Since early 2020, Nepal has been working to expand and adapt its epidemiological and laboratory influenza surveillance networks to enable an effective COVID-19 response.
Integration has long been at the heart of pandemic preparedness and response capacity building in Nepal, supported by the Pandemic Influenza Preparedness Framework Partnership Contribution. For example, since 2018, the country has linked its influenza-like illness and severe acute respiratory infection sentinel surveillance network with the sites in its Early Warning, Alert and Response System to enable greater disease surveillance coverage.
When the COVID-19 pandemic spread in early 2020, Nepal’s Ministry of Health and Population again used integration to enable a more effective response, acting quickly to adapt and expand existing influenza surveillance systems on three fronts so that they could also be used to detect and monitor the new virus.
- Expanding the laboratory network
The National Influenza Centre (NIC) at the National Public Health Laboratory became the first reference laboratory for SARS-CoV-2 testing in January 2020 when the first case was diagnosed. Under the guidance of the NIC, Nepal quickly expanded its network of SARS-CoV-2 diagnostic laboratories, reaching 104 provincial public health laboratories (PPHLs) by December 2021. To ensure quality throughout the network, the PPHLs adapted the WHO External Quality Assessment Programme focusing on proficiency panels, parallel testing of samples, monthly re-testing, and on-site reviews.
- Harmonizing surveillance networks
Following a kick-off meeting in October 2021, Nepal began a multisectoral process involving human and animal health authorities to harmonize its surveillance networks for influenza and SARS-CoV-2. Authorities integrated sentinel surveillance across both viruses, thus expanding the existing influenza laboratory surveillance network to include the PPHLs being used for SARS-CoV-2 testing. Coupled with retrospective testing using multiplex testing kits from the US Centers for Disease Control and Prevention, further training and validation of laboratory staff and processes ensured concurrent surveillance of both high-risk pathogens would be maintained and sustained, and that outbreaks of influenza and SARS-CoV-2 would be detected quickly and accurately.
Building capacity for genetic sequencing
In March 2021, led by the Nepal NIC and supported by WHO, the National Pathogen Genetic Sequencing Consortium was established to boost capacity to sequence both influenza and SARS-CoV-2 viruses. In October 2021, the consortium became operational; and by mid-December, members of the consortium had sequenced around 100 genomes of SARS-CoV-2 and had detected and confirmed the latest SARS-CoV-2 variant of concern, Omicron. Data from the consortium are now being regularly shared with GISAID, a global sequencing data sharing platform.
The steps taken by Nepal to integrate and expand their influenza and SARS-CoV-2 surveillance networks at a national and provincial level are a testament to the multisectoral commitment to effective respiratory pathogen detection and monitoring in the country. They have proved vital in supporting the COVID-19 response over the past two years, and will further support influenza preparedness and response in the years to come.