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

Funder: OUCRU (Wellcome funding)

Principal Investigators: Rogier van Doorn and Le Van Tan

Location of activity: Vietnam

Purpose / Hypothesis

We will study the epidemiology of the early epidemic of COVID-19 in Vietnam by establishing a sequencing pipeline at the National Hospital for Tropical Diseases and the National Institute of Hygiene and Epidemiology and investigating viral diversity at both population and within host level, and among clusters from January onward. We also propose to add SARS-CoV-2 diagnostics to two ongoing projects: 1) a National sentinel influenza-like illness (ILI) surveillance system to detect early community transmission and describe the contribution of COVID-19 to ILI and 2) a household community cohort in Ha Nam to study within-household transmission, including the role of children, respectively.


By implementing and applying molecular diagnostics we will contribute to understanding local epidemiology and generate higher resolution baseline and follow-up data to inform the national response against COVID-19 in Vietnam. Study of within host evolution would shed light on the pathogenesis of the infection, important to inform clinical management and development and intervention strategies.


Our objectives are to gain insight from diagnostics at three different levels and stages of the epidemic.

We aim to:

  1. Implement direct sequencing of SARS-CoV-2 from clinical specimens using Nanopore technology (ARTIC network protocols) and to study the molecular epidemiology of the first cases and clusters of COVID-19 in Vietnam;
  2. Investigate intra host evolution of SARS-CoV-2 using samples collected as part of our observational study in the Cu Chi site;
  3. Add SARS-CoV-2 diagnostics to samples collected through the sentinel ILI surveillance system to detect cryptic circulation of SARS-CoV-2 during the first wave (JAN-MAY) and detect potential community transmission going forward; and
  4. Conduct a household transmission study in an existing household cohort in northern Vietnam should household transmission occur.