Service Description:

The Center of Immunophenomics (CIPHE) provides advanced infrastructure and expertise to accelerate the development of therapies and vaccines targeting immune-related and infectious diseases. Our ANSM-accredited 400 m² BSL-2 and BSL-3 facilities enable secure, compliant research on high-risk pathogens.

We develop and offer access to precision in vivo and in vitro disease models including mice, lung organoids, and aerosol infection systems – for respiratory viruses (Coronaviruses, Influenza A/B, RSV, Rhinoviruses, Pneumoviruses) in collaboration with VirPath, and for arboviruses and flaviviruses (Zika, Chikungunya, Dengue) in partnership with CEMIPAI. CIPHE delivers mechanistic insights via high-resolution clinical, virological, immunological, behavioural, and neuroinflammatory readouts, including viral load quantification, multi-omics (scRNAseq) studies, cytokine profiling, flow, spectral and mass cytometry, pulmonary function tests, behavioural assessments, lung and CNS histopathology, and advanced imaging.

CIPHE is collaborating on studies from early discovery to preclinical validation, with academic, biotech, and pharmaceutical partners. As a key contributor to national and international research infrastructure such as Celphedia, Virocrib, ISIDORe, INFRAFRONTIER, or IMPC; CIPHE has played a pivotal role in COVID-19 preclinical research since 2020, driving innovation in infectious and immune-mediated diseases.

Included in the Service:

CIPHE’s platform generates multi-parametric data across clinical, virological, immunological, behavioural, and neuroinflammatory domains. Key readouts include:

• Clinical scoring and infection kinetic with comprehensive assessment of disease progression and host response
• Daily clinical scoring using standardised scales to quantify key parameters such as body weight, body temperature, posture, fur condition, respiratory distress, and overall activity level.
• Survival monitoring and humane endpoint tracking to evaluate lethality and time-to-event data in acute or chronic infection models.
• Infection kinetics profiling, including longitudinal sampling of biological fluids to quantify viral load over time.
• Monitoring of physiological parameters, such as body temperature, via implanted sensors where applicable
• Visual assessment and digital video tracking for real-time behaviour and distress monitoring, when integrated with smart-cage technologies (e.g., DVC).
• Correlation of clinical findings with pathogen replication dynamics in target organs and tissues, enabling evaluation of therapeutic efficacy or pathogenic mechanisms.
• Viral replication and tissue tropism (e.g., RT-qPCR, TCID50 assays)
• Cytokine and chemokine profiling (ELISA, Luminex)
• Flow, spectral, and mass cytometry for immune cell phenotyping
• Pulmonary function analysis (plethysmography, lung resistance/compliance)
• Behavioural and neurocognitive assessments (nesting, locomotion, feeding)
• Peripheral tissue histopathology, immunostaining, and advanced imaging
• Multi-omics integration, including single-cell RNA sequencing, for mechanistic insight

Additional Support:

CIPHE develops its activities around several integrated technological platforms that contribute to infection research axis providing powerful tools for translational applications:

• Development and characterisation of murine models that replicate human disease phenotypes, including susceptibility to viral and bacterial infections, using advanced genome editing technologies.
• Study of immunopathological mechanisms, triggered by infection (e.g., acute inflammation, immune exhaustion, cytokine storms)
• High-throughput multi-omics immune phenotyping (flow and mass cytometry, single-cell RNA-seq, proteomics), applied to decipher host responses to infection and identify biomarkers of disease progression or therapeutic response.
• Modelling of respiratory infections, with validated systems for pathogens such as Influenza, RSV, SARS-CoV-2, and an emerging focus on lung–brain interactions and post-infectious neuroinflammation.
• Integrated in vivo/in vitro therapeutic evaluation pipelines, used to assess antivirals, vaccines, and immunotherapies

These platforms position CIPHE as a key contributor to infectious disease research, while maintaining a broader impact across immunology and precision medicine.