Biology subjects

Mateu, E.

Publications and source records attributed to Mateu, E..

4 recordsLinked to original sources

bioRxiv2026

Genetic diversity and phylogeography of swine influenza A virus in 2013-2022 in Europe using a harmonized genotyping nomenclature

Swine Influenza A virus (swIAV) poses constant health threat for both humans and animals. This study comprehensively analysed the genetic diversity and evolution of European swIAVs from 2013 to 2022. To address existing classification gaps, an easily accessible full-genome genotyping tool based on Nextclade was developed alongside a global nomenclature system. Application of this tool to European sequence data revealed unprecedented genetic diversity, successfully identifying 150 swIAV genotypes mixing segments of both swine and human origin. Bayesian phylogeographic models, combined with economic data, identified that the trade of live weaner pigs for fattening drove the transboundary spread of swIAVs across Europe. The study detected repeated human-to-swine reverse-zoonotic events across multiple European countries. These findings clearly highlight the role of commercial pig movements in viral dissemination and emphasize the critical importance of harmonized genomic surveillance to monitor swIAV viral evolution to inform global pre-pandemic preparedness strategies.

microbiology↗

bioRxiv2025

Rodent Origins and Human-Mediated Evolutionary Dynamics of PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) is among the most economically damaging swine pathogens worldwide, yet its evolutionary origins and the forces driving its diversification remain unclear. Using complete arterivirus genomes, we applied an integrative, high-resolution phylogenomic framework that combined time-calibrated evolutionary inference with recombination- and introgression-aware analyses. This approach resolved the divergence history of PRRSV and uncovered a cryptic mosaic genome and reticulation shaped by recurrent recombination and interspecies viral gene flow. We show that North American and European lineages diverged in the late 19th century - long before the emergence of disease on either continent and that their closest relatives are rodent arteriviruses, indicating a rodent ancestry. Genome-wide scans further reveal that PRRSV evolution is driven by adaptive changes in the glycoprotein ORF3, whereas the replicase genes remain a conserved genomic backbone. Demographic reconstructions suggest that the intensification of pig farming in the mid-20th century-imposed transmission bottlenecks that amplified genetic drift and accelerated the fixation of advantageous variants. Together, these findings rewrite the evolutionary timeline of PRRSV and provide a framework for understanding how human practices shape the emergence and spread of viral pathogens across animal and human health.

evolutionary biology↗

bioRxiv2020

SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naive human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.

evolutionary biology↗

bioRxiv2018

Bottlenecks in the transmission of Porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs

The existence of bottlenecks during infection of Porcine reproductive and respiratory syndrome virus (PRRSV) was studied in an experimental one-to-one model of transmission in pigs. Besides, the differences between viral quasi-species in vaccinated pigs that developed shorter or longer viremias after natural challenge were analysed. The results consistently reported the existence of bottlenecks during transmission. Several positions along the PRRSV genome were identified as being selected in partially immune animals that developed short viremias. Those positions accumulated in GP2, nsp9 and M proteins and resulted in changes in the protein structure and in the interactions of those proteins with their targets. The fact that the affected proteins are known targets of the immunity against PRRSV suggested that the immune response selected those changes. This pig model can be useful for the study of other pathogens of interest in animals and humans.\n\nAuthor summaryPorcine reproductive and respiratory syndrome (PRRS) is one of the most economically important disease of pigs. It is caused by PRRS virus (PRRSV), a positive-sense, single-stranded RNA virus in the Arteriviridae family within the order Nidovirales. Here, we study the existence of bottlenecks during disease transmission and the differences between viral quasi-species in vaccinated pigs that developed shorter or longer viremias after natural challenge. Our results consistently report the existence of bottlenecks during PRRSV1 transmission and identify several mutations along the viral genome selected by the host immune response that can be clear targets for new vaccine development.

microbiology↗