As the world has become more interconnected, our vulnerability to devastating pandemics following rapid dissemination of novel emerging pathogens has never been greater. The global SARS-COV-2 pandemic engulfed the world in 2020 with unprecedented social, economic and political consequences. The events surrounding the pandemic caused a chaotic mass return-migration event from India, the Middle East and South East Asia following the loss of employment. To date there has only been sequencing of limited numbers of SARS CoV-2 isolates from Nepal and there is no clear understanding of the origin, evolution or transmission dynamics of the strains circulating within the country. Understanding of the true patterns of introduction and subsequent transmission of the virus has the potential to inform our understanding and response to future pandemics.

The vaccines currently available may also be less protective against some emerging new strains. It is of urgent importance therefore that we understand when and how new variants of SARS CoV-2 are emerging and spreading in Nepal.

The Epidemic Intelligence project will recruit a cohort of participants with confirmed COVID-19 infection from three hospitals spanning Nepal: Bheri hospital, Nepalgunj, Koshi hospital, Biratnagar and Sukraraj Tropical Infectious Diseases hospital, Kathmandu. We will collect and sequence SARS CoV-2 samples from patients with their consent in order to understand the evolution, transmission and effects of the COVID19 pandemic in the country.

We will follow-up the participants at three and six months to understand the frequency and symptoms of long-term complications of COVID-19 illness (LONG COVID) in the Nepali population.

The project will also help build in-country capacity to rapidly sequence any new pathogens which cause diseases, as well as old enemies like dengue, malaria, TB and typhoid, and build capacity in Nepal to protect against future disease epidemics with molecular surveillance.

The project is a collaboration between consortium partners BNMT, Centre for Molecular Dynamics Nepal, Nepal Health Research Council, Oxford University Clinical Research Unit, Nepal, Liverpool School of Tropical Medicine, UK and University of Cambridge, UK. It is funded by the UK medical research charity, the Wellcome Trust.

Specific Objectives:

  1. Establish SARS Cov-2 sample bank from three locations spanning Nepal: the capital city, and two major urban centres bordering India (Eastern and Western Nepal) with high levels of migrant workers returning from international locations.
  2. Sequence a large cohort of coronavirus samples to understand the different patterns of introduction, seeding and transmission occurring in rural and urban areas of Nepal.
  3. Document any introduction and dissemination of the newly emerged highly transmissible SARS Cov-2 variants.
  4. Analyse demographic and clinical factors associated with circulating strains of SARS Cov-2 in Nepal to understand any variation in virulence associated with genetic variation.
  5. Determine the prevalence, risk factors and clinical presentation of LONG-COVID symptoms in the Nepali population.
  6. Describe mental health consequences of COVID-19 in a Nepali cohort with confirmed COVID-19 infection.