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Cécile Tran Kiem

@ceciletk.bsky.social
601 followers 156 following 13 posts

Research fellow at Imperial College London on infectious disease modelling and genomic epidemiology, she/her. ceciletk.github.io

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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026
Saltational-like branches carry a distinct mutational signature, enriched in Spike mutations particularly in the receptor-binding domain. This signature quantitatively matches that of persistent human infections, confirming the role of chronic infections as a major source for such events. 3/
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Cécile Tran Kiem @ceciletk.bsky.social · 01/07/2026
We systematically investigated saltational evolution, developing a scalable approach to detect long branches with evidence for positive selection in a SARS-CoV-2 phylogeny of 4.4M high-quality genomes. We identified 1576 saltational-like branches across every year and nearly every region sampled. 2/
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Cécile Tran Kiem @ceciletk.bsky.social · 19/03/2026
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.
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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025
Patterns of occurrence of identical sequences between age groups show assortativity in age mixing and transmission between generations. Jointly analyzing the ages & geographies of pairs of identical sequences, we find that age transmission patterns vary across spatial scales. 5/
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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025
The location of pairs of identical sequences is in line with expectations from cell phone derived mobility data. Outliers in the relationship between genetic and mobility data can be explained by large clusters of identical sequences shared between male prisons' postal codes. 4/
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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025
Applying the framework to more than 114,000 SARS-CoV-2 sequences collected through genomic sentinel surveillance in WA, USA between Mar 2021 & Dec 2022, we find a strong signal for local spread, with identical sequences having an increased risk of being observed between nearby counties. 3/
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Cécile Tran Kiem @ceciletk.bsky.social · 05/03/2025
Genetic proximity between infecting viruses indicates epidemiological linkage. Here, we introduce a relative risk (RR) metric that quantifies how the number of pairs of identical sequences in two groups differs from what we expect from the sequencing effort. 2/
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