Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights.

Background: Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants. Materials and methods: We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility ( Δ ß ) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants. Results: Our model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Δ ß between variants, revealing that: ( i ) Δ ß increased progressively from the Alpha to the Omicron variant; ( i i ) Δ ß showed a high degree of variability within Omicron variants; ( i i i ) a higher Δ ß was associated with a later emergence of the variant within a country; ( i v ) a higher degree of immunization of the population against previous variants was associated with a higher Δ ß for the Delta variant; ( v ) larger countries exhibited smaller Δ ß , suggesting regionally diverse outbreaks within the same country; and finally ( v i ) the model reliably captures the dynamics of competing variants, even in complex scenarios. Conclusion: The use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Δ ß , we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries.

Severity of Omicron Subvariants and Vaccine Impact in Catalonia, Spain.

In the current COVID-19 landscape dominated by Omicron subvariants, understanding the timing and efficacy of vaccination against emergent lineages is crucial for planning future vaccination campaigns, yet detailed studies stratified by subvariant, vaccination timing, and age groups are scarce. This retrospective study analyzed COVID-19 cases from December 2021 to January 2023 in Catalonia, Spain, focusing on vulnerable populations affected by variants BA.1, BA.2, BA.5, and BQ.1 and including two national booster campaigns. Our database includes detailed information such as dates of diagnosis, hospitalization and death, last vaccination, and cause of death, among others. We evaluated the impact of vaccination on disease severity by age, variant, and vaccination status, finding that recent vaccination significantly mitigated severity across all Omicron subvariants, although efficacy waned six months post-vaccination, except for BQ.1, which showed more stable levels. Unvaccinated individuals had higher hospitalization and mortality rates. Our results highlight the importance of periodic vaccination to reduce severe outcomes, which are influenced by variant and vaccination timing. Although the seasonality of COVID-19 is uncertain, our analysis suggests the potential benefit of annual vaccination in populations >60 years old, probably in early fall, if COVID-19 eventually exhibits a major peak similar to other respiratory viruses.

DNMR measurements of an asymmetric odd liquid crystal dimer: determination of the intramolecular angle and the degree of order of the two rigid cores.

In this work, we present a Deuteron Nuclear Magnetic Resonance (DNMR) study of the non-symmetric odd liquid crystal dimer α-(4-cyanobiphenyl-4'-yloxy)-ω-(1-pyrenimine-benzylidene-4'-oxy) heptane (CBO7O.Py), formed by a pro-mesogenic cyanobiphenyl unit and a bulky pyrene-containing unit, linked via alkoxy flexible chain. We have synthesized two partially deuterated samples: one with the deuterium atoms in the cyanobiphenyl moiety (dCBO7O.Py) and the other one with the deuterium atoms in the pyrenimine-benzylidene unit (CBO7O.dPy). We have performed angular distribution analysis in the SmA glassy state, obtaining the degree of order of both rigid cores and an estimation of the internal molecular angle between both structures. With the results from the angular study, we have been able to determine the degree of order of both rigid units in either the N phase and the SmA phase, far enough from the glass transition. Both rigid cores have the same degree of order close to the nematic-isotropic phase transition, but as the compound is cooled down, the degree of order of the cyanobiphenyl moiety is clearly higher than that of the pyrene-containing unit. The critical behaviour of the order parameter of the pyrene-containing moiety is consistent with the fact that, for CBO7O.Py, the N-I phase transition is tricritical, which seems to indicate that the uniaxial order parameter of the dimer is dominated by the degree of order of the pyrene-containing core.

A semi-empirical risk panel to monitor epidemics: multi-faceted tool to assist healthcare and public health professionals.

Introduction: Bronchiolitis, mostly caused by Respiratory Syncytial Virus (RSV), and influenza among other respiratory infections, lead to seasonal saturation at healthcare centers in temperate areas. There is no gold standard to characterize the stages of epidemics, nor the risk of respiratory infections growing. We aimed to define a set of indicators to assess the risk level of respiratory viral epidemics, based on both incidence and their short-term dynamics, and considering epidemical thresholds. Methods: We used publicly available data on daily cases of influenza for the whole population and bronchiolitis in children <2 years from the Information System for Infection Surveillance in Catalonia (SIVIC). We included a Moving Epidemic Method (MEM) variation to define epidemic threshold and levels. We pre-processed the data with two different nowcasting approaches and performed a 7-day moving average. Weekly incidences (cases per 105 population) were computed and the 5-day growth rate was defined to create the effective potential growth (EPG) indicator. We performed a correlation analysis to define the forecasting ability of this index. Results: Our adaptation of the MEM method allowed us to define epidemic weekly incidence levels and epidemic thresholds for bronchiolitis and influenza. EPG was able to anticipate daily 7-day cumulative incidence by 4-5 (bronchiolitis) or 6-7 (influenza) days. Discussion: We developed a semi-empirical risk panel incorporating the EPG index, which effectively anticipates surpassing epidemic thresholds for bronchiolitis and influenza. This panel could serve as a robust surveillance tool, applicable to respiratory infectious diseases characterized by seasonal epidemics, easy to handle for individuals lacking a mathematical background.

A mathematical approach to virus therapy of glioblastomas.

BACKGROUND: It is widely believed that the treatment of glioblastomas (GBM) could benefit from oncolytic virus therapy. Clinical research has shown that Vesicular Stomatitis Virus (VSV) has strong oncolytic properties. In addition, mathematical models of virus treatment of tumors have been developed in recent years. Some experiments in vitro and in vivo have been done and shown promising results, but have been never compared quantitatively with mathematical models. We use in vitro data of this virus applied to glioblastoma. RESULTS: We describe three increasingly realistic mathematical models for the VSV-GBM in vitro experiment with progressive incorporation of time-delay effects. For the virus dynamics, we obtain results consistent with the in vitro experimental speed data only when applying the more complex and comprehensive model, with time-delay effects both in the reactive and diffusive terms. The tumor speed is given by the minimum of a very simple function that nonetheless yields results within the experimental measured range. CONCLUSIONS: We have improved a previous model with new ideas and carefully incorporated concepts from experimental results. We have shown that the delay time τ is the crucial parameter in this kind of models. We have demonstrated that our new model can satisfactorily predict the front speed for the lytic action of oncolytic VSV on glioblastoma observed in vitro. We provide a basis that can be applied in the near future to realistically simulate in vivo virus treatments of several cancers.