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 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. 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 have developed a method for isolating and genome sequence thousands of individual viral particles from individual patients. We are finding variance among the genomes of the individual viral particles in the 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. We are collaborating with other Norwegian Research Council projects at NPHI and FFI to study transmission and evolution between linked cases of covid -19. This will allow us to make models and estimates of getting infected, which will inform epidemiological studies.

Our current, actual outcomes are mostly technical as there were more obstacles than we anticipated. We have found optimal procedures for producing long (full genome length ~29k basepairs), high quality RNA strands for single-molecule sequencing. We developed assays which can determine the quantity of specific target cDNA strands in several length groups and methods for PCR of 9kb DNA fragments for PacBio HiFi sequencing. We are able to tag individual cDNA molecules with unique molecular identifiers for grouping consensus sequences using custom bioinformatic pipelines. We are currently comparing our data with Illumina short-read data from the same samples, where we think our data can enlighten the Illumina data by identifying true polymorphisms with the ability to group these polymorphisms by viral particle. After we finish analyzing the data we anticipate we will be able to measure viral starting population size and potential risk when coming into contact with sick individuals although this will be retrospective as the virus is significantly different in terms of infectiousness. Follow studies of how the virus has changed would stil be interesting.

The COVIDOSE project has a goal-oriented and straightforward approach to its 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.