Risk assessment of COVID-19 epidemic resurgence in relation to SARS-CoV-2 variants and vaccination passes

The introduction of COVID-19 vaccination passes (VPs) by many countries coincided with the Delta variant fast becoming dominant across Europe. A thorough assessment of their impact on epidemic dynamics is still lacking. Here, we propose the VAP-SIRS model that considers possibly lower restrictions for the VP holders than for the rest of the population, imperfect vaccination effectiveness against infection, rates of (re-)vaccination and waning immunity, fraction of never-vaccinated, and the increased transmissibility of the Delta variant. Some predicted epidemic scenarios for realistic parameter values yield new COVID-19 infection waves within two years, and high daily case numbers in the endemic state, even without introducing VPs and granting more freedom to their holders. Still, suitable adaptive policies can avoid unfavorable outcomes. While VP holders could initially be allowed more freedom, the lack of full vaccine effectiveness and increased transmissibility will require accelerated (re-)vaccination, wide-spread immunity surveillance, and/or minimal long-term common restrictions

National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021

We compare forecasts of weekly case and death numbers for COVID-19 in Germany and Poland based on 15 different modelling approaches. These cover the period from January to April 2021 and address numbers of cases and deaths one and two weeks into the future, along with the respective uncertainties. We find that combining different forecasts into one forecast can enable better predictions. However, case numbers over longer periods were challenging to predict. Additional data sources, such as information about different versions of the SARS-CoV-2 virus present in the population, might improve forecasts in the future

Risk of COVID-19 epidemic resurgence with the introduction of vaccination passes

Many countries hit by the COVID-19 epidemic consider the introduction of vaccination passes. So far, no thorough impact assessment of vaccination passes and of lower restrictions for their holders has been conducted. Here, we propose the VAP-SIRS model that accounts for susceptible, infected, and recovered subpopulations, also within the group of vaccinated pass holders. The model accounts for imperfect vaccination effectiveness, revaccinations and waning immunity. Different restrictions for pass holders and the rest of the population result in different scenarios of the epidemic evolution, some of which yield unfavourable COVID-19 dynamics and new waves. We identify critical variables that should be considered by policymakers and show how unfavourable outcomes can be avoided using adaptive policies. In particular, while pass holders could initially be allowed large freedoms, the gradual loss of immunity will require either increased restrictions for pass holders, or accelerated revaccination. In the long-term, common restrictions for both the pass holders and the rest of the population will have to be kept to avoid epidemic resurgence. Such minimum required restrictions depend on vaccination effectiveness, revaccination rate, waning rate and fraction of never-vaccinated population, and, for realistic combinations of these parameters, range between 29% and 69% reduction of contacts

A robust algorithm for segmenting and tracking clustered cells in time-lapse fluorescent microscopy

We present herein a robust algorithm for cell tracking in a sequence of time-lapse 2-D fluorescent microscopy images. Tracking is performed automatically via a multiphase active contours algorithm adapted to the segmentation of clustered nuclei with obscure boundaries. An ellipse fitting method is applied to avoid problems typically associated with clustered, overlapping, or dying cells, and to obtain more accurate segmentation and tracking results. We provide quantitative validation of results obtained with this new algorithm by comparing them to the results obtained from the established CellProfiler, MTrack2 (plugin for Fiji), and LSetCellTracker software

Vaccination passes: Chariot to freedom or a Trojan horse?

An interdisciplinary collaboration to provide model-based evidence to inform policy decisions on vaccination passes and on how they shape pandemic dynamics. Do they allow us to safely navigate epidemic waves? Or can they prove treacherous, compromising all sacrifices and efforts previously made

Risk assessment of COVID-19 epidemic resurgence in relation to SARS-CoV-2 variants and vaccination passes

The introduction of COVID-19 vaccination passes (VPs) by many countries coincided with the Delta variant fast becoming dominant across Europe. A thorough assessment of their impact on epidemic dynamics is still lacking. Here, we propose the VAPSIRS model that considers possibly lower restrictions for the VP holders than for the rest of the population, imperfect vaccination effectiveness against infection, rates of (re-)vaccination and waning immunity, fraction of never-vaccinated, and the increased transmissibility of the Delta variant. Some predicted epidemic scenarios for realistic parameter values yield new COVID-19 infection waves within two years, and high daily case numbers in the endemic state, even without introducing VPs and granting more freedom to their holders. Still, suitable adaptive policies can avoid unfavorable outcomes. While VP holders could initially be allowed more freedom, the lack of full vaccine effectiveness and increased transmissibility will require accelerated (re-)vaccination, wide-spread immunity surveillance, and/or minimal long-term common restrictions.peer-reviewe

Threshold-based epidemic dynamics in systems with memory

In this article we analyze an epidemic dynamics model (SI) where we assume that there are k susceptible states, that is a node would require multiple $(k)$ contacts before it gets infected. In specific, we provide a theoretical framework for studying diffusion rate in complete graphs and d-regular trees with extensions to dense random graphs. We observe that irrespective of the topology, the diffusion process could be divided into two distinct phases: i) the initial phase, where the diffusion process is slow, followed by ii) the residual phase where the diffusion rate increases manifold. In fact, the initial phase acts as an indicator for the total diffusion time in dense graphs. The most remarkable lesson from this investigation is that such a diffusion process could be controlled and even contained if acted upon within its initial phase

Estimation of the Severeness Rate, Death Rate, Household Attack Rate and the Total Number of COVID-19 Cases Based on 16 115 Polish Surveillance Records

Background: Estimating the actual number of COVID-19 infections is crucial for steering through the COVID-19 pandemic crisis. It is, however, notoriously difficult, as many cases have no or only mild symptoms. Surveillance data for in-household secondary infections offers unbiased samples for COVID-19 prevalence estimation. Methods: We analyse 16 115 Polish surveillance records to obtain key figures of the COVID-19 pandemic. We propose conservative upper and lower bound estimators for the number of SARS-CoV-2 infections. Further, we estimate age-dependent bounds on the severe case rate, death rate, and the in-household attack rate. Results: By maximum likelihood estimates, the total number of COVID-19 cases in Poland as of July 22nd, 2020, is at most around 13 times larger and at least 1.6 times larger than the recorded number. The lower bound on the severeness rate ranges between 0.2% for the 0–39 year-old to 5.7% for older than 80, while the upper bound is between 2.6% and 34.1%. The lower bound on the death rate is between 0.04% for the age group 40–59 to 1.34% for the oldest. Overall, the severeness and death rates grow exponentially with age. The in-household attack ratio is 8.18% for the youngest group and 16.88% for the oldest. Conclusions: The proposed approach derives highly relevant figures on the COVID-19 pandemic from routine surveillance data, under assumption that household members of detected infected are tested and all severe cases are diagnosed.MedRxiv</p

National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021

We compare forecasts of weekly case and death numbers for COVID-19 in Germany and Poland based on 15 different modelling approaches. These cover the period from January to April 2021 and address numbers of cases and deaths one and two weeks into the future, along with the respective uncertainties. We find that combining different forecasts into one forecast can enable better predictions. However, case numbers over longer periods were challenging to predict. Additional data sources, such as information about different versions of the SARS-CoV-2 virus present in the population, might improve forecasts in the future