arXiv subjects

Jakob Jonnerby

Publications and source records attributed to Jakob Jonnerby.

4 recordsLinked to original sources

arXiv2026

Inferring infectiousness: a joint model of the within-host viral kinetics of SARS-CoV-2

During an infectious disease outbreak, providing accurate answers to policy questions about transmission requires a detailed model of the natural history of infectiousness. Unfortunately, direct measures of infectiousness are generally unavailable. Instead, we often rely on indirect proxies, such as viral load measured by PCR or antigen tests, viral culture to detect replication-competent virus, or symptom onset, each of which reflects different aspects of viral dynamics or host response. However, these proxies vary in terms of the ease of collection, scalability, and their relationship to viral shedding and therefore underlying infectiousness. Here, we use data from five prospective, densely sampled cohorts with longitudinal data on multiple proxies of viral shedding for approximately 2,000 infections to develop a Bayesian joint model for the within-host viral kinetics of SARS-CoV-2 infection. Modeling the joint distribution allows us to infer the trajectory of infectious virus shedding -- the most direct correlate of infectiousness -- for individuals who contribute only PCR data, and to compute derived quantities that are inaccessible from any single proxy alone. These include the population-level probability and expected duration of ongoing infectiousness as a function of time since diagnosis, stratified by variant, vaccination status, and infection history; the residual risk of releasing an individual from isolation; and personalized, real-time estimates of infectiousness that are sequentially updated as new test results become available.

stat.ME↗

arXiv2023

Optimal Testing and Containment Strategies for Universities in Mexico amid COVID-19

This work sets out a testing and containment framework developed for reopening universities in Mexico following the lockdown due to COVID-19. We treat diagnostic testing as a resource allocation problem and develop a testing allocation mechanism and practical web application to assist educational institutions in making the most of limited testing resources. In addition to the technical results and tools, we also provide a reflection on our current experience of running a pilot of our framework within the Instituto Tecnológico y de Estudios Superiores de Monterrey (ITESM), a leading private university in Mexico, as well as on our broader experience bridging research with academic policy in the Mexican context.

cs.GT↗

arXiv2020

Maximising the Benefits of an Acutely Limited Number of COVID-19 Tests

We propose a novel testing and containment strategy in order to contain the spread of SARS-CoV2 while permitting large parts of the population to resume social and economic activity. Our approach recognises the fact that testing capacities are severely constrained in many countries. In this setting, we show that finding the best way to utilise this limited number of tests during a pandemic can be formulated concisely as an allocation problem. Our problem formulation takes into account the heterogeneity of the population and uses pooled testing to identify and isolate individuals while prioritising key workers and individuals with a higher risk of spreading the disease. In order to demonstrate the efficacy of our testing and containment mechanism, we perform simulations using a network-based SIR model. Our simulations indicate that applying our mechanism on a population of $100,000$ individuals with only $16$ tests per day reduces the peak number of infected individuals by approximately $20\%$, when compared to the scenario where no intervention is implemented.

q-bio.PE↗

arXiv2019

Hydrodynamic, Optically-Field-Ionized (HOFI) Plasma Channels

We present experiments and numerical simulations which demonstrate that fully-ionized, low-density plasma channels could be formed by hydrodynamic expansion of plasma columns produced by optical field ionization (OFI). Simulations of the hydrodynamic expansion of plasma columns formed in hydrogen by an axicon lens show the generation of \unit[200]{mm} long plasma channels with axial densities of order $n_e(0) = 1 \times 10^{17} cm^{-3}$ and lowest-order modes of spot size $W_M \approx 40 μm$. These simulations show that the laser energy required to generate the channels is modest: of order 1 mJ per centimetre of channel. The simulations are confirmed by experiments with a spherical lens which show the formation of short plasma channels with $1.5 \times 10^{17}cm^{-3} \lesssim n_e(0) \lesssim 1 \times 10^{18} cm^{-3}$ and $61 μm \gtrsim W_M \gtrsim 33 μm$. Low-density plasma channels of this type would appear to be well-suited as multi-GeV laser-plasma accelerator stages capable of long-term operation at high pulse repetition rates.

physics.plasm-ph↗