Charlotte J. Houldcroft

Statistical inference of virus evolution using ancestral recombination graphs

This paper develops ARG-based methods to analyze virus evolution, showing EBV coalesces predominantly inter-host and revealing gene-level selective structure.

COVID-19 vaccination induces cross-neutralisation of sarbecoviruses related to SARS-CoV-2

This study assesses cross-neutralisation of sarbecoviruses by COVID-19 vaccines in older adults, finding reduced neutralisation of Omicron variants and some animal sarbecoviruses but enhanced neutralisation of specific bat and pangolin coronaviruses.

2500 Years of Human Betaherpesvirus 6A and 6B Evolution Revealed by Ancient DNA

This study analyzes ancient DNA to reveal the 2500-year evolutionary history of human betaherpesviruses 6A and 6B, showing established diversity by the 14th century and ancient integration into the human genome.

Viral Diversity Influences T Cell Responses to Enteric Human Adenoviruses F40 and F41

The paper identifies CD8+ T cell epitopes in HAdV-F40 and F41 hexon and penton proteins, showing they elicit IFNγ responses in healthy donors and could inform vaccine design.

Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

The paper presents ancient HSV-1 genomes from Europe, estimates mutation rates, and suggests lineage replacement during the Bronze Age.

Patterns of within-host genetic diversity in SARS-CoV-2

This study analyzes within-host genetic diversity in 1,181 SARS-CoV-2 samples, finding high mutation rates, strand asymmetries, and purifying selection, with implications for transmission chain reconstruction.