Modeling infectious diseases for innovative therapies

A secure platform for academics & pharmas

CIPHE’s dedicated team specializes in infection models under controlled BSL-2 and BSL-3 environments, providing extensive expertise in pathogen handling, disease modeling, and host–pathogen functional analysis. Using genetically modified mouse models, including hACE2 knock-in strains, we perform detailed characterization of antiviral immune responses and support the preclinical evaluation of antivirals, antibodies, vaccines, and anti-inflammatory therapies.

With ANSM-accredited 400 m² facilities and advanced in vivo and in vitro models, including lung organoids and aerosol infection systems, CIPHE conducts research on respiratory viruses (Coronaviruses, Influenza, RSV) and arboviruses (Zika, Dengue, Chikungunya) in collaboration with VirPath and CEMIPAI.

Our studies have highlighted distinct pulmonary and cerebral impacts of infections, offering valuable insights into respiratory viral diseases. New platforms for plethysmography, nebulization, and behavioral analyses, expected to be operational by 2026, will further strengthen CIPHE’s capacity to respond rapidly to emerging viral threats and support high-impact translational research.

Head of Platform: Ana Zarubica, PhD

Team & experts

major research infrastructures

+10

multiparametric readouts

400 m²

BSL-2/3

Integrated preclinical solutions for infectious disease research

The platform delivers multi-parametric readouts, including virological and immunological profiling, pulmonary and behavioral function, lung and CNS histopathology, multi-omics (e.g., scRNA-seq), metabolic markers, and advanced imaging.
Outcomes include validated disease models, mechanistic insights, therapeutic and vaccine efficacy data, and robust, publication-ready datasets.

CIPHE’s BSL-2 and BSL-3 facilities and cutting-edge platforms are accessible to research teams via collaborative partnerships or fee-for-service models. In addition, training programs and expert consultation foster capacity building in infectious disease modeling and translational immunology.

CIPHE supports projects from early discovery to preclinical validation, offering full experimental design, model development, and regulatory expertise (biosafety, biosecurity, GMO, DUO).

The center is engaged in an ISO 9001 quality management system approach to ensure high standards and continuous improvement. It also adheres to the 3Rs principles and animal welfare and care guidelines in all preclinical studies.

The platform delivers multi-parametric readouts, including virological and immunological profiling, pulmonary and behavioral function, lung and CNS histopathology, multi-omics (e.g., scRNA-seq), metabolic markers, and advanced imaging.

Quality-driven preclinical innovation at CIPHE

Outcomes include validated disease models, mechanistic insights, therapeutic and vaccine efficacy data, and robust, publication-ready datasets. CIPHE is a key contributor to research infrastructures such as PHENOMIN, CELPHEDIA, INFRAFRONTIER, IMPC, and ISIDORe, positioning it as a trusted partner in translational infectious disease research.

Delivering validated models and translational research outcomes

CIPHE’s platform delivers multi-parametric datasets spanning clinical, virological, immunological, metabolic, behavioral, and neuroinflammatory domains.

Key readouts include:

Clinical monitoring: Standardized daily scoring (body weight, temperature, posture, fur condition, respiratory distress, activity), survival tracking, and humane endpoint evaluation for acute and chronic infection models.
Infection kinetics: Longitudinal sampling of biological fluids (e.g., blood, BAL) to assess viral load dynamics; physiological monitoring (e.g., telemetry sensors for body temperature).
Behavioral monitoring: Real-time tracking using visual inspection and smart-cage technologies (e.g., DVC) to detect changes in activity or distress.
Virology: Viral replication and tissue tropism via RT-qPCR, TCID₅₀, and immunostaining.
Immunology: Cytokine/chemokine profiling (ELISA, Luminex), flow, spectral, and mass cytometry for immune cell phenotyping, Immunogenicity and efficacy, ELISpot
Immune metabolism: High-content single-cell immune-metabolic profiling by mass cytometry.
Pulmonary function: Plethysmography and lung mechanics (resistance/compliance) for respiratory assessment.
Behavior and neuroinflammation: Cognitive and behavioral assays, CNS histopathology, and neuroinflammatory markers.
Histopathology and imaging: Peripheral tissue analysis with immunostaining and advanced imaging modalities.
Multi-omics: Integration of transcriptomic data, including single-cell RNA sequencing, to reveal underlying mechanisms.

Included in the service

CIPHE develops and integrates advanced technological platforms to support infectious disease research and translational applications:

Precision rodent models development: Design and characterization of genetically engineered mice and rats using CRISPR-Cas9, and other advanced genome editing tools, immunodeficient, humanized mice, and bone marrow chimera models, that replicate human susceptibility to infections and infection-related disorders (e.g., inflammation, autoimmunity).
Host-pathogen interactions: Dissection of immunopathological responses to infection - acute and chronic inflammation, immune dysregulation, cytokine storms, and auto-immune sequelae.
High-throughput functional screening: In development, a CRISPR-Cas9 knockout library for genome-wide screens of host genes controlling susceptibility/resistance to pathogens.
Immune phenotyping and biomarker discovery: Multi-omics platforms (flow/spectral/mass cytometry, single-cell RNA-seq, proteomics) to profile host responses and identify therapeutic targets or disease biomarkers.
Infectious disease modeling: Preclinical systems for respiratory viruses (SARS-CoV-2, Influenza, RSV), arboviruses and flaviviruses (Zika, Dengue, Chikungunya), and emerging pathogens, including models addressing lung–brain axis and infection-induced neuroinflammation.
Organoids & 3R innovation: As part of PRIMTECH 3R (INFRAFRONTIER), CIPHE develops lung organoids co-cultured with stromal and immune cells using 3D bioprinting and microfluidics, benchmarked against in vivo models via transcriptomic, proteomic, and imaging readouts.
Therapeutic pipelines: Integrated in vivo/in vitro workflows to evaluate antivirals, vaccines, and immunotherapies.