Involvement of the France Genomique Platforms in the battle against SARS Cov2
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.
[13] Bui LTet al. (2021) Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity. Nat Commun. 2021 Jul 14;12(1):4314.
[14] Muus C et al. (2021) Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 27(3):546-559.
[15] Tucker NR et al. (2020) Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2-Mediated Myocarditis. Circulation. 142(7):708-710.
[16] Ziegler CGK et al. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. Cell. 2020 181(5):1016-1035.e19.
[17] Flament et al. (2021) Outcome of SARS-CoV-2 infection is linked to MAIT cell activation and cytotoxicity Nature Immunology 22, pages322–335
[18] de Melo et al. (2021) Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin, EMBO Mol Med 9;13(8):e14122
[19] de Melo et al. (2021) COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters Science Transl Med 2;13(596):eabf8396
[20] Di Meglio et al. (2021) Influence of age on the spread of SARS-CoV-2 variant B.1.1.7, J Clin Virol 141: 104872
[21] Epidémiologie génétique de la Covid-19 : projet EpiGenCOV
Pro-inflammatory cytokines regulation through Ikaros
GenomEast is co-authors of a multi-omics study (RNA, ATAC, CHIPseq) that elucidates the role of the Ikaros repressor in the regulation of pro-inflammatory cytokines that, when overexpressed, lead to tissue damage in autoimmune diseases. With these findings, Ikaros could be considered as a biomarker of the autoimmune response in patients with Covid-19.
PNAS April 2020 doi.org/10.1073/pnas.2023172118
UCA GenomiX tracks SARS-CoV-2 variants in waste water
The UCA GenomiX (IPMC) platform has been developing for several months a method to measure the levels of the different forms of the SARS-CoV-2 virus circulating in the wastewater of the Nice area. The detection of high levels of SARS-CoV2 in patients' faeces has indeed suggested the interest of monitoring its levels in wastewater treatment facilities. The emergence of new variants makes the sequencing approach particularly interesting, as it allows easy detection. The entire viral genome (30,000 nucleotides) is sequenced using an Oxford Nanopore technique on a set of amplicons from sewage extracts. In September 2020, UCA GenomiX started to establish a partnership with the City of Nice to carry out the sequencing of samples collected in twenty different districts, providing a precise quantification of the different variants present in the region. This collection by district enabled to alert the Nice Metropôle very quickly on the circulation of certain "at-risk" variants in particular districts of the city. While continuing this monitoring, the team is now working with the company Véolia, which wants to industrialise this approach, building on the expertise developed by UCA GenomiX. The first analyses required the implementation of a complete processing chain, from sample collection to library production, sequencing and bioinformatics analysis. This initiative was followed by others, such as the Ôbépine monitoring unit (https://www.reseau-obepine.fr/), to be extended to the whole of France.
IPMC staff involved in the project: Géraldine Rios, CNRS Assistant Engineer; Rainer Waldmann, INSERM researcher; Caroline Lacoux (Bernard Mari team), CNRS researcher; Kévin Lebrigand, CNRS engineer; Anna Diamant, Master student; Pascal Barbry, CNRS Research Director.
Mission « Microbiomes » for Tara
The schooner sails back to the oceans to study their microbiomes (https://oceans.taraexpeditions.org/m/science/les-actualites/mission-microbiomes-la-nouvelle-expedition-de-tara/). As partner of the expedition, Genoscope will be providing its expertise in sequencing and multi-metaomic analyses for the identification of micro-organisms and their ecosystems in the context of environmental changes.
Identification of SARS-COV2 host cells
As part of the Human Cell Atlas Lung Biological Network consortium and research to understand the mechanism of infection of Covid-19 disease, IPMC/UCAGenomiX scRNAseq studies have identified respiratory cells as targets for SARS-COV2 .
Nature Medecine 2020; doi: 10.1038/s41591-020-0868-6
Cell 2020; doi: 10.1016/j.cell.2020.04.035
CAF-S1 fibroblast clusters and immunotheraty response
The sequencing platform of Institut Curie has participated to a significant advance in the identification of CAF-S1 fibroblast clusters associated with resistance to cancer immunotherapies ( CANCER DISCOVERY 2020 ; doi: 10.1158/2159-8290.CD-19-1384)
SCNaUMI
K Lebrigand et al. describe a new approach for assigning UMIs "SCNaUMI" ( Nat.Commun. 2020 ;doi: 10.1038/s41467-020-17800-6), which allows the precise identification, from single cells, of transcripts and their isoforms by long fragment sequencing (Oxford Nanopore) .
The 1st cell atlas of the human airways
P Barbry's team and the UCAGenomiX platform publish the 1st human airway cell atlas by scRNA-seq analysis (Am. J. Respir. Crit. Care. Med 2020; doi: 10.1164/rccm.201911-2199OC). This study demonstrates that transcriptome differs for a cell type according to its location along the respiratory tract while the expression of cell-specific genes remains stable.
Oak genomics
The consortium in which Genoscope is a major contributor is publishing a special issue of the "New Phytologist" devoted to the genomics of oak and its genetic flexibility that allows its adaptability to the environment, its robustness and its longevity.
The PED-COVID project
The CNRGH is one of the partners in the PED-COVID project coordinated by the Necker Hospital to carry out genomic analyses for the study of immunoprevalence and immunoprotection against SARS-CoV2 in young children and their parents.