A. Katzourakis

The paper identifies new endogenous viral elements in vertebrate genomes, expanding the known diversity of non-retroviral EVEs by 44%.

This study applies a mechanistic model to correct for time-dependent rate phenomena in plant viruses, revealing an ancient origin for sobemoviruses over four million years ago.

The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.

This study identifies novel rodent hosts of hepaciviruses, documents their diversity, and estimates the origin of the genus to be about 22 million years ago.

This paper reconstructs the evolutionary history of SIVs and pSIVs across timescales using a time-dependent rate model, finding the most recent common ancestor of extant SIVs dates to ~1 million years ago.

This study uses mathematical models and simulations to explore how virophage integration affects cell-virus dynamics and identifies antiviral strategies like PCD and multicellularity.

The paper discovers novel papillomaviruses in Malayan and Chinese pangolins using genome mining and identifies their prevalence and phylogenetic relationships.

This study investigates the evolutionary origins of the first three SARS-CoV-2 variants of concern, finding that they likely evolved within long-term infections in single individuals through multiple mutations.

This paper identifies two ancient Maverick-like viral integrations in the human genome, estimates their age at ~105 My and infers the viral ancestor at 268.61 My.

The paper tests evolutionary hypotheses about the origins of viruses, virophages, and eukaryotes using phylogenetic analysis of viral proteins.

The paper introduces a mechanistic model explaining time-dependent substitution rate decay in viruses, showing it applies across virus types and revises evolutionary timescales for HCV and sarbecoviruses.