S. Lytras

A Protein Language Model for Exploring Viral Fitness Landscapes

This paper introduces CoVFit, a protein language model that predicts SARS-CoV-2 variant fitness using spike protein sequences, identifying fitness-enhancing mutations and predicting emerging variants.

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

The paper maps glycoprotein structures across Flaviviridae to identify evolutionary events shaping their virology and ecology.

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.

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

This study identifies XBB as a SARS-CoV-2 variant resulting from recombination of BA.2 subvariants, showing increased resistance to neutralizing antibodies and enhanced fusogenicity compared to BA.2.75.

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

The paper investigates convergent evolution in SARS-CoV-2 Omicron subvariants, identifying five critical spike protein substitutions in BQ.1.1 that enhance viral fitness and antibody resistance.

Zoonotic avian influenza viruses evade human BTN3A3 restriction

This study identifies BTN3A3 as a human restriction factor that inhibits avian influenza viruses but not human IAVs, with resistance linked to specific NP mutations.

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

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

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

This paper traces the origins of SARS-CoV-2 to horseshoe bats in China and Southeast Asia, identifies recombination events in Sarbecoviruses, and highlights the need for more wildlife sampling to understand zoonotic spillover risks.

Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion H69/V70

This paper identifies a recurrent SARS-CoV-2 Spike deletion (H69/V70) that increases infectivity and compensates for RBD mutations, suggesting it may facilitate immune escape and variant emergence.

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

The paper shows the N439K SARS-CoV-2 spike variant maintains replication fitness while evading antibody neutralization.

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes.

This study identifies and analyzes endogenous hepatitis B viruses (eHBVs) in vertebrate genomes, revealing their evolutionary history and impact on saurian genomes.

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

The paper shows SARS-CoV-2's ability to infect humans stems from its evolutionary history in bats, not human adaptation, with evidence of positive selection in bat viruses and weak purifying selection in SARS-CoV-2.