Bhagawan Shrestha, Country Director, FHI 360 Nepal
Rajesh Khanal, Project Director-EpiC, FHI 360 Nepal
Andrea Surette, Technical Advisor, FHI 360
Saroj Dhakal, Team Leader, COVID-19 Response
Sanjeet Pandit, Laboratory Specialist, FHI 360 Nepal

On December 5, 2021, Nepal’s National Public Health Laboratory (NPHL) identified the country’s first two cases of the Omicron variant of COVID-19 in patients who had recently traveled to Nepal. The identification came just 10 days after the World Health Organization (WHO) declared Omicron a variant of concern. 

Detection of the variant was possible because the NPHL had the capacity and equipment needed to sequence the genetic material from the patients’ virus samples. This genomic sequencing, which enables scientists to spot mutations and identify specific variants, is an essential tool for COVID-19 surveillance as the virus continues to mutate.

Over the past year, the USAID-funded Meeting Targets and Maintaining Epidemic Control (EpiC) project has collaborated with the Government of Nepal, WHO, and other stakeholders to build surveillance and genome sequencing capacity within the NPHL. EpiC Nepal supported planning; developed standard operating procedures and training packages on genome sequencing; and coordinated with the NPHL to roll out training sessions. The project also provided the reagents required to conduct 500 COVID-19 genomic sequencing tests.

EpiC Nepal’s support prepared the NPHL to perform genome sequencing for the first time in Nepal in September 2021, helping to identify the Delta variant in most samples. “USAID’s support for the initiation of the testing is highly appreciated; now we can detect COVID variants on our own,” said Dr. Runa Jha, Director of the NPHL.

On October 8, 2021, the NPHL convened a meeting with EpiC Nepal’s assistance to present Nepal’s successful experience with COVID-19 genome sequencing and seek support to continue the effort. The participants included members of the COVID-19 genomic sequencing technical working group, government health officials, scientists and medical experts from the country’s leading medical research institutions, and international partners, including WHO, USAID, and the EpiC project. Meeting participants discussed challenges to genomic sequencing as well as the progress made and the impressive results to date. As a result of the meeting, EpiC Nepal and WHO committed to providing continued procurement and human resources support to NPHL for COVID-19 genome sequencing.

To do so, EpiC Nepal is providing a computer with the capacity for faster analysis of sequencing results. The project will also provide a short-term consultant who will help the NPHL perform COVID-19 genomic sequencing and will procure an additional 500 reagents to help the laboratory sequence 100 COVID-19 samples per month.

NHPL and EpiC Nepal are pleased to continue their productive partnership. “EpiC Nepal’s continuous support and motivation has made this COVID-19 gene sequencing possible,” noted Lok Bandhu Chaudhary, an NHPL Medical Technologist.

With EpiC’s support, NPHL has developed systems, platforms, and capacity for COVID-19 genome sequencing in the country. The Government of Nepal plans to continue sequencing samples from COVID-19 patients to track potential new variants. The country’s increased capacity has implications for other diseases as well—NPHL now has the option to apply the same skills to sequence genomes for HIV, hepatitis, Japanese Encephalitis, measles, and other viruses.

Photo Credit: EpiC Nepal