Real-Time Estimation of Rt for Supporting Public-Health Policies Against COVID-19

Contreras, Sebastián; Villavicencio, Humberto; Medina-Ortiz, David; Saavedra, Claudia P.; Olivera-Nappa, Álvaro

doi:10.3389/fpubh.2020.556689

Cited by 25 publications

(28 citation statements)

References 21 publications

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“…Early in the pandemic, the SARS-CoV-2 epidemic in Spain displayed an R t of 2.83 to 2.9, meaning that each case spread to an average of 2 to 3 other exposed persons [ 17 ]. Similar findings were reported for Latin America where early evaluations on the impact of transmission through the first 10 days of the pandemic revealed an exponential growth with an R t greater than 2 [ 16 , 55 ]. Amongst these, Brazil was the country that exhibited the highest R t at the beginning of the pandemic ( R t of 2.96), with Colombia scoring an R t of 2.67, consistent with the results obtained in this study, which is now starting to level-off throughout specific regions ( Figure 4 c,d and Figure S1 ) [ 16 ].…”

Section: Discussionsupporting

confidence: 82%

Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic

et al. 2021

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Current efforts to understand the epidemiology, transmission dynamics and emergence of novel SARS-CoV-2 variants worldwide has enabled the scientific community to generate critical information aimed at implementing disease surveillance and control measures, as well as to reduce the social, economic and health impact of the pandemic. Herein, we applied an epidemic model coupled with genomic analysis to assess the SARS-CoV-2 transmission dynamics in Colombia. This epidemic model allowed to identify the geographical distribution, Rt dynamics and predict the course of the pandemic considering current implementation of countermeasures. The analysis of the incidence rate per 100,000 inhabitants carried out across different regions of Colombia allowed visualizing the changes in the geographic distribution of cases. The cumulative incidence during the timeframe March 2020 to March 2021 revealed that Bogotá (8063.0), Quindío (5482.71), Amazonas (5055.68), Antioquia (4922.35) and Tolima (4724.41) were the departments with the highest incidence rate. The highest median Rt during the first period evaluated was 2.13 and 1.09 in the second period; with this model, we identified improving opportunities in health decision making related to controlling the pandemic, diagnostic testing capacity, case registration and reporting, among others. Genomic analysis revealed 52 circulating SARS-CoV-2 lineages in Colombia detected from 774 genomes sequenced throughout the first year of the pandemic. The genomes grouped into four main clusters and exhibited 19 polymorphisms. Our results provide essential information on the spread of the pandemic countrywide despite implementation of early containment measures. In addition, we aim to provide deeper phylogenetic insights to better understand the evolution of SARS-CoV-2 in light of the latent emergence of novel variants and how these may potentially influence transmissibility and infectivity.

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Section: Discussionsupporting

confidence: 82%

Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic

et al. 2021

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“…For this type of study, it is important to highlight the limitations and hypotheses since media, health authorities, and people can reach wrong conclusions under a variety of scenarios. Nonetheless, the findings are useful to scientifically support health policies [146][147][148][149][150][151][152][153][154][155]. There are several assumptions and limitations in this study.…”

Section: Discussionmentioning

confidence: 90%

Analysis of Delayed Vaccination Regimens: A Mathematical Modeling Approach

González-Parra

2021

Epidemiologia

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The first round of vaccination against coronavirus disease 2019 (COVID-19) began in early December of 2020 in a few countries. There are several vaccines, and each has a different efficacy and mechanism of action. Several countries, for example, the United Kingdom and the USA, have been able to develop consistent vaccination programs where a great percentage of the population has been vaccinated (May 2021). However, in other countries, a low percentage of the population has been vaccinated due to constraints related to vaccine supply and distribution capacity. Countries such as the USA and the UK have implemented different vaccination strategies, and some scholars have been debating the optimal strategy for vaccine campaigns. This problem is complex due to the great number of variables that affect the relevant outcomes. In this article, we study the impact of different vaccination regimens on main health outcomes such as deaths, hospitalizations, and the number of infected. We develop a mathematical model of COVID-19 transmission to focus on this important health policy issue. Thus, we are able to identify the optimal strategy regarding vaccination campaigns. We find that for vaccines with high efficacy (>70%) after the first dose, the optimal strategy is to delay inoculation with the second dose. On the other hand, for a low first dose vaccine efficacy, it is better to use the standard vaccination regimen of 4 weeks between doses. Thus, under the delayed second dose option, a campaign focus on generating a certain immunity in as great a number of people as fast as possible is preferable to having an almost perfect immunity in fewer people first. Therefore, based on these results, we suggest that the UK implemented a better vaccination campaign than that in the USA with regard to time between doses. The results presented here provide scientific guidelines for other countries where vaccination campaigns are just starting, or the percentage of vaccinated people is small.

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“…We obtain a data-driven value for the observed

, adapting the methodology presented in Contreras et al. [17] , Medina-Ortiz et al. [34] :

…”

Section: Resultsmentioning

confidence: 99%

On the heterogeneous spread of COVID-19 in Chile

Freire-Flores

Llanovarced-Kawles

Sanchez-Daza

et al. 2021

Chaos, Solitons & Fractals

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Non-pharmaceutical interventions (NPIs) have played a crucial role in controlling the spread of COVID-19. Nevertheless, NPI efficacy varies enormously between and within countries, mainly because of population and behavioral heterogeneity. In this work, we adapted a multi-group SEIRA model to study the spreading dynamics of COVID-19 in Chile, representing geographically separated regions of the country by different groups. We use national mobilization statistics to estimate the connectivity between regions and data from governmental repositories to obtain COVID-19 spreading and death rates in each region. We then assessed the effectiveness of different NPIs by studying the temporal evolution of the reproduction number . Analyzing data-driven and model-based estimates of , we found a strong coupling of different regions, highlighting the necessity of organized and coordinated actions to control the spread of SARS-CoV-2. Finally, we evaluated different scenarios to forecast the evolution of COVID-19 in the most densely populated regions, finding that the early lifting of restriction probably will lead to novel outbreaks.

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Real-Time Estimation of Rt for Supporting Public-Health Policies Against COVID-19

Cited by 25 publications

References 21 publications

Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic

Evolution and Epidemic Spread of SARS-CoV-2 in Colombia: A Year into the Pandemic

Analysis of Delayed Vaccination Regimens: A Mathematical Modeling Approach

On the heterogeneous spread of COVID-19 in Chile

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