Jeffrey B. Joy

The emergence and molecular evolution of H5N1 influenza viruses in United States dairy cattle

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

Functional genomic analysis reveals mechanisms of epigenetic interference in SARS-CoV-1 and SARS-CoV-2

The paper identifies novel svRNA-triplex-forming oligonucleotides in SARS-CoV-2 and their evolutionary conservation and potential role in host adaptation and viral evolution.

HIV reservoirs are dominated by genetically younger and clonally enriched proviruses

This study identifies that HIV reservoirs consist mainly of genetically younger, clonally enriched proviruses from the pre-ART period, with defective proviruses persisting longer.

HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy

This study analyzes HIV proviral diversity and compartmentalization in blood and lung during suppressive ART, finding shared sequences and limited genetic compartmentalization.

The emergence of SARS-CoV-2 in Europe and the US

January 2020 cases in Germany and Washington State were contained, while separate later introductions from China seeded the first sustained SARS-CoV-2 transmission networks in Italy and Washington State.