Tanmoy Bhattacharya A

Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection

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.

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

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

VRC01 Selects Rare HIV Escape Mutations After Acquisition in Antibody-Mediated Prevention Trials

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.

Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility

The paper shows that recombination and low diversity reduce the sensitivity of homoplasy-based methods to detect increased transmissibility of the G614 SARS-CoV-2 variant.

Quantifying uncertainty in the inference of generalized coalescents

The paper develops methods to infer generalized coalescent models and quantify uncertainty in their parameters using site-frequency spectra from Atlantic cod mitochondrial data.