Molecular epidemiology and within host evolution of COVID-19/SARS-CoV-2 in Vietnam

Purpose / Hypothesis We will study the early epidemiology of the COVID-19 epidemic in Vietnam, by establishing a sequence sequence at the National Hospital of Tropical Diseases and the National Institute of Hygiene and Epidemiology, and by studying study virus diversity at the host and population level, and between clusters from January onwards. We also recommend adding SARS-CoV-2 diagnostics to two ongoing projects: 1) National surveillance and control systems for influenza-like diseases for early detection of community transmission, and describe the contribution of the COVID-19 epidemic for influenza-like illness and 2) a household community cohort study in Ha Nam to study family transmission, including the role of children. - Importance By implementing and applying molecular diagnostics, we will contribute to understanding local epidemiology, and generate higher resolution monitoring and background data to inform action. national response to the COVID-19 epidemic in Vietnam. The study of evolution in the host organism, will elucidate the pathogenesis of infection, which is important to inform interventional strategies, development and clinical management. - Target Our goal is to gain insights from diagnoses at three different levels and stages of the epidemic. We aim at: Perform direct sequencing of SARS-CoV-2 from patient samples using Nanopore technology ( ARTIC technical network outline ), and study the molecular epidemiology of the first COVID-19 cases and clusters in Viet Nam; Study the evolution in the host organism of SARS-CoV-2, using samples collected as part of our observational study at the Cu Chi site; Add a diagnosis of SARS-CoV-2 to samples collected through an influenza-like disease control surveillance system, to detect the puzzling circulation of SARS-CoV-2 during the first outbreak (January-January). 5), and detecting the potential for future community transmission; Conduct a household transmission study on an existing family cohort in northern Vietnam, to see if there is a possibility of household transmission.