Doctoral candidate 14
Mechanisms of PLpro-mediated host-cell reprogramming in SARS-CoV-2 infection and persistence
About MERIT
MERIT (MEtabolic Reprogramming in viral pathogenesis: from Infection to Therapeutic innovations) is an EU-funded MSCA training programme aimed at better understanding how viruses affect the human body. Coordinated by Dr. Adithya Sridhar, Assistant Professor, and Prof. Dr. Dasja Pajkrt, Professor of Pediatric Infectious diseases, from the OrganoVIR Labs at Amsterdam UMC (location AMC), this project brings together 7 academic institutions and 12 associated partners from across Europe.
Within MERIT, researchers will take a new, holistic approach that focuses on infections and host metabolism to unravel virus-induced metabolic reprogramming and its impact on human health. The project’s objective lies in understanding the complex interplay between viruses and host cells, focusing on metabolic reprogramming, and long-term consequences of infection. This will be achieved by combining three methodological pillars: human organoids, integrative and spatial omics, and advanced microscopy.
Background of project
SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and immune suppression. Acting as a deISGylase, PLpro cleaves ISG15, suppressing host immune responses. Since ISGylation regulates metabolic pathways such as glycolysis, fatty acid oxidation, and mitochondrial function, PLpro’s activity may indirectly impact these processes, promoting viral persistence in gut and lung tissues. This persistence may drive chronic inflammation, potentially leading to neuroinflammation via the gut-lung-brain axis. Using advanced multi-scale models and autopsy-derived tissues, this study aims to explore the systemic effects of PLpro-mediated viral persistence, including neuroinflammation, to better understand long-term COVID-19 complications.
Job description
At Karolinska Institutet in Sweden, MERIT is looking for a highly motivated doctoral candidate (DC) to join the Systems Virology Lab. As DC14, your objectives are:
Define how PLpro-mediated deISGylation reprogrammes host-cell metabolism and antiviral signalling during SARS-CoV-2 infection, integrating molecular and biochemical approaches.
Determine how this PLpro-driven reprogramming shapes SARS-CoV-2 persistence in physiologically relevant organoid models of the gut and lung.
Explore the broader consequences of PLpro-mediated persistence, including links to chronic inflammation and neuroinflammation, using organoid systems and patient-derived tissue.
You will be directly supervised during your research project by Dr. Soham Gupta and Dr. Magdalini Lourda. You will work in close synergy with the broader team at the Center for Systems Infection Biology, including network principal investigators Dr. Ujjwal Neogi and Dr. Iva Filipovic, leveraging their cutting-edge pipelines in single-cell techniques, spatial multi-omics, and immunometabolic engineering.
A central component of the MSCA Doctoral Network is international and interdisciplinary training. Planned secondments include:
Complex tissue and barrier models: Dr. Adithya Sridhar, Amsterdam UMC, the Netherlands.
Metabolic alteration analysis: Prof. Gisa Gerold, Medical University Innsbruck, Austria
In addition, the candidate will participate in MERIT-wide scientific meetings, hands-on workshops (including an AI/LLM workshop and an Integrative Omics workshop), transferable skills training, and a tailored pre-MBA certificate course.
You can apply for this position until 30 October 2026. Applications submitted after this date will not be considered.
Please note: You must submit your application through both the MERIT website and the Karolinska Institutet’s website. Your application will only be considered complete once both submissions have been made.
Requirements
Experience in one or more of the following areas would be particularly advantageous:
Protein biochemistry: Experience with protein handling, Western blotting, functional enzyme kinetics, or investigating protein-protein interactions.
Histopathology & tissue processing: Hands-on experience sectioning, fixing, embedding, and analyzing tissue samples or complex cell layers.
Immunohistochemistry & advanced microscopy: Proficiency in tissue staining protocols (e.g., IHC, multiplex immunofluorescence, or in situ hybridization) and confocal imaging.
Advanced cell culture: Routine maintenance of mammalian cell systems, primary immune cells, or 3D/iPSC-derived tissue models.
Virology & molecular immunology: Experience studying virus-host interactions, innate immune signaling pathways, or cell-type specific host responses.
An interest in working in a highly multidisciplinary, intersectoral, and international research network.
MSCA Doctoral Network eligibility
At the time of recruitment, applicants must:
Not hold a doctoral degree.
Be eligible for enrolment in a doctoral program.
Be of any nationality.
ulfil the MSCA mobility rule: applicants must not have resided or carried out their main activity, such as work or studies, in Sweden for more than 12 months during the 36 months immediately preceding the recruitment date.
Eligibility for doctoral education at Karolinska Institutet
Applicants must meet the general eligibility requirements for doctoral education at Karolinska Institutet by having:
been awarded a degree at the advanced/second-cycle level; or
completed at least 240 ECTS credits, of which at least 60 ECTS credits are at advanced/second-cycle level; or
acquired substantially equivalent knowledge in another way in Sweden or abroad.
applicants must also demonstrate proficiency in English equivalent to the Swedish upper-secondary course English 6/English Level 2, according to Karolinska Institutet's requirements for doctoral education.
More information regarding general and specific entry requirements to Karolinska Institute: https://education.ki.se/doctoral-education.
What we offer
A doctoral student position for four years at Karolinska Institutet, one of the world's leading medical universities.
An interdisciplinary research project at the frontier of emerging viruses, immunometabolism, and host-directed therapeutics.
Extensive training in human iPSC-derived models, organoids, multi-omics, metabolic modelling, and advanced microscopy.
International secondments (to the Netherlands and Austria) and access to expertise and infrastructure across the MERIT MSCA Doctoral Network.
An opportunity to take part in a tailor-made pre-MBA programme to develop entrepreneurial and commercial skills and other network-wide training opportunities including conferences and courses, a Personal Development Plan, non-academic coaching, and workshops on topics including ethics and sustainability and AI/LLM.
Participation in an international network of doctoral candidates, leading researchers, and partner organizations.
Structured scientific and transferable skills training supporting future careers in academia, biotechnology, pharmaceutical research, and other sectors.
Employment according to Karolinska Institutet's conditions for doctoral students and applicable MSCA Doctoral Network provisions.
Access to KI employee benefits, including occupational pension, annual leave, wellness facilities and reimbursement schemes according to applicable university regulations.
About the host institution
The Systems Virology Lab and Center for Systems Infection Biology at Karolinska Institutet sit at the forefront of understanding how viruses interact with the human host at a systems level. Integrating cutting-edge single-cell and spatial multi-omics approaches with advanced experimental models such as human organoids, the lab deciphers the molecular and cellular mechanisms that govern viral pathogenesis, immune evasion, and disease progression.
Our research spans a broad spectrum of clinically relevant viruses, with a particular focus on retroviruses and arboviruses, interrogating how host-virus dynamics shape outcomes across tissues. By combining computational systems biology with rigorous experimental virology, we translate complex biological data into mechanistic insights with direct relevance to therapeutic and diagnostic innovation.
Based at one of the world’s leading medical universities, the lab fosters an international, collaborative, and intellectually ambitious environment where early-career scientists are empowered to develop as independent research and contribute to science that matters. The group is coordinating and involved in several EU projects, as well as supported by the Swedish Research Council and other funders.