Estimates of COVID-19 cases based on SARS-CoV-2 genome mutations.

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Estimates of COVID-19 cases based on SARS-CoV-2 genome mutations.

A new study published in Nature Communications reconstructs regional incidence profiles of, emphasizing the effects of non-pharmaceutical interventions (NPI) and various testing methodologies.

Daily counts of new COVID-19 cases are crucial for making educated judgments about public actions and assessing the state of the pandemic. These case counts, on the other hand, are based on positive diagnostic test results and so are largely reliant on the testing approach used. However, testing procedures vary by location and have evolved dramatically over time, making their precise impact on the number of daily new diagnoses difficult to estimate. For pandemic surveillance, more accurate estimates of the number of newly infected individuals are required.

Researchers devised and tested a new computational method that infers temporal profiles of viral incidence solely from genomic sequences and their sampling dates in order to better estimate new infection rates. Because the viral genome is subject to a constant mutation process, changes in its sequence over time can be used to trace the virus’s progress across the population.

“The mutations that occur in viral genomes leave a signal that allows us to link genetic diversity with viral population size and, in this example, incidence,” explains Denise Kühnert, co-author of the paper and chief of the tide research group at MPI-SHH.

The study highlights potential implications of public initiatives on the spread of COVID-19 by producing piece-wise constant estimations of the effective reproductive number between major changes in non-pharmaceutical treatments.

Many European countries’ lockdown measures are an instructive example. The effective reproductive number plummeted rapidly to below 1 in the spring of 2020, following the installation of tight lockdown measures throughout Europe. When these restrictions were relaxed in most countries at the start of Summer 2020, the effective reproductive number grew to more than 1.

To confirm the new method, the scientists performed rigorous state-of-the-art phylodynamic analyses utilizing genomes from four different areas (Denmark, Scotland, Switzerland, and Victoria, Australia).

“We were able to uncover periods of underreporting by comparing our results with reported case numbers,” explains Ariane Weber, a PhD student in the tide research group and co-author of the study. “These include the initial wave of infections in Scotland and Victoria, as well as lesser epidemic waves across Europe during the summer… Summary of the latest news from Brinkwire.

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