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Objectives
The objective of this WP is to study sub-specific
systematic and genetic variation of the masked palm civet in order
to determine:
- Population structure and validity of subspecies;
- Geographic origin of the infected animals (from markets, farms
and the wild);
- Gene flows between the civet populations in order to determine
the contact zones between civet populations, and possible virus
transmission between populations.
- Comparison of the phylogeography of this species and of the presence
of the SARS-like CoV in the different populations.
Similar comparative animal/Coronavirus phylogeographic
studies of other species of Viverridae, notably of the common genet
(Genetta genetta occurring in Africa and southern Europe) would
be of great importance in order to foresee if similar events may
occur in the future in other parts of the world. A particular attention
has to be put on other species of small carnivores in contact with
human (farming, food, trade; e.g. African civet).
Finally, comparative phylogeny of animals and Coronavirus
will help to understand the evolutionary history of this virus group.
This could help to understand any new emerging zoonotic disease
and provide a model for similar epidemiological studies.
Description of work
Task 1: Training to molecular
and phylogenetic analysis methods.
Task 2: Collect of samples,
linked with WP 1 and WP 4. Collect of samples will also be made
on African viverrids,
particularly on captive animals (farms, markets). This can be done
through collaborations already established. Material from the tissue
and DNA bank of G. Veron will also be available for these studies.
Task 3: Microsatellites
design.
Task 4: DNA extraction,
amplification and sequencing of mitochondrial genes (cytochrome
b, D-Loop) and study of
microsatellites in order to determine geographic structure of the
populations and gene flows between populations of the masked palm
civet. Previous markers used for similar viverrids studies can be
used.
Task 5: Systematics study
of the masked palm civet, morphological and molecular comparative
work.
Task 6: Population study
of genets in Europe (mitochondrial genes, microsatellites).
Task 7: Molecular phylogeographic
and phylogenetic studies of other viverrids, in Asia, Europe and
Africa.
Task 8: Comparative phylogeographic
and phylogenetic studies: Paguma/SARS-like Coronavirus,
Viverridae/Coronavirus, Carnivore/Coronavirus and Synthesis.
Deliverables
D3 Training of students to field
work on small carnivores and to molecular techniques and methods
of phylogenetic analysis.
D4 Identification of the SARS-like
Coronavirus reservoir
D5 Specimen collection, animal
virology and civet population study will contribute to identify
the wild reservoir of the SARS-like Coronavirus.
D6 Production of an identification
tool (DNA sequence bank) for market and farm infected animals (species
identification, geographic origin identification).
D7 Identification of route and
mechanism of transmission of SARS-like Coronavirus.
D8 Virology and biological studies
on masked palm civet will conduct to understand mechanism of transmission
of this virus.
D9 Comparative evolutionary history
of Coronavirus and of carnivores.
D10 This may have outputs in evolutionary
biology, virology and human and animal epidemiology.
D11 Recommendation for capture,
farming, consumption, handling and trade of wild viverrids and wild
animals.
Milestones and expected result
M0-M12:
- Field work, sampling, training of Chinese collaborators to phylogenetic
analysis methods.
- Collection of samples of civets.
- Microsatellites design.
- Species checking and identification of the infected animals
on the basis of sequences bank already acquired by G.
Veron.
- Identification of infected animal.
M12-M24:
Sequencing work and microsatellites analysis.
-Population structure, identification of geographic origin of infected
animals
-Route of transmission between populations
-Recommendation for wild animals handling.
-Comparative phylogeography and phylogeny of viverrids (and other
small carnivores) and Coronaviruses.
M24-M30
- Reconstruction of evolution history of Coronaviruses
- Recommendation for small carnivores handling and farming (preparation
of the report).
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