Post-doctoral research position in Detection of SARS-CoV-2 in coastal environment

Post-doctoral research position in Detection of SARS-CoV-2 in coastal environment.

Reference: PV-2020-836/1

A pioneer in ocean science, IFREMER’s cutting-edge research is grounded in sustainable development and open science. Our vision is to advance science, expertise and innovation to:
– Protect and restore the ocean
– Sustainably use marine resources to benefit society
– Create and share ocean data, information & knowledge.
With more than 1,500 personnel spread along the French coastline in more than 20 sites, the Institute explores the 3 great oceans: the Indian, Atlantic and Pacific oceans. A leader in ocean science, IFREMER is managing the French Oceanographic Fleet and its dedicated scientists create ground-breaking technology to push the boundaries of ocean exploration and knowledge, from the abyss to the atmosphere-ocean interface.
Well-established in the international scientific community, our scientists, engineers and technicians are committed to advance knowledge about our planet’s last unexplored frontiers. They provide the science we need for informed decision-making and public policy and they transfer this knowledge and technology to businesses to fulfill public and private needs. Core to our mission is also to strengthen public awareness about the importance of understanding the ocean and its resources, and empowering future generations of leaders through education and outreach national campaigns.
Founded in 1984, IFREMER is a French public organization and its budget approximates 240 million euros. It is operating under the joint authority of the French Ministry for Higher Education, Research and Innovation, the French Ministry for the Ecological and Solidary Transition, and the French Ministry of Agriculture and Food.

The Laboratory
The Santé Environnement et Microbiologie laboratory (LSEM) develops research activities related to human pathogenic micro-organisms (viruses, bacteria and parasites) in the marine environment and shellfish to understand microbial contamination through watershed and coastal environment. This laboratory has a long experience on virus detection in sewage, shellfish and the coastal environment, and is a partner of several national or European projects.

To answer the possible issue regarding environmental contamination by SARS-CoV-2 from human releases, this project aims to optimize methods for detecting the virus in the nearshore environment, assess its spread along the French coastline and its ability to persist in coastal water.
SARS-Cov2 belong to the coronavirus family. SARS-CoV2 is a respiratory virus mainly transmitted through exposure to droplets generated by coughing, sneezing or breathing, especially at the onset of symptoms. The presence of SARS-CoV2 RNA in feces of infected people has also been reported several times, with concentrations up to 107 genomic copies /g of stool) even if the presence of infectious viral particles is
not so clear (V. Marechal, unpublished data).
Stool excretion leads to the presence of SARS CoV2 particles in wastewater as demonstrated by different works in France or in various countries. In response to potential environmental contamination by SARS CoV-2 from human sewage, this project aims to optimize methods to detect the virus in the coastal environment, assess its spread along the French coastline and its ability to persist in coastal water.

Indeed, its detection could help the monitoring of clusters on the national territory in wastewater (OBEPINE project) but also in shellfish, considered here as an integrator of contamination (Ifremer action plan). Furthermore, it seems appropriate to validate a surrogate virus to assess the stability of this virus in seawater during the emission of aerosols by infected persons, or inactivation processes in case of
shellfish contamination

Main tasks
The main purpose of this work consist in three tasks:
Task 1 : Method optimization to detect SARS-CoV2 and to select a surrogate: enteric or respiratory animal coronavirus (in collaboration with ANSES).
Porcine coronavirus belonging to the three main genus, alpha, beta, and gamma, will be compared based on similarity in the host (respiratory/gastro-intestinal), their similarity with SARS-CoV-2, their simplicity of multiplication, and their resistance to salt or pH conditions.
Extraction method from shellfish tissue and coastal seawater: this work has partially been made but need to be fully investigated.
Yield calculation for each method and matrices, digital RT-PCR optimization.
Choice of membrane for passive sample ing in seawater.
Task 2 : Detection of SARS-CoV-2 in coastal environment using shellfish as sentinel for viral contamination and reflecting sweater quality,
Analysis of samples and coordination of sampling. Collaboration to the OBEPINE network to survey the SARSCoV2 in raw sewage and to link with Human clusters on the coastal area.
– Follow up of samples collected with the help of colleagues from Ifremer
– Validation and results synthesis,
– OBEPINE network: collaboration with the laboratories, data collection and interpretation.
Task 3 : Persistence of infectious coronavirus in the coastal environment. For this task the surrogate selected in task 1 will be used to mimic the behavior of the human strain. Different parameters will be investigated:
temperature and salinity, selection of different experimental conditions,
sample preparation: contration and purification to recover infectious particles,
persitence in shellfish: RT-PCR concentration follow up in shellfish kept in tanks oor out of water at 4°C to mimick storage in a fridge.
This researcher will be in charge of the follow up on sampling already set up at Ifremer, to coordinate the work of different collaborators, to contribute to results analysis, and exchange with other laboratories.

PhD thesis
Knowledge in Human virology, and if possible on environmental samples analysis.
Contact :

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