Carolyn E. Williamson

The paper uses long-read sequencing to study HIV transmission and population dynamics in acute infection, finding high multilineage transmission rates and rapid viral evolution.

This paper develops updated HIV-1 pseudovirus panels to better detect and assess B cell lineages with potential to produce broadly neutralizing antibodies against contemporary HIV-1 variants.

The paper analyzes HIV breakthrough virus populations in antibody-mediated prevention trials, finding high rates of multilineage infections and recombination under VRC01 treatment.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

This study identifies VRC01-mediated viral escape mutations in HIV-infected participants from antibody-mediated prevention trials, showing that VRC01 can select for escape variants with cross-resistance to other CD4bs bnAbs.

This study investigates how HIV-1 Nef's ability to downregulate MHC-I affects the size of the replication-competent viral reservoir in South African women on ART, finding a significant association between MHC-I downregulation and reservoir size.

The paper identifies rare twin cysteine residues in HIV-1 Env V1 linked to neutralization escape and breadth development.

The paper identifies that HIV-1 rebound virus primarily originates from a small number of lineages that entered the reservoir near ART initiation, despite the reservoir containing older sequences.

The paper presents an optimized SMRT-UMI protocol and bioinformatics pipeline to generate highly accurate sequence datasets from diverse pathogens, demonstrated on HIV-1 quasispecies.