Browsing by Autor "Philippe Lemey"

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Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean
(Nature Portfolio, 2024) Tiago Gräf; Alexander A. Martínez; Gonzalo Bello; Simon Dellicour; Philippe Lemey; Vittoria Colizza; Mattia Mazzoli; Chiara Poletto; Vanessa Leiko Oikawa Cardoso; Alexandre Freitas da Silva
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
Diversity and dissemination of viruses in pathogenic protozoa
(Nature Portfolio, 2023) Senne Heeren; Ilse Maes; Mandy Sanders; Lon‐Fye Lye; Vanessa Adaui; Jorge Arévalo; Alejandro Llanos‐Cuentas; Lineth García; Philippe Lemey; Stephen M. Beverley
Parasite hybridization promotes spreading of endosymbiotic viruses
(2023) Senne Heeren; Ilse Maes; Mandy Sanders; Lon‐Fye Lye; Jorge Arévalo; Alejandro Llanos‐Cuentas; Lineth García; Philippe Lemey; Stephen M. Beverley; James A. Cotton
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of <i>Leishmania braziliensis</i> parasites and their endosymbiotic <i>Leishmania</i> RNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.