Réseau Scientifique PhyloMAP

PhyloMAP#3 + GDR-phylodynamique#1

Les prochaines rencontres sont co-organisées par le réseau PhyloMAP de l’INRAE et le GDR phylodynamique du CNRS. Ces recontres communes seront l’occasion d’initier un nouveau format, sur plusieurs jours, mêlant exposés scientifiques et formations.

Le symposium de phylodynamique aura lieu du mercredi 5 octobre 2022 à 14h au vendredi 7 octobre à 12h, en salle D2, CIRB, Collège de France, (11 place Marcellin Berthelot, 75005 Paris). La journée du mercredi sera suivi d’un diner au restaurant et la journée du jeudi se terminera par un cocktail dinatoire (lieu encore à préciser), permettant de prolonger les échanges.

Nous aurons le grand plaisir d’acceuillir comme orateurs:

Simon Dellicour - Molecular epidemiological approaches to investigate the dispersal dynamic of viruses and the environmental factors impacting it

Recent advances in genomics, mathematical modelling and computational biology have enabled molecular approaches to become key methods to investigate the spread of viral infectious diseases. In the emerging field of molecular epidemiology, genetic analyses of pathogens are used to complement traditional epidemiological methods in various ways. For instance, genetic analyses offer the possibility to infer linkages between infections that are not evident without analysing viral genomes. In particular, the development of phylogeographic methods has enabled to reconstruct dispersal history of epidemics in a discretised or on a continuous space, using only a relatively limited number of viral sequences sampled from known locations and times. At the Spatial Epidemiology Lab (SpELL, ULB), we develop and apply new analytical approaches exploiting such phylogeographic reconstructions to test epidemiological hypotheses about the external and environmental factors impacting the dispersal history and dynamic of viral epidemics.

Maude Jacquot - Linking disease monitoring and eco-evolution of marine mollusc pathogens

Pathogen surveillance and diagnostic methods are constantly evolving. Sequencing can provide critical information to diagnose diseases and to inform control and mitigation strategies by identifying genetically distinct pathogen variants that may have different host reservoir species or geographic distributions. However, most reference laboratories for marine mollusc diseases lack the resources or expertise for sequencing and data analysis. In order to overcome these limitations, we developed an easy to use, high throughput in-field mollusc pathogen sequencing suitcase, using the Oxford Nanopore MinION portable sequencer, and set up collaborative tools for data sharing, visualisation and analysis. In addition, using phylodynamic approaches we also addressed fundamental epidemiological questions such as inferring pathogen transmission dynamics from genetic data of the main oyster pathogen, the Ostreid Herpersvirus-1 (OsHV-1). Sequencing suitcases were deployed and used by five different shellfish industry actors including, farmers, hatchers and laboratories of veterinary analyses during oyster mortality events. Data obtained were analysed by our dedicated bioinformatics pipeline and allowed us to identify agents potentially responsible for mortalities within few days. Sequence data were shared on MoPSeq-DB which is a web-based platform we developed to reference curated genomic data related to mollusc pathogens. It also gives users opportunities to interactively visualise data and provides integrated analysis tools. The database currently focuses on OsHV-1, but will later include data from other mollusc pathogens such as the bacterium Vibrio aestuarianus or the protozoan Marteilia refringens. Genomic analyses showed OsHV-1 is a measurably evolving pathogen [1] and a first attempt of phylogeographic inference allowed us to determine that frequent pathogen transfers occur across shellfish production areas [2]. Moreover, population genetics analyses of multiple samples collected from different host species suggested that co-evolution between host-species and OsHV-1 has played a major role in the appearance of new variants and divergence of clades. Finally, current OsHV-1 evolutionary rates are quite similar to those estimated from firsts outbreaks indicating comparable epidemiological dynamics across time. We provide here robust bases to unify all sequence-based work related to mollusc pathogens which will offer unprecedented opportunities to carry out monitoring and diagnosis in near-real time as well as genomic inferences for a better understanding of transmission dynamics of marine mollusc diseases.

  1. Morga, B. et al. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species. Front. Microbiol. 12, (2021).
  2. Delmotte, J. et al. Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease. Virus Evol. 8, 1–14 (2022).

Chris Wymant - A highly virulent variant of HIV-1 circulating in the Netherlands

We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV—CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences—is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.

Les inscriptions se font via un formulaire en ligne

Comme d’habitude, le but de ces rencontres est d’initier une dynamique pour la communauté française en phylodynamique et les participant⋅e⋅s sont très fortement encouragé⋅e⋅s à présenter leur travaux de recherches (au moins par équipe).

Le réseau PhyloMAP et le GDR phylodynamique pourront prendre en charge une partie des frais d’hébergement et de transport (idéalement tous les frais pour les jeunes chercheur⋅se⋅s).