Siobain Duffy

The paper analyzes sweet potato-infecting begomoviruses and finds that genome-sequence identity thresholds fail to produce monophyletic species due to recombination and paraphyly.

This study shows that RNA phage phi6 specialists can re-expand their host ranges through mutations, including reversion of narrowing mutations or parallel mutations, indicating no constraint from their mutational backgrounds.

The paper reevaluates begomovirus phylogeographic groupings using coat and replication-associated proteins, finding broad support for AAEO and Americas groupings but not fine-scaled divisions.

The paper analyzes 3D structural changes in SARS-CoV-2 proteins during the first six months of the pandemic, showing amino acid substitutions primarily affect surfaces and boundary layers.