Lung cells infected with SARS

Viral Immunology

Welcome to the Čičin-Šain Lab of Viral immunology. We study cytomegalovirus (CMV) and other major viral pathogens to decode host-pathogen interactions, map immune longevity, and design next-generation prophylactic and diagnostic tools.

Prof Dr Dr Luka Cicin-Sain

Head

Prof Dr Dr Luka Cicin-Sain
Head of Research Group

Our Research

Our work is organized into four major research pillars:

Next-Generation CMV Vaccine Platforms and Bioprocessing

We leverage the unique immunobiological properties of the Cytomegalovirus to develop highly effective, long-lasting vaccines against respiratory pathogens. A major focus of this work is our vaccine candidate for Respiratory Syncytial Virus (RSV), which is being advanced toward clinical trials through our spin-off initiative, ENDURIVAC. In parallel, we are also developing vaccine candidates against influenza. To bring these discoveries to reality, our team actively optimizes cell-culture production strategies while simultaneously refining standard analytical assays to achieve exceptional precision in virus quantification.

Viral Latency, Cellular Reservoirs, and Mucosal Immunity

Cytomegalovirus establishes lifelong latency, fundamentally alters the host immune landscape, and, from a scientific perspective, requires a deep understanding of where the virus hides and how it shapes regional immunity. We systematically investigate the specific cellular niches that harbor latent human CMV (HCMV), moving beyond traditional monocyte reservoirs to characterize the role of stromal cells and alternative cell types across multiple tissues. Furthermore, we explore how these persistent latent infections imprint the host immune system, both systemically and at mucosal surfaces. Specifically, we study the generation and maintenance of tissue-resident memory T cells (Trm) in the lung, which act as pre-positioned local sentinels capable of providing rapid, early cross-protection against heterologous respiratory threats, including COVID-19.

High-Throughput Functional Assays and Patient Monitoring Platforms

To translate laboratory findings directly into clinical utility, we design dynamic assay systems that provide real-time, functional assessments of antiviral immune responses. We established ARMATA (Assay for Rapid Measurement of Antiviral T-cell Activity), a live-cell imaging platform that uses automated fluorescence microscopy to quantify how CD8 T cells control HCMV infection in real time. We have since expanded this into ARMADA (Antiviral Response Monitoring Assay for Dynamic Analysis), a comprehensive translational platform that incorporates total PBMC populations from transplant recipients. By pairing longitudinal patient sampling with real-time imaging, we can analyze complex, patient-specific immunity and map individual differences in viral control. 

Antigenic Cartography, Immune Escape, and Post-Viral Pathogenesis

We track viral evolution in real time to predict how mutations bypass host defenses while concurrently studying the debilitating, long-term systemic consequences of viral infections. Our group deploys multi-pathogen pseudoviral systems spanning SARS-CoV-2, flaviviruses, and CMV to quantify the evolving landscape of neutralizing antibodies. By utilizing antigenic cartography and advanced reverse mutational scanning, we systematically visualize antigenic distances and identify the exact structural epitopes that drive immune escape from polyclonal sera and therapeutic treatments. This structural work directly informs our research into post-viral conditions, particularly long COVID. We are actively investigating the mechanisms behind post-acute sequelae, focusing on how viral infections trigger systemic inflammation and cross into the central nervous system to drive neuroinflammation through brain microglia, while also evaluating how prior vaccination modifies these long-term neurological outcomes.