Natural history of SARS-CoV-2 in comparison to influenza A virus: a multi-site study focused in the Southern Hemisphere and equatorial regions

Funder: US NIH

Principal Investigators: Scientific Leadership Group with representatives from 7 consortia including the 5 CEIRS (Centres of Excellence in Influenza Research and Surveillance) centres

OUCRU Principal Investigator: Rogier van Doorn

Locations of activity: Ha Nam and Hanoi, Viet Nam

Status: Ongoing until May 2022



This study aims to conduct human surveillance for SARS-CoV-2 and influenza virus at eight sites across the Southern Hemisphere and equatorial regions. Each of these sites has an established research relationship with one of the five Centers of the CEIRS Network. Each site has the clinical and laboratory infrastructure needed to support enrollment, data and sample collection, and analysis of virological and serological parameters using qPCR and ELISA assays, respectively. Each site is furthermore able to ship biospecimens to US-based CEIRS laboratories for more in-depth analyses. One of the sites is the Ha Nam community household cohort that is led by OUCRU Hanoi and the National Institute of Hygiene and  Epidemiology, Viet Nam.



Major knowledge gaps remain around the natural history of infection, the spectrum of disease, risk factors for severe outcomes and the magnitude, quality and longevity of immune responses. To address these gaps, systematic and in-depth analyses of viral load, clinical outcomes, and immune responses of infected individuals are rapidly needed. We propose to undertake such an effort. To give context to the results obtained and better understand their implications for human health, we will examine SARS-CoV-2 and influenza virus infection in parallel.



  1. Document clinical outcomes and risk factors for severe disease in individuals with SARS-CoV-2 infection.
  2. Define virology features of SARS-CoV-2 infection.
  3. Define the magnitude, quality and longevity of immune responses to SARS-CoV-2.
  4. Importantly, as a reference for comparison, parallel examination of influenza will be undertaken in each of these aims.



The study aims to enroll 40 index cases with influenza and 40 index cases with COVID-19. We will follow-up patients in 12 months. According to the recommended schedule (10 sampling time points), acutely infected participants will be more intensively sampled to determine virus infection dynamics and kinetics, humoral and cellular immune responses, co-infections, and host gene expression.

Currently, the project is active. We are screening patients with respiratory illness in the cohort. At the time of writing, no patients have tested positive for influenza or SARS-CoV-2 viruses.