Epidemic Inteligence: Understanding how returning migrant waves drive epidemic seeding and community transmission events in the South Asian context to inform epidemic preparedness

Nepal, as for much of Asia, has high levels of labour migration, particularly to neighbouring India and the Middle East. The SARS-CoV-2 pandemic has caused a chaotic mass return migration event. While the government has attempted to quarantine and test returning migrants the fragile infrastructure has been rapidly overwhelmed and repeated migration waves have occurred into remote rural areas. The epidemic in Nepal is now entering the rapid escalation phase. Despite this surge, the government has been forced to raise the lockdown, imposed since March 24th, due to the economic and political consequences. There is limited understanding of the pattern and extent of transmission in this context due to limited and sporadic testing. Understand how return migration is influencing the epidemic dynamics in rural vs. urban contexts. Understand how the reported data from the core government testing system compares to estimated community prevalence dynamics to predict testing capacity gaps and refine future response. Determine sensitivity and specificity of GeneXpert Xpress testing using nasopharageal swabs or saliva against RT-PCR for SARS CoV-2 infection. Sequence a cohort of 500 SARS CoV-2 samples to understand the patterns of repeated introduction, seeding and transmission occurring in rural and urban areas as the epidemic unfolds.