This project is a part of the Norwegian SARS-CoV-2 study (NCT04381819), a multicentre (10 hospitals) cohort study on COVID-19 initiated through a joint collaboration between the Dep. of Microbiology and Dep. of Infectious disease, Oslo University Hospital, and national and international partners. The study investigates adult hospitalized COVID-19 patients by serial clinical data collection according to the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC)/World Health Organization (WHO) Clinical Characterization Protocol (CCP) (isaric.tghn.org).
The purpose of this project is to gain new knowledge about the genomic evolution and clinical correlation of viral variants (quasispecies) of the previously unknown virus, SARS-CoV-2, in both hospitalized and outpatients. Clinical data and biological sampling materials will be collected from a total of 4 collaborating studies: (i) the NOR Solidarity RCT study, (ii) “The Household Study”, a prospective study initiated by Folkehelseinstituttet, which gathers data and samples from asymptomatic patients, (iii) the “Korona study”, led by Arne Søraas, which collects prospective data and samples from outpatients, and (iv) from our own multicentre observational cohort study.
Viral quasispecies refer to a population, or mutant cloud, consisting of large numbers of genomic viral variants. This is based upon the quasispecies theory, which describes the replicon population as an organized mutant spectra with the dominating sequence being the “master sequence”. The master sequence is determined by viral fitness. Verification of quasispecies is done through molecular biological methods, and this project intends to utilize quantitative real-time polymerase chain reaction (qPCR), Next generation sequencing (NGS), and Whole genome sequencing (WGS) in blood and respiratory samples, as well as samples from other bodily fluids/excrements such as urine and feces to assess SARS-CoV-2 quasispecies.
Quasispecies recognition is important for identification of pathogenic RNA virus variants leading to selection of treatment or vaccine-escape variants, immune escape, increased virulence and development of future anti-viral therapies. To summarize, in the short-term, this project expects to provide much needed quality data about viral pathogenicity and data on full genome sequence of the SARS-CoV-2 in mild versus severe cases. In the long-term, we hope that the knowledge from this study will provide scientific information on diagnostic and prognostic markers and knowledge about viral pathogenesis needed for future drug and vaccine development for later epidemics.
The project was granted funds from the Research Council of Norway grant number 312780.
The PhD project is located at Institute for Clinical Medicine at Faculty of Medicine at University of Oslo.
Main supervisor is dr. Jan Cato Holter and co-supervisors are dr. Andreas Lind and dr. med. ass.prof Susanne Dudman