Jakob Jonnerby
Tagline:Research Associate in Epidemiology at Imperial College London
London, UK
About Me
I provide actionable, evidence-based advice to public health agencies to strengthen pandemic preparedness as a researcher in the Health Protection Research Unit in Respiratory Infections,
My research interests span infectious disease transmission risk modelling, health economics, and immunology.
Research Interests
- Infectious disease transmission dynamics
- Health economics
- Immunology
- Public health
- Biosecurity
- Public health
- Pandemic preparedness
Projects
Understanding seasonal infection dynamics using blood samples
date: 2025Organization:Imperial College London and UK Health Security Agency
Description:Every year, thousands of blood samples are collected from GP surgeries and hospitals and sent to the UK Health Security Agency for processing. In this project, we aim to develop models to make the most use of these samples to understand what infections are currently circulating, and how many people are infected.
Preparing for pathogen X
date: 2025Organization:Imperial College London and UK Health Security Agency
Description:The next pandemic is a question of when, not if. Together with colleagues at the UK Health Security Agency, we have secured funding from the National Institute for Health and Care research to build and test the next generation pandemic response studies that can be rapidly deployed to answer questions about asymptomatic spread, duration of infectiousness, and modes of transmission of emerging pathogens.
Exploring the early immune response to infection
date: 2024Organization:Imperial College London
Description:Why are some people more likely to get infected with seasonal respiratory viruses than others? How exactly does the immune system respond to a virus in the critical first few hours and days of infection? By using high-resolution data from people infected with respiratory viruses, we aim to develop mathematical models that can recreate the interaction we observe between a viral infection and the immune response. This knowledge can help us develop powerful antiviral drugs and new types of vaccines that can protect against multiple types of viruses.
Delineating the pathways of SARS-CoV-2 transmission
date: 2023Organization:Imperial College London
Description:It has been well established that SARS-CoV-2 is primarily spreading through the air. In this project, I used data from human challenge and observational studies to quantify the risk of transmission through both aerosol and surfaces and evaluate the potential impact of non-pharmaceutical interventions.
Work Experiences
Research Associate
from: 2021, until: presentOrganization:Health Protection Research Unit, Imperial College LondonLocation:London, United Kingdom
Description:Generated ambitious pandemic preparedness research agendas in partnership with experts in clinical research, public health, immunology, and epidemiology from academia, government, and non-profit organisations. Coordinated budget proposals worth more than £20 million.
Responded to urgent requests from the UK Government by providing tailored, evidence-based advice on lateral flow test and PCR-based diagnostic testing strategies during the COVID-19 pandemic.
Advised £50 million UK Government biosecurity research fund on strengthening its scientific aims, deliverables, and programme structure to maximise impact.
Led research projects to quantitatively assess personal protective equipment and air filtration, integrating data from multiple studies.
Maintained funder relations, held project partners to account to meet agreed objectives, highlighted projects at risk of delay and suggesting modifications in scope in response to changing circumstances.
Co-supervised and mentored students to develop their research and public communication skills.
Advised on epidemiology and statistical practice to non-experts from clinical research, immunology, and bioinformatics.
Prepared scientific manuscripts for publication, presented research findings at conferences, and sought feedback from other attendees. Presented complex technical content to both expert and lay audiences.
Used emerging AI tools including large language models to facilitate scoping literature reviews, code development, and scientific writing.
Achievements
Provided tailored advice to England’s Chief Medical Officer, the CDC, and the Robert Koch Institute on testing and isolation policies for SARS-CoV-2, resulting in a reduced self-isolation period with negative lateral flow tests. This is estimated to have saved the UK economy over £600 million.Coordinated and co-developed a successful grant application which secured a £5.5 million grant for pandemic preparedness research from National Institute for Health and Care Research (NIHR).
Co-founder
from: 2020, until: 2021Organization:Test & Contain (Independent Research Organisation)Location:Oxford, United Kingdom
Description:Researching diagnostic testing strategies against respiratory infections
Honors & Awards
NIHR Career Development Award
date: 2025-03-31Issuer:National Institute for Health and Care Research
Description:Awarded £2600 to attend courses in health economics and infectious disease modelling
Market Shaping Accelerator Innovation Prize in Pandemic Preparedness
date: 2023-08-22Issuer:University of Chicago
Description:Awarded $4000 for my proposal to develop cheap, rapid, easy-to-use diagnostics to respond to the next pandemic
Elected Fellow of the Royal Society of Arts
date: 2023-04-26Issuer: Royal Society for the encouragement of arts, manufactures and commerce
COVID-19 Microgrant
date: 2021-03-21Issuer:Zvi Mowshowitz
Description:Awarded $4,500 to apply reinforcement learning approaches to diagnostic testing strategies during the COVID-19 pandemic
Research grant
date: 2020-08-01Issuer:ACM (supported by Facebook Research)
Description:Received $20,000 to develop group-based testing strategies during the COVID-19 pandemic
Education
Short course
from: 2025, until: presentField of study:Modelling Cost-Effectiveness in HealthcareSchool:London School of EconomicsLocation:London, United Kingdom
DPhil
from: 2016, until: 2021Field of study:PhysicsSchool:University of OxfordLocation:Oxford, United Kingdom
DescriptionLed planning, budgeting and execution of physics experiments at a UK national laboratory. Performed particle-in-cell plasma simulations using a high-performance computer cluster and carried out statistical analysis of large datasets in Python.
MSc
from: 2015, until: 2016Field of study:PhysicsSchool:ETHZLocation:Zurich, Switzerland
DescriptionJoint degree in high energy physics
MSc
from: 2014, until: 2015Field of study:PhysicsSchool:Ecole PolytechniqueLocation:Paris, France
DescriptionJoint degree in high energy physics
BSc
from: 2011, until: 2014Field of study:PhysicsSchool:Uppsala UniversityLocation:Uppsala, Sweden
DescriptionIncluding Erasmus exchange to EPFL in Lausanne, Switzerland
Publications
Measurement of the decay rate of laser-driven linear wakefields
Journal ArticleDate:2025Authors:J JonnerbyJ HollowayAV BoetticherA PicksleyAJ RossC ArranRJ ShallooL CornerSM HookerR WalczakothersEarly de novo T cell expansion following SARS-CoV-2 infection predicts favourable clinical and virological outcomes
Journal ArticlePublisher:EBioMedicineDate:2025Authors:Joe FennAleksandra KoychevaRhia KunduMica Tolosa-WrightLulu WangJanakan Sam NareanEmily ConibearSeran HakkiJakob JonnerbySamuel BaldwinothersInvestigations of Optical Guiding through Hydrodynamic Optical-Field Ionised Plasma Channels
Journal ArticleDate:2025Authors:A PicksleyA AlejoJ CowleyJ JonnerbyAJ RossJ HollowayA BoetticherR WalczakSM HookerL FederothersInferring transmission risk of respiratory viral infection from the viral load kinetics of SARS-CoV-2, England, 2020 to 2021 and influenza A virus, Hong Kong, 2008 to 2012
Journal ArticlePublisher:EurosurveillanceDate:2025Authors:Jakob JonnerbyJoe FennSeran HakkiJie ZhouKieran J MadonAleksandra KoychevaSean NevinRhia KunduMichael A CroneTimesh D PillayothersAuthor’s response: Viral load decline time offers theoretical insight rather than practical value
Journal ArticlePublisher:EurosurveillanceDate:2025Authors:Jakob JonnerbyAjit LalvaniothersAn ultra-early, transient interferon-associated innate immune response associates with protection from SARS-CoV-2 infection despite exposure
Journal ArticlePublisher:EBioMedicineDate:2025Authors:Joe FennKieran MadonEmily ConibearRomain DerelleSean NevinRhia KunduSeran HakkiJohn S TregoningAleksandra KoychevaNieves DerquiothersSusceptibility and infectiousness of SARS-CoV-2 in children versus adults, by variant (wild-type, alpha, delta): A systematic review and meta-analysis of household contact studies
Journal ArticlePublisher:Plos oneDate:2024Authors:Olalekan A UthmanFrederik Plesner LyngseSeun AnjorinBarbara HauerSeran HakkiDiego A MartinezYang GeJakob JonnerbyCathinka Halle JulinGary LinothersRapid emergence of transmissible SARS-CoV-2 variants in mild community cases
Journal ArticlePublisher:Microbiology SpectrumDate:2024Authors:Michael A CroneSeran HakkiJoe FennJie ZhouCarolina Rosadas de OliveiraKieran J MadonAleksandra KoychevaAnjna BadhanJakob JonnerbySean NevinothersMeasurement of the decay of laser-driven linear plasma wakefields
Journal ArticlePublisher:Physical Review EDate:2023Authors:J JonnerbyA BoetticherJ HollowayL CornerA PicksleyAJ RossRJ ShallooC ThorntonN BourgeoisR WalczakothersSARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY. 4.2
Journal ArticlePublisher:BMC infectious diseasesDate:2022Authors:Oliver EalesAndrew J PageLeonardo Oliveira MartinsHaowei WangBarbara BodinierDavid HawJakob JonnerbyChristina AtchisonDeborah Ashbyothers