Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data

2022/01/01 by Brian Lee, Ahmed Abdul Quadeer, Muhammad Saqib Sohail +4 · 1 voice
Biochemistry, Genetics and Molecular Biology · Mathematics · Medicine · #COVID-19 epidemiological studies #Evolution and Genetic Dynamics #SARS-CoV-2 and COVID-19 Research

paper · pdf · doi:10.1101/2021.12.31.21268591

openalex publication_date 2022/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

New and more transmissible variants of SARS-CoV-2 have arisen multiple times over the course of the pandemic. Rapidly identifying mutations that affect transmission could improve our understanding of viral biology and highlight new variants that warrant further study. Here we develop a generic, analytical epidemiological model to infer the transmission effects of mutations from genomic surveillance data. Applying our model to SARS-CoV-2 data across many regions, we find multiple mutations that substantially affect the transmission rate, both within and outside the Spike protein. The mutations that we infer to have the largest effects on transmission are strongly supported by experimental evidence. Importantly, our model detects lineages with increased transmission even at low frequencies. As an example, we infer significant transmission advantages for the Alpha, Delta, and Omicron variants shortly after their appearances in regional data, when their local frequencies were only around 1-2%. Our model thus facilitates the rapid identification of variants and mutations that affect transmission from genomic surveillance data.

Citations

• The estimation of the basic reproduction number for infectious diseases
• Diffusion models in population genetics
• Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak
• Serial interval of novel coronavirus (COVID-19) infections
• Serial Interval of COVID-19 among Publicly Reported Confirmed Cases
• Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures
• Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
• Evasion of Type I Interferon by SARS-CoV-2
• MPL resolves genetic linkage in fitness inference from complex evolutionary histories
• The fate of competing beneficial mutations in an asexual population

Discussions

• We used a similar method to study SARS-CoV-2 evolution over the first four years of the pandemic. There's clear selection for Spike mutations, but we also see mutations with large effects in different [bsky, 0 points, 1 comments]