Retrospective Cohort Study of COVID-19 in Patients of the Brazilian Public Health System with SARS-CoV-2 Omicron Variant Infection.

Several vaccines against COVID-19 are now available, based on different techniques and made by different laboratories spread around the world. With the roll out of the vaccination process in an advanced stage in many countries, the reduced risk of hospitalization due to the Omicron variant relative to the Delta variant infection, despite the higher transmission risk of Omicron, may lead to a misinterpretation of the results, as infection by Omicron is associated with a significant reduction in severe outcomes and shorter hospitalization time than the Delta variant. We compared the in-hospital mortality due to the Omicron (Jan-Mar 2022) with Gamma (Jan 2021) and Delta (Oct-Dec 2021) variants of patients in the Brazilian public health system. This study also discusses the decrease in booster vaccine effectiveness in patients hospitalized due to the Omicron variant compared with the Delta variant. Without a remodeling of vaccines for new variants, booster doses may be necessary with a shorter time interval.

Relating SARS-CoV-2 variants using cellular automata imaging.

We classify the main variants of the SARS-CoV-2 virus representing a given biological sequence coded as a symbolic digital sequence and by its evolution by a cellular automata with a properly chosen rule. The spike protein, common to all variants of the SARS-CoV-2 virus, is then by the picture of the cellular automaton evolution yielding a visible representation of important features of the protein. We use information theory Hamming distance between different stages of the evolution of the cellular automaton for seven variants relative to the original Wuhan/China virus. We show that our approach allows to classify and group variants with common ancestors and same mutations. Although being a simpler method, it can be used as an alternative for building phylogenetic trees.

Optimization of COVID-19 vaccination and the role of individuals with a high number of contacts: A model based approach.

We report strong evidence of the importance of contact hubs (or superspreaders) in mitigating the current COVID-19 pandemic. Contact hubs have a much larger number of contacts than the average in the population, and play a key role on the effectiveness of vaccination strategies. By using an age-structures compartmental SEIAHRV (Susceptible, Exposed, Infected symptomatic, Asymptomatic, Hospitalized, Recovered, Vaccinated) model, calibrated from available demographic and COVID-19 incidence, and considering separately those individuals with a much greater number of contacts than the average in the population, we show that carefully choosing who will compose the first group to be vaccinated can impact positively the total death toll and the demand for health services. This is even more relevant in countries with a lack of basic resources for proper vaccination and a significant reduction in social isolation. In order to demonstrate our approach we show the effect of hypothetical vaccination scenarios in two countries of very different scales and mitigation policies, Brazil and Portugal.