The emergence and spread of highly mutated variants have shaped the COVID-19 pandemic. In our new work (tinyurl.com/ncov-saltati...), we find that such jumps aren’t rare anomalies but a recurring feature of SARS-CoV-2 evolution, occurring at low but detectable rates over time & across geographies.

SARS-CoV-2 saltational events are recurrent and trace to persistent human infections

SARS-CoV-2 evolution is characterized by gradual mutation accumulation but has been punctuated by rare yet impactful highly mutated variants. Whether such saltational jumps are a broad feature of SARS...

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Excited to share our work w/ @justinlessler.bsky.social, Trevor Bedford & Amanda Perofsky: doi.org/10.1098/rspb.... We investigate when sequence datasets are informative about between-group transmission, and how this depends on the relative pace of mutation, between-group transmission and sampling.

Pathogen genomes can provide insights into underlying disease transmission patterns but new methods are needed to analyze large genome datasets. Our work using identical pathogen sequences to characterize fine scale SARS-CoV-2 transmission was just published in @nature.com tinyurl.com/bdzk9xjj 🥳

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences - Nature

The analysis of pairs of identical SARS-CoV-2 genome sequences enables characterization of transmission patterns between geographies and age groups.

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During COVID years in France, the SocialCov survey showed major evolution and strong heterogeneities in contact patterns according to age, employment, weekend/vacation. Led by @paolobosetti.bsky.social and @lullaopatowski.bsky.social. bmcinfectdis.biomedcentral.com/articles/10....

Evolution of social contacts patterns in France over the SARS-CoV-2 pandemic: results from the SocialCov survey - BMC Infectious Diseases

Background Non-pharmaceutical measures such as lockdowns, curfews and place closures were implemented in France during 2020–2022 to reduce contacts in the population, to limit the spread of SARS-CoV-2...

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