR surveillance. 

The AMR surveillance network started with nine laboratories, which now has 26 participating laboratories. NPHL conducts capacity building training for the site personnel on bacterial identification, antibiotic susceptibility testing, biosafety and biosecurity practices as well as quality assurance in bacteriology laboratory. The sites are monitored and onsite orientation provided to the lab personnel with technical support and logistics supply from Fleming Fund Country Grant for Nepal. External Quality assessment of sites is performed on a quarterly basis.

Protocol for Laboratory based Surveillance of antimicrobial resistance in clinical bacterial isolates in Nepal was printed and distributed to the surveillance sites. SOP on Bacteriology for AMR Surveillance was also printed after interactions with microbiologists and specialists from various institutions. The SOP and bench aids were distributed to the surveillance sites in valley as other sites were unapproachable due to lockdown. Three batches of Microbiology EQAS were sent to the AMR surveillance sites including two unknown organisms per panel sent. This year, Molecular laboratory was established in the department. It will be used for detection of resistance genes in multi-drug resistant strains received at NPHL from the surveillance sites.

The AMR surveillance data received from all the sites was collected, collated and the complete data from 23 sites was submitted to Global AMR Surveillance System (GLASS) with the help of WHO country office and FHI 360 (Fleming Fund).