The other immune landscape of SARS-CoV-2 evolution

Researchers used to think that HIV and its relatives were pretty recent things, maybe only a few hundred years old. But a growing body of evidence now suggests their history is far more ancient, with ...

Researchers used to think that HIV and its relatives were pretty recent things, maybe only a few hundred years old. But a growing body of evidence now suggests their history is far more ancient, with viruses closely related to HIV circulating in primates for tens or hundreds of thousands of years, and the very roots of their family tree perhaps stretching back millions of years.

Advances in virus genomics have made it increasingly possible to track evolutionary changes at the population level over the timescales of outbreaks and epidemics (1). Before the current era of large-...

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...

High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically ...

Abstract. The evolutionary history of simian and prosimian immunodeficiency viruses (SIVs and pSIVs) remains difficult to resolve, because divergence-time

Spyros Lytras is one of four young scientists selected in 2025 to lead new research groups at the Institut Pasteur. He has headed the “Antigen Evolution & Design laboratory” 5-year Group (G5) since Ju...

Authors: Gina Cuomo-Dannenburg and Mahan Ghafari Note on data use This is an informal analysis and is not intended as a formal preprint or manuscript in its current form. The aim of this post is to p...

Preliminary reconstruction of the current MV Hondius Andes virus outbreak sequences Note on data use This is an informal analysis of currently available consensus sequences and is not intended as a fo...

AbstractSummary. Endogenous viral elements (EVEs) offer valuable insights into virus and host evolution, but their detection remains computationally and bi

Key findings England is currently experiencing a high growth rate of infections caused by the influenza A/H3N2 K clade. Antigenic change from the previously dominant clade, a rapid selective sweep evi...

Annual competition for early-career virologists to publish a minireview in JVI. Their minireviews will be peer reviewed & published in a collection.

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Oxford’s Prof Katrina Lythgoe and Mahan Ghafari, DPhil, report ONS-CIS data on 576 persistent UK infections with rapid within-host evolution and rare transmission after one month.

This talk brings together experts in pathogen genomics, virology, ecology, climate science, and data science to explore how AI, genomic surveillance, and…

Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as recently as one to six years before their respective dates of human emergence. These inferred virus ancestors likely needed to travel faster than closely related bat viruses in order to reach their respective sites of emergence.

Viral phylodynamics focuses on using sequence data to make inferences about the population dynamics of viral diseases. These inferences commonly include estimation of growth rates, reproduction numbers and times of most recent common ancestor. With few ...

Tracking the spread of emerging pathogens is critical to the design of timely and effective public health responses. Policymakers face the challeng...

In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-h...