Hi!
I'm Spyros

An evolutionary virologist at the Systems Virology lab of the University of Tokyo. I study the arms race evolution between viruses and host immune responses and how this process can explain when viruses spill over into new species.
From June 2026 I will be leading the Antigen Evolution & Design laboratory at Institut Pasteur, where we will use AI-based approaches to better understand the evolutionary properties of pathogen antigen proteins.

myphoto
Coming soon...
At institut pasteur, paris.


Publications

From single-sequences to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2

Nature Communications, 2026

Inferring context-specific site variation with evotuned protein language models

NAR Genomics & Bioinformatics, 2026

Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals

Science, 2025

Genetic diversity in horseshoe bat ACE2 and sarbecovirus spike proteins mutually shape one another

Preprint, 2025

Structural and phenotypic plasticity of the RBD loop2 region is a key determinant for HKU5r-CoVs’ emergence in mink

Preprint, 2025

Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans

Cell Reports, 2025

Viro3D: a comprehensive database of virus protein structure predictions

Molecular Systems Biology, 2025

Integrative modeling of seasonal influenza evolution via AI-powered antigenic cartography

Preprint, 2025

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

Cell, 2025

Artificial intelligence for modelling infectious disease epidemics

Nature, 2025

Beyond MERS: Merbecovirus receptor plasticity calls for emergence preparedness

Cell Host & Microbe, 2025

A Protein Language Model for Exploring Viral Fitness Landscapes

Nature Communications, 2025

Pathogen genomic surveillance and the AI revolution

Journal of Virology, 2025

Expanding the genomic diversity of human anelloviruses

Virus Evolution, 2025

Mapping glycoprotein structure reveals defining events in the evolution of the Flaviviridae

Nature, 2024

Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV

Virology Joural, 2024

Resurrection of 2′-5′-oligoadenylate synthetase 1 (OAS1) from the ancestor of modern horseshoe bats blocks SARS-CoV-2 replication

PLOS Biology, 2023

BTN3A3 evasion promotes the zoonotic potential of influenza A viruses

Nature, 2023

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

Nature Communications, 2023

Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

Nature Communications, 2023

Exploring the natural origins of SARS-CoV-2 in the light of recombination

Genome Biology and Evolution, 2022

A Prenylated dsRNA Sensor Protects Against Severe COVID-19

Science, 2021

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

PLOS Biology, 2021

The animal origin of SARS-CoV-2

Science, 2021

Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses

Viruses, 2020

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Virus Evolution, 2021

No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota

Journal of Virology, 2024

Recombination as an evolutionary driver of MERS-related coronavirus emergence

The Lancet Infectious Diseases, 2024

A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

Genome Biology, 2024

Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Cell Reports, 2021

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Cell, 2021

Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function

Molecular Biology and Evolution, 2022

Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike

EMBO Reports, 2022

Conserved recombination patterns across coronavirus subgenera

Virus Evolution, 2022

Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms

Vaccines, 2023

No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues

PNAS, 2021

Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2

Molecular Biology and Evolution, 2020

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Public Engagement

Exploring the molecular interplay between viruses and their reservoir hosts' immune systems can aid our understanding of how these viruses can potentially spill over into new hosts. Have a watch of the clip below where I explain our work on resurrecting an ancient bat defence against SARS-related coronaviruses

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Understanding the origins of the COVID-19 pandemic will help us to stop coronavirus pandemics from happening in the future. Have a watch of my short interview and our animated video explaining how we study the evolutionary history and likely origins of SARS-CoV-2 and its relative coronaviruses.

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Blogs & Media

Sick animals suggest COVID pandemic started in Wuhan market

Nature News

Breathless: The Scientific Race to Defeat a Deadly Virus

David Quammen

Newly Discovered Bat Viruses Give Hints to Covid’s Origins

New York Times

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Chasing the bat origins of SARS-CoV-2

Protagonist Science

Science in Action

BBC Radio

How much should we worry about avian flu? (in Greek)

Iatronet

The coronavirus origins and the 'SARS-CoV-3' that's somewhere out there (in Greek)

Iatronet

Chances of finding COVID-virus ancestor ‘almost nil’, say virologists

Nature News

Looking for trouble

Science Magazine

Where did Omicron come from? Three key theories

Nature News

Where did the SARS-CoV-2 Omicron variant come from?

Philipp Markolin

BBC Essex with Emma Bullimore (2:17:00)

BBC Essex

Want to Avoid Omicron Two? We Have to Start Supporting Poorer Countries, Scientists Say

Newsweek

Omicron Variant May Have Spread From Animal to Human, Scientists Suggest

Newsweek

Conference Talks

Software & Resources

The plm_entropy Python3 package can be used for embedding sequences though ESM-2 and protT5 based models and calculating pLM entropy, a protein language model-based metric to assess protein site conservation and variability, along with a number of helper functions


plm_entropy

Viro3D is a comprehensive, searchable and browsable database of viral protein structure predictions, containing over 85,000 structural models from more than 4,400 human and animal viruses. The database is designed to support fundamental research into viral protein structure, function, and evolution, as well as to explore the contribution of viruses to overall protein structure diversity.


Viro3D

The DinuQ (Dinucleotide Quantification) Python3 package provides a range of metrics for quantifying nucleotide, dinucleotide representation and synonymous codon usage in a DNA/RNA sequence. These include the recently developed corrected Synonymous Dinucleotide Usage (SDUc) and corrected Relative Synonymous Dinucleotide Usage (RSDUc).


DinuQ
Want to chat science / start a project together? Get in touch!
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