Objectives
The objectives of this WP are to collect samples
for:
- detection and characterisation of SARS-like
CoV in animals;
- population study, phylogeography and systematic study of SARS
animal reservoir.
This WP will focus on all animal species with links
to masked palm civets in China, and civets and other species of
Viverridae in Asia, southern Europe and Africa. Sampled animals
will be both captive (farms) and wild.
Description of work
Task 1: Processing of authorizations
for animal sampling.
Task 2: Sampling techniques:
A/ for animal species other than civets in Guangdong
and neighbouring provinces: targeted inventory of vertebrate animals
in the region; risk ranking for harbouring SARS-like CoV based on
type of contacts with civets (prey, predator, proximity, etc…);
convenient sampling of animal species with the highest risk ranking
score.
B/ for civets and other Viverridae in China: stratified
(by geography and farm/market/wild origin) random cluster
sampling, proportional to estimated size.
C/ for civets and other Viverridae in Southern
Europe and Africa: convenience sampling.
Wild animals will be live trapped, with daily revised box traps
measuring 1.5 x 0.5 x 0.5 m and immobilized using an intramuscular
injection in the hindquarters of a combination of ketamine hydrochloride
(KE) and xylazine hydrochloride (XY). Initial doses of 7 mg/kg KE
and 10 mg/km XY should be enough to safely handle animals. For all
animal sampling, staff will be protected by 2 pairs of plastic disposable
gloves overlapping (tape may be used to hold the gloves over the
coat sleeves) with disposable overcoats and disposable hats as well
as EN95 compliant face masks and protective glasses.
Task 3: Type of samples:
A/ for virology: oral, nasal, and faecal swabs.
If possible, blood samples on dry tubes for future serological confirmation
of viral infection and basic studies on serological cross reactivity
between animal and human strains.
B/ for zoology (animal identification): hair samples
or skin biopsies
Task 4: Sample sizes:
A/ for animal species other than civets in Guangdong:
20 animals per species; 30 animal species sampled based on risk
ranking.
B/ for civets and other Viverridae in China and
Vietnam: 400 civets from farms (20 animals per civet farms from
20 civet farms (5% of the total number of civet farms of China));
200 civets and other Viverridae from markets (20 animals per market
from 10 markets); 200 wild civets and other Viverridae.
C/ for wild civets and other Viverridae in Southern
Europe and Africa: 100 animals in each continent (including tissue
collection from the MNHN)
Task 5: Laboratory analysis:
A/ Virology: techniques are detailed in WP3, and
will be standardised across the virology laboratories of the network
(Wuhan, Shanghai and Paris). All infectious samples transport will
be made according to the IATA regulation, using specialised couriers
with international recognition.
B/ Phylogeography and molecular systematics: techniques
are detailed in WP2. At least 30 animals per subspecies will be
analysed for phylogeography and systematic studies, resulting roughly
in 300 civets and 100 genets samples analysed. In addition, samples
from animals positive by PCR for SARS-like viruses will be analysed
for proper identification of the animal.
Deliverables
D1 Acquisition of material for WP2 and WP3,
D2 Identification of the animal species naturally
harbouring the SARS-like CoV.
Milestones and expected result
M0-M6:
- sampling in Chinese farms and Chinese and Vietnamese
markets and restaurants for civets and other Viverridae. Sampling
for other animal species in Guangdong province.
- live trapping of masked palm civets in China.
- request for samples to animal keepers in African civet farms.
M6-M12:
- samples shipment to Europe for phylogeographic analysis.
- preparation of the a short report of collected data.
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