Jonathan E. Pekar

The paper analyzes the spread of H5N1 B3.13 in U.S. dairy cattle using genomic data and movement networks, finding that cattle movement, not birds, drives the outbreak.

This study shows bovine H5N1 influenza viruses have adapted to efficiently use NeuGc receptors in cattle, enhancing replication without significantly altering zoonotic risk.

The paper identifies the emergence of D1.1 reassortant H5N1 viruses in North America, which show increased transmissibility, host range, and human spillover potential.

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.

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

The paper uses phylogenetic analysis to examine natural selection in zoonotic viruses, finding no evidence of pre-zoonotic adaptation for human transmission but detecting selection changes in the 1977 H1N1 reemergence.

Delphy provides a fast, scalable Bayesian phylogenetic analysis tool for outbreak tracking, achieving 1,000x speedups while maintaining state-of-the-art accuracy.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

This study analyzes MPXV genomic data from NYC during the 2022 outbreak, identifying NYC-specific lineages and estimating multiple infections, while highlighting gaps in epidemiological-genetic concordance.

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.