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Article
Open AccessDrivers and impact of the early silent invasion of SARS-CoV-2 Alpha
SARS-CoV-2 variants of concern (VOCs) circulated cryptically before being identified as a threat, delaying interventions. Here we studied the drivers of such silent spread and its epidemic impact to inform fut...
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Article
Open AccessEpistatic interactions between the high pathogenicity island and other iron uptake systems shape Escherichia coli extra-intestinal virulence
The intrinsic virulence of extra-intestinal pathogenic Escherichia coli is associated with numerous chromosomal and/or plasmid-borne genes, encoding diverse functions such as adhesins, toxins, and iron capture sy...
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Article
From individual-based epidemic models to McKendrick-von Foerster PDEs: a guide to modeling and inferring COVID-19 dynamics
We present a unifying, tractable approach for studying the spread of viruses causing complex diseases requiring to be modeled using a large number of types (e.g., infective stage, clinical state, risk factor c...
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Article
Phage–host coevolution in natural populations
Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage–host evolution in wild populations, we isolated 195 Vi...
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Article
Open AccessNosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020
France went through three deadly epidemic waves due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing major public health and socioeconomic issues. We proposed to study the course of...
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Article
Open AccessHeritability of the HIV-1 reservoir size and decay under long-term suppressive ART
The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 res...
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Protocol
Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
We describe a detailed protocol for the manual workup of blood (plasma/serum) samples from individuals infected with the human immunodeficiency virus type 1 (HIV-1) for deep sequence analysis of the viral geno...
