Involvement of the France Genomique Platforms in the battle against SARS Cov2

8 December 2021

Detection and sequencing of the SARS-Cov2 virus and its variants

Faced with the spread of SARS-Cov2 in France, many platforms and associated platforms of France Génomique have been mobilised to contribute to the research on this virus and in particular to developping or testing different approaches for the sequencing of the SARS-Cov2 virus and its variants, based on the specific capture or amplification of viral sequences. The Biomics platform (Pasteur Paris) has collaborated with the Pasteur National Reference Centre (CNR) to rapidly implement sequencing. Go@l (Lille) relied on expertise already developed on another coronavirus [1] to amplify SARS-Cov2, MGX (Montpellier) also developed custom amplicons, but quite quickly the ARTIC primer set developed by Nic Loman’s team in England became the preferred choice, and was integrated as the basis for various kits, in particular those proposed by Nanopore and Illumina. Biomics (Pasteur Paris) has also implemented a protocol using viral sequence capture, allowing high quality sequencing of the SARS-CoV-2 genome from samples with very low viral abundance. The CNRGH (Evry) has tested and compared the commercial solutions proposed by Paragon Genomics, Agilent and Illumina (publication in progress). To go further, the CNRGH is developing new approaches using Illumina and Nanopore sequencing methods for analyses on “extreme” samples (low viral load with CT>28, fragmented genomes, etc.), and by evaluating statistical and bioinformatics strategies for haplotype and mixture reconstruction.

The UCAGenomix platform (Nice) showed the very rapid increase in the frequency of the English variant among people hospitalised for Covid in Nice between December 2020 and February 2021, and the admission in intensive care of a younger population without comorbidity [2]. Over the same period, GeT-PlaGe (Toulouse) collaborated with the Toulouse University Hospital to show the very rapid increase in the frequency of this same English variant in SARS-Cov2 positive nasopharyngeal swabs from early 2021 in Toulouse [3]. In addition, the UCAGenomix platform (Nice) developed the detection of the virus from wastewater samples and thus defined how the English variant appeared in the different districts of the city of Nice in early 2021 [4]. In a publication, the Biomics platform (Pasteur) presented the organisation that enabled it to continue to operate in conjunction with the Pasteur CNR during the confinements, in order to meet the needs for sequencing, by prioritising the projects related to the SARS-Cov2 study [5]. The UCAGenomix platform (Nice) also participated in a working group set up by the HESI (Health and Environmental Sciences Institute) to develop rapid, sensitive and affordable tests that could be used in the event of a shortage of SARS-Cov2 screening reagents [6]^, [7].

Before the national network was effectively structured, the FPs LIGAN (Lille) [8] and GeT-PlaGe (Toulouse) [9] contributed to the national effort to search for variants by sequencing a total of over 10,000 samples. More recently, GeT-PlaGe (again in collaboration with the Toulouse University Hospital) was one of a small number of sites worldwide involved in the validation of a new approach proposed by PacBio, which is less sensitive to contamination than approaches based on the ARTIC primer set, as the amplification and barcoding of the fragments amplified from each sample are performed during the same PCR [10].

Finally, the CNRGH coordinates with the Obépine network a consortium of 10 teams aiming to develop tools for the discovery and long-term monitoring of viral variants in wastewater [11].

Research on SARS-Cov2

Understanding how the virus interacts with cells is essential to be able to divert its attack and proliferation strategies. UCAGenomiX (Nice) generated a cellular atlas of the human airways in 2020, which allowed identifying the receptor cells of SARS-CoV-2 [12]. This work has led to various analyses of the impact of several factors on the development of the disease, in partnership with the UCAGenomiX platform (Nice) through the Human Cell Atlas Consortium [13] [14], [15], [16]

GenomIC (Cochin Paris) produced single cell RNAseq data and participated in their analysis to establish the role played by mucosa-related T lymphocytes (called MAIT) during Sars cov-2 infection, showing a correlation between the symptoms severity and the hyperactivation of MAIT lymphocytes and their cytotoxic effect in the lungs [17].

Biomics (Pasteur) has participated in several projects of the Pasteur teams on humans or on hamster cell models, in particular for the study of the modulating effect of ivermectin [18] and the study of anosmia [19].

The sequences produced by GeT-PlaGe (Toulouse) on longitudinal data from the Toulouse University Hospital have contributed to the study of the effectiveness of various public health measures in the Toulouse area ³ [20].

In terms of host genetics, the CNRGH (Evry) is, along with Imagine, the Pasteur Institute and the Bordeaux University Hospital, one of the 4 coordinators of the genomic screening (GWAS) currently underway to identify susceptibility factors for the severity of Covid19 [21].

[1] Maurier F. et al. (2019). A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology, 531:141-148.

[2] Courjon J et al. (2021). COVID-19 patients age, comorbidity profiles and clinical presentation related to the SARS-CoV-2 UK-variant spread in the Southeast of France. Sci Rep. Sep 16;11(1):18456.

[3] Di Meglio et al. (2021) Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2, Viruses 13(5), 898

[4] Rios G. et al. (2021). Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. Lancet Regional Health Europe

[5] Najar et al. (2021) How Did Institut Pasteur’s NGS Core Facility, Biomics, Manage the Coronavirus Disease 2019 Crisis? J Biomol Tech 32(2):50-56

[6] Pettit SD et al. (2020) ‘All In’: a pragmatic framework for COVID-19 testing and action on a global scale. EMBO Mol Med.

[7] Fassy J et al. (2021) Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples. PLoS One. Apr 14;16(4):e0243333.

[8] LIGAN platform at the heart of Covid-19 screening

[9] Un traçage des variants du SARS-CoV-2 en Occitanie

[10] HiFi Viral SARS-CoV-2 kit for Covid19 whole genome sequencing

[11] Consortium EMERGEN : Le séquençage pour la santé publique au service du contrôle de la pandémie Covid19

[12] Sungnak W. et al. (2020). SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine, 26(5):681-687.