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

IFREMER

Nantes, , FR

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up to 107 genomic copies /g of stool) even if the presence of infectious viral particles is not so clear (V. Marechal, unpublished data).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.

Principal activities

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/gastrointestinal), 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 RTPCR optimization.
  • Choice of membrane for passive sampleing in seawater.
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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 SARS-CoV2 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.

Taask 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: RTPCR 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.


POSITION TYPE

ORGANIZATION TYPE

EXPERIENCE-LEVEL

DEGREE REQUIRED