COVIDOSE: Determining infectious dose for SARS-CoV-2 and assessing contact/proximity risk

The main aim of the COVIDOSE project is to estimate the infectious dose for the coronavirus SARS-COV2 (former COVID-19) in humans, and use this knowledge to develop risk models for getting sick from coming into contact with the virus in various ways.

About the Project

Infectious dose for a pathogen (virus, bacteria, fungus, etc.) is the number of individual particles that needs to enter your body in order to make you sick. This dose varies with many orders of magnitude between different pathogens, and may also vary with what route it entered the body.

Having an infectious dose is very useful for designing practical security measures, as it lets you know how effective, thorough, time-consuming and expensive they - and how sensitive the controls -needs to be. It also allows you to calculate the risk imposed by coming into contact with multiple small doses of the pathogen and so on.

To estimate the infectious dose for SARS-CoV-2 in humans, we will isolate and genome sequence hundreds of individual viral particles from individual patients. We are expecting to find variance among the genomes of the individual viral particles in form of mutations. However, these mutations occur over time at a fairly regular rate, so large genomic data sets will allow us to calculate the rate at which these mutations occur. This is called a molecular clock. Combining the genetic variability between patients and within patients with this molecular clock allows us to estimate how large a “population” (dose) of viruses initially started the infection in each patient.

 

Diagram showing transmission scenarios
Figure 1: Panel A: Using single-genomes from a chain of transmissions it appears that one virus strain is present through columns 1-3 and suddenly a mutation occurs leading to a new strain. Panel B: We hypothesize that the process has more nuanced underlying dynamics. Here we suggest possible scenario where drift and/or selection occur to change strain frequencies through infection and transmission. Taking one consensus sequence gives the appearance of events in panel A.

In collaboration with other projects, we will analyze virus samples from contaminated air and different surfaces and other places in the environment and see how these relate to the infectious dose. This will allow us to make models and estimates of getting infected through different routes, which will inform epidemiological studies, choice of protective equipment and procedures for medical personnel and the general public.

Objectives

1. Derive infectious doses for individual SARS-CoV-2 infections

2. Risk of infection analysis of contact with patients and surfaces, based on infectious doses

3. Outreach and transparency during the research process where we update results and methods while produced to public, academic and medical communities.

Background

The COVIDOSE project has a goal-oriented and straightforward approach to it's first and main goal: determining the infectious dose, i.e. the minimum number of SARS-CoV-2 virus particles needed to start an infection resulting in disease, achieved through coalescent analysis on population-based viral genomics sampled from Norwegian patients. Furthermore, this will be compared to samples from likely contact points in the environment to contribute to risk assessment and transmission dynamics. Lastly, an innovative outreach plan enables an open platform for our research. It draws on a small, dedicated team of specialists well placed for such a study. The team consists of highly creative, ambitious and talented researchers in established yet highly productive career stages with the ability, experience and drive to accomplish our objectives. Our work is highly visible and has been featured in Nature, Science, PNAS, Nature Communications, Nature Ecology & Evolution, among other top journals.

Financing

This Project is funded by the Research Council of Norway (RCN)

RCN Project Number: 312751 (Project data bank at RCN)

UiO Project Number: 145020

Period

15.06.2020 - 31.12.2022

 

Published Nov. 30, 2020 11:03 AM - Last modified Dec. 3, 2020 1:44 PM