Katrina Lythgoe

Identification and Masking of Artefactual and Misleading Within-Host Variants in Deep-Sequencing SARS-CoV-2 Data

The paper identifies and masks artefactual variants in SARS-CoV-2 sequencing data to improve the accuracy of within-host diversity and transmission analysis.

Natural selection driven by escape from shifting antibody classes shapes SARS-CoV-2 evolution

This study traces how natural selection on SARS-CoV-2 has shifted during the pandemic, favoring antibody escape and ACE2 binding, with dynamic pressures across antibody classes.

Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution.

The paper shows that slightly deleterious mutations, rather than a few large-effect mutations, explain slow viral load changes and heritability in HIV evolution.

Lineage-aware evolutionary analysis of hepatitis C virus within-host dynamics

This study analyzes HCV within-host dynamics post-DAA treatment failure, finding persistent viral subpopulations and lineage-specific evolutionary rates.

Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods

This paper develops scalable machine learning methods to identify significant SARS-CoV-2 lineages from genomic data, offering a complementary approach to traditional phylogenetic analysis.

Directional predictions of HIV transmission with optimised genomics in cohorts of serodiscordant couples

The paper evaluates two tools for HIV transmission direction prediction using short and long-read sequencing data from serodiscordant couples, showing long reads improve phylogenetic resolution and transmission prediction accuracy.

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

This study adjusts for sampling bias in SARS-CoV-2 Ct values and finds that viral variant and age affect within-host viral burdens, with variant effects varying by vaccination status.

Within-host genomics of SARS-CoV-2

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.