A. Katzourakis

Deep-mining of vertebrate genomes reveals an unexpected diversity of endogenous viral elements

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

Revisiting the origins of the Sobemovirus genus: a case for ancient origins of plant viruses

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 recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

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.

The evolutionary history of hepaciviruses

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.

A unified evolutionary framework to reconstruct the viral histories of human, simian, and prosimian immunodeficiency viruses across timescales

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.

Ecological and evolutionary dynamics of cell-virus-virophage systems

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

Discovery of novel papillomaviruses in the critically-endangered Malayan and Chinese pangolins

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

Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern

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.

An ancient endogenous DNA virus in the human genome

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.

A billion years arms-race between viruses, virophages and eukaryotes

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

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

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.