Population mobility, well-mixed clustering and disease spread: a look at COVID-19 Spread in the United States and preventive policy insights.

The epidemiology of pandemics is classically viewed using geographical and political borders; however, these artificial divisions can result in a misunderstanding of the current epidemiological state within a given region. To improve upon current methods, we propose a clustering algorithm which is capable of recasting regions into well-mixed clusters such that they have a high level of interconnection while minimizing the external flow of the population towards other clusters. Moreover, we analyze and identify so-called core clusters, clusters that retain their features over time (temporally stable) and independent of the presence or absence of policy measures. In order to demonstrate the capabilities of this algorithm, we use USA county-level cellular mobility data to divide the country into such clusters. Herein, we show a more granular spread of SARS-CoV-2 throughout the first weeks of the pandemic. Moreover, we are able to identify areas (groups of counties) that were experiencing above average levels of transmission within a state, as well as pan-state areas (clusters overlapping more than one state) with very similar disease spread. Therefore, our method enables policymakers to make more informed decisions on the use of public health interventions within their jurisdiction, as well as guide collaboration with surrounding regions to benefit the general population in controlling the spread of communicable diseases.

Maritime transportation and people mobility in the early diffusion of COVID-19 in Croatia.

Introduction: The outbreak of COVID-19 in Europe began in early 2020, leading to the emergence of several waves of infection with varying timings across European countries. The largest wave of infection occurred in August-September. Croatia, known for being a hotspot of tourism in the Mediterranean region, raised concerns that it might have played a role in incubating the pandemic during the summer of 2020. Methods: To investigate this possibility, we conducted a data-driven study to examine the potential influence of passenger mobility to and within Croatia, utilizing various modes of transportation. To achieve this, we integrated observational datasets into the "epidemic Renormalization Group" modeling framework. Results: By comparing the models with epidemiological data, we found that in the case of Croatia in 2020, neither maritime nor train transportation played a prominent role in propagating the infection. Instead, our analysis highlighted the leading role of both road and airborne mobility in the transmission of the virus. Discussion: The proposed framework serves to test hypotheses concerning the causation of infectious waves, offering the capacity to rule out unrelated factors from consideration.

The quantification of vaccine uptake in the Nordic countries and impact on key indicators of COVID-19 severity and healthcare stress level via age range comparative analysis.

In this paper we analyze the impact of vaccinations on spread of the COVID-19 virus for different age groups. More specifically, we examine the deployment of vaccines in the Nordic countries in a comparative analysis where we focus on factors such as healthcare stress level and severity of disease through new infections, hospitalizations, intensive care unit (ICU) occupancy and deaths. Moreover, we analyze the impact of the various vaccine types, vaccination rate on the spread of the virus in each age group for Denmark, Finland, Iceland, Norway and Sweden from the start of the vaccination period in December 2020 until the end of September 2021. We perform a threefold analysis: (i) frequency analysis of infections and vaccine rates by age groups; (ii) rolling correlations between vaccination strategies, severity of COVID-19 and healthcare stress level and; (iii) we also employ the epidemic Renormalization Group (eRG) framework. The eRG is used to mathematically model wave structures, as well as the impact of vaccinations on wave dynamics. We further compare the Nordic countries with England. Our main results outline the quantification of the impact of the vaccination campaigns on age groups epidemiological data, across countries with high vaccine uptake. The data clearly shows that vaccines markedly reduce the number of new cases and the risk of serious illness.

Variant-driven early warning via unsupervised machine learning analysis of spike protein mutations for COVID-19.

Never before such a vast amount of data, including genome sequencing, has been collected for any viral pandemic than for the current case of COVID-19. This offers the possibility to trace the virus evolution and to assess the role mutations play in its spread within the population, in real time. To this end, we focused on the Spike protein for its central role in mediating viral outbreak and replication in host cells. Employing the Levenshtein distance on the Spike protein sequences, we designed a machine learning algorithm yielding a temporal clustering of the available dataset. From this, we were able to identify and define emerging persistent variants that are in agreement with known evidences. Our novel algorithm allowed us to define persistent variants as chains that remain stable over time and to highlight emerging variants of epidemiological interest as branching events that occur over time. Hence, we determined the relationship and temporal connection between variants of interest and the ensuing passage to dominance of the current variants of concern. Remarkably, the analysis and the relevant tools introduced in our work serve as an early warning for the emergence of new persistent variants once the associated cluster reaches 1% of the time-binned sequence data. We validated our approach and its effectiveness on the onset of the Alpha variant of concern. We further predict that the recently identified lineage AY.4.2 ('Delta plus') is causing a new emerging variant. Comparing our findings with the epidemiological data we demonstrated that each new wave is dominated by a new emerging variant, thus confirming the hypothesis of the existence of a strong correlation between the birth of variants and the pandemic multi-wave temporal pattern. The above allows us to introduce the epidemiology of variants that we described via the Mutation epidemiological Renormalisation Group framework.

Epidemiological theory of virus variants.

We propose a physics-inspired mathematical model underlying the temporal evolution of competing virus variants that relies on the existence of (quasi) fixed points capturing the large time scale invariance of the dynamics. To motivate our result we first modify the time-honoured compartmental models of the SIR type to account for the existence of competing variants and then show how their evolution can be naturally re-phrased in terms of flow equations ending at quasi fixed points. As the natural next step we employ (near) scale invariance to organise the time evolution of the competing variants within the effective description of the epidemic Renormalisation Group framework. We test the resulting theory against the time evolution of COVID-19 virus variants that validate the theory empirically.

Impact of US vaccination strategy on COVID-19 wave dynamics.

We employ the epidemic Renormalization Group (eRG) framework to understand, reproduce and predict the COVID-19 pandemic diffusion across the US. The human mobility across different geographical US divisions is modelled via open source flight data alongside the impact of social distancing for each such division. We analyse the impact of the vaccination strategy on the current pandemic wave dynamics in the US. We observe that the ongoing vaccination campaign will not impact the current pandemic wave and therefore strict social distancing measures must still be enacted. To curb the current and the next waves our results indisputably show that vaccinations alone are not enough and strict social distancing measures are required until sufficient immunity is achieved. Our results are essential for a successful vaccination strategy in the US.

Multiwave pandemic dynamics explained: how to tame the next wave of infectious diseases.

Pandemics, like the 1918 Spanish Influenza and COVID-19, spread through regions of the World in subsequent waves. Here we propose a consistent picture of the wave pattern based on the epidemic Renormalisation Group (eRG) framework, which is guided by the global symmetries of the system under time rescaling. We show that the rate of spreading of the disease can be interpreted as a time-dilation symmetry, while the final stage of an epidemic episode corresponds to reaching a time scale-invariant state. We find that the endemic period between two waves is a sign of instability in the system, associated to near-breaking of the time scale-invariance. This phenomenon can be described in terms of an eRG model featuring complex fixed points. Our results demonstrate that the key to control the arrival of the next wave of a pandemic is in the strolling period in between waves, i.e. when the number of infections grows linearly. Thus, limiting the virus diffusion in this period is the most effective way to prevent or delay the arrival of the next wave. In this work we establish a new guiding principle for the formulation of mid-term governmental strategies to curb pandemics and avoid recurrent waves of infections, deleterious in terms of human life loss and economic damage.

Mining Google and Apple mobility data: temporal anatomy for COVID-19 social distancing.

We employ the Google and Apple mobility data to identify, quantify and classify different degrees of social distancing and characterise their imprint on the first wave of the COVID-19 pandemic in Europe and in the United States. We identify the period of enacted social distancing via Google and Apple data, independently from the political decisions. Our analysis allows us to classify different shades of social distancing measures for the first wave of the pandemic. We observe a strong decrease in the infection rate occurring two to five weeks after the onset of mobility reduction. A universal time scale emerges, after which social distancing shows its impact. We further provide an actual measure of the impact of social distancing for each region, showing that the effect amounts to a reduction by 20-40% in the infection rate in Europe and 30-70% in the US.

Second wave COVID-19 pandemics in Europe: a temporal playbook.

A second wave pandemic constitutes an imminent threat to society, with a potentially immense toll in terms of human lives and a devastating economic impact. We employ the epidemic Renormalisation Group (eRG) approach to pandemics, together with the first wave data for COVID-19, to efficiently simulate the dynamics of disease transmission and spreading across different European countries. The framework allows us to model, not only inter and extra European border control effects, but also the impact of social distancing for each country. We perform statistical analyses averaging on different level of human interaction across Europe and with the rest of the World. Our results are neatly summarised as an animation reporting the time evolution of the first and second waves of the European COVID-19 pandemic. Our temporal playbook of the second wave pandemic can be used by governments, financial markets, the industries and individual citizens, to efficiently time, prepare and implement local and global measures.