Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains

F Aubry, S Jacobs, M Darmuzey, S Lequime… - Nature …, 2021 - nature.com
The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-
borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all …

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

M Giovanetti, E Cella, F Benedetti… - Communications …, 2021 - nature.com
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest
by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We …

Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus

S Lequime, JS Dehecq, S Matheus, F de Laval… - PLoS …, 2020 - journals.plos.org
Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized
areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can …

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction

C Sun, R Fang, M Salemi, M Prosperi… - PLOS Computational …, 2024 - journals.plos.org
In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks
and patterns of spread is critical to inform public health programs. Projections of …

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics

S Marini, C Mavian, A Riva, M Prosperi, M Salemi… - …, 2022 - academic.oup.com
TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both
genetic diversity and temporal distribution through a genetic algorithm. Availability and …

[HTML][HTML] Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods

BR Magalis, A Riva, S Marini, M Salemi… - Infection, Genetics and …, 2024 - Elsevier
Molecular data analysis is invaluable in understanding the overall behavior of a rapidly
spreading virus population when epidemiological surveillance is problematic. It is also …

e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology

P Xu, S Liang, A Hahn, V Zhao, WTJ Lo, BC Haller… - bioRxiv, 2024 - biorxiv.org
Infectious disease dynamics are driven by the complex interplay of epidemiological,
ecological, and evolutionary processes. Accurately modeling these interactions is crucial for …

Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission

IH Goldstein, D Bayer, I Barilar, B Kizito… - PLoS Computational …, 2022 - journals.plos.org
Identifying host factors that influence infectious disease transmission is an important step
toward developing interventions to reduce disease incidence. Recent advances in methods …

Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier's …

B Viginier, L Cappuccio, C Garnier… - Peer Community …, 2023 - peercommunityjournal.org
Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity
formula, depends on host and vector parameters, including the vector's intrinsic ability to …

[HTML][HTML] Untangling the stranglehold through mathematical modelling of Streptococcus equi subspecies equi transmission

R Houben, JR Newton, C van Maanen… - Preventive Veterinary …, 2024 - Elsevier
Strangles, a disease caused by infection with Streptococccus equi subspecies equi (S.
equi), is endemic worldwide and one of the most frequently diagnosed infectious diseases of …