Mathematical modeling and impact analysis of the use of COVID Alert SA app.
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ABSTRACT:
SUBMITTER: Kinyili M
PROVIDER: S-EPMC8755967 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectivesWe analyzed the effectiveness of the Canadian COVID Alert app on reducing COVID-19 infections and deaths due to the COVID-19 virus.MethodsTwo separate but complementary approaches were taken. First, we undertook a comparative study to assess how the adoption and usage of the COVID Alert app compared to those of similar apps deployed in other regions. Next, we used data from the COVID Alert server and a range of plausible parameter values to estimate the numbers of infections and deaths averted in Canada using a model that combines information on number of notifications, secondary attack rate, expected fraction of transmissions that could be prevented, quarantine effectiveness, and expected size of the full transmission chain in the absence of exposure notification.ResultsThe comparative analysis revealed that the COVID Alert app had among the lowest adoption levels among apps that reported usage. Our model indicates that use of the COVID Alert app averted between 6284 and 10,894 infections across the six Canadian provinces where app usage was highest during the March-July 2021 period. This range is equivalent to 1.6-2.9% of the total recorded infections across Canada in that time. Using province-specific case fatality rates, 57-101 deaths were averted during the same period. The number of cases and deaths averted was greatest in Ontario, whereas the proportion of cases and deaths averted was greatest in Newfoundland and Labrador. App impact measures were reported so rarely and so inconsistently by other regions that the relative assessment of impact is inconclusive.ConclusionWhile the nationwide rates are low, provinces with widespread adoption of the app showed high ratios of averted cases and deaths (upper bound was greater than 60% of averted cases). This finding suggests that the COVID Alert app, when adopted at sufficient levels, can be an effective public health tool for combatting a pandemic such as COVID-19.
| S-EPMC9172601 | biostudies-literature
Project description:Prior to vaccination or drug treatment, non-pharmaceutical interventions were almost the only way to control the coronavirus disease 2019 (COVID-19) epidemic. After vaccines were developed, effective vaccination strategies became important. The prolonged COVID-19 pandemic has caused enormous economic losses worldwide. As such, it is necessary to estimate the economic effects of control policies, including non-pharmaceutical interventions and vaccination strategies. We estimated the costs associated with COVID-19 according to different vaccination rollout speeds and social distancing levels and investigated effective control strategies for cost minimization. Age-structured mathematical models were developed and used to study disease transmission epidemiology. Using these models, we estimated the actual costs due to COVID-19, considering costs associated with medical care, lost wages, death, vaccination, and gross domestic product (GDP) losses due to social distancing. The lower the social distancing (SD) level, the more important the vaccination rollout speed. SD level 1 was cost-effective under fast rollout speeds, but SD level 2 was more effective for slow rollout speeds. If the vaccine rollout rate is fast enough, even implementing SD level 1 will be cost effective and can control the number of critically ill patients and deaths. If social distancing is maintained at level 2 at the beginning and then relaxed when sufficient vaccinations have been administered, economic costs can be reduced while maintaining the number of patients with severe symptoms below the intensive care unit (ICU) capacity. Korea has wellequipped medical facilities and infrastructure for rapid vaccination, and the public's desire for vaccination is high. In this case, the speed of vaccine supply is an important factor in controlling the COVID-19 epidemic. If the speed of vaccination is fast, it is possible to maintain a low level of social distancing without a significant increase in the number of deaths and hospitalized patients with severe symptoms, and the corresponding costs can be reduced.
| S-EPMC9512395 | biostudies-literature
Project description:Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. In this study, we refined the previously published mathematical model for bloodstream form parasites and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Through this study, we conclude that lLevels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting acquisition of new control mechanisms during adaptation to mammalian parasitism. Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro PCF and in duplicate from in vitro T. brucei Lister427, to understand global differntial gene transcription.
2016-03-16 | E-GEOD-79208 | biostudies-arrayexpress
Project description:IntroductionPrevention of mother-to-child HIV transmission (PMTCT) strategies include combined short-course antiretrovirals during pregnancy (Option A), triple-drug antiretroviral treament (ART) during pregnancy and breastfeeding (Option B), or lifelong ART (Option B+). The WHO also recommends ART for HIV treatment and prevention of sexual transmission of HIV. The impact of PMTCT strategies on prevention of sexual HIV transmission of HIV is not known. We estimated the population-level impact of PMTCT interventions on heterosexual HIV transmission in southwestern Uganda and KwaZulu-Natal, South Africa, two regions with different HIV prevalence and fertility rates.Materials and methodsWe constructed and validated dynamic, stochastic, network-based HIV transmission models for each region. PMTCT Options A, B, and B+ were simulated over ten years under three scenarios: 1) current ART and PMTCT coverage, 2) current ART and high PMTCT coverage, and 3) high ART and PMTCT coverage. We compared adult HIV incidence after ten years of each intervention to Option A (and current ART) at current coverage.ResultsAt current coverage, Options B and B+ reduced heterosexual HIV incidence by about 5% and 15%, respectively, in both countries. With current ART and high PMTCT coverage, Option B+ reduced HIV incidence by 35% in Uganda and 19% in South Africa, while Option B had smaller, but meaningful, reductions. The greatest reductions in HIV incidence were achieved with high ART and PMTCT coverage. In this scenario, all PMTCT strategies yielded similar results.DiscussionImplementation of Options B/B+ reduces adult HIV incidence, with greater effect (relative to Option A at current levels) in Uganda than South Africa. These results are likely driven by Uganda's higher fertility rates.
| S-EPMC4532442 | biostudies-literature
Project description:Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. In this study, we refined the previously published mathematical model for bloodstream form parasites and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Through this study, we conclude that lLevels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting acquisition of new control mechanisms during adaptation to mammalian parasitism.
2016-03-16 | GSE79208 | GEO
Project description:IntroductionDiagnostic tests can play an important role in reducing the transmission of infectious respiratory diseases, particularly during a pandemic. The potential benefit of diagnostic testing depends on at least 4 factors: (1) how soon testing becomes available after the beginning of the pandemic and (2) at what capacity; (3) compliance with isolation after testing positive; and (4) compliance with isolation when experiencing symptoms, even in the absence of testing.MethodsTo understand the interplay between these factors and provide further insight into policy decisions for future pandemics, we developed a compartmental model and simulated numerous scenarios using the dynamics of COVID-19 as a case study.ResultsOur results quantified the significant benefits of early start of testing and high compliance with isolation. Early start of testing, even with low testing capacity over time, could significantly slow down the disease spread if compliance with isolation is high. By contrast, when the start of testing was delayed, the benefit of testing on reducing infection spread was limited, even when testing capacity was high; the additional testing capacity required increased superlinearly for each day of delay to achieve a similar infection attack rate as in starting testing earlier.ConclusionsOur study highlighted the importance of the early start of testing and public health messaging to promote isolation compliance when needed for an ongoing effective response to COVID-19 and future pandemics.
| S-EPMC9119710 | biostudies-literature
Project description:This study started from the request of providing predictions on hospitalization and Intensive Care Unit (ICU) rates that are caused by COVID-19 for the Umbria region in Italy. To this purpose, we propose the application of a computational framework to a SEIR-type (Susceptible, Exposed, Infected, Removed) epidemiological model describing the different stages of COVID-19 infection. The model discriminates between asymptomatic and symptomatic cases and it takes into account possible intervention measures in order to reduce the probability of transmission. As case studies, we analyze not only the epidemic situation in Umbria but also in Italy, in order to capture the evolution of the pandemic at a national level. First of all, we estimate model parameters through a Bayesian calibration method, called Conditional Robust Calibration (CRC), while using the official COVID-19 data of the Italian Civil Protection. Subsequently, Conditional Robustness Analysis (CRA) on the calibrated model is carried out in order to quantify the influence of epidemiological and intervention parameters on the hospitalization rates. The proposed pipeline properly describes the COVID-19 spread during the lock-down phase. It also reveals the underestimation of new positive cases and the need of promptly isolating asymptomatic and presymptomatic cases. The results emphasize the importance of the lock-down timeliness and provide accurate predictions on the current evolution of the pandemic.
| S-EPMC7697740 | biostudies-literature
Project description:With the recent licensure of mRNA vaccines against COVID-19 in the 5- to 11-year-old age group, the public health impact of a childhood immunization campaign is of interest. Using a mathematical epidemiological model, we project that childhood vaccination carries minimal risk and yields modest public health benefits. These include large relative reductions in child morbidity and mortality, although the absolute reduction is small because these events are rare. Furthermore, the model predicts "altruistic" absolute reductions in adult cases, hospitalizations, and mortality. However, vaccinating children to benefit adults should be considered from an ethical as well as a public health perspective. From a global health perspective, an additional ethical consideration is the justice of giving priority to children in high-income settings at low risk of severe disease while vaccines have not been made available to vulnerable adults in low-income settings. IMPORTANCE Countries have recently begun implementation of childhood vaccination against SARS-CoV-2 with the Pfizer/BioNTech mRNA vaccine in children 5 to 11 years of age. Because SARS-CoV-2 disease severity is remarkably age dependent, vaccinating children may have modest public health benefits, relative to the unequivocal benefit of vaccinating vulnerable older adults. Furthermore, vaccinating children to "altruistically" increase herd immunity should be considered from an ethical as well as a public health perspective. An additional question is related to global social justice: should priority be given to vaccinating children in high-income settings while older adult populations in low-resource settings have limited access to vaccine? To address the risks and benefits of childhood vaccination, we provide a balanced commentary, supported by a mathematical epidemiological model, using Australia and Alberta, Canada, as case studies. We give highlights of the modeling findings in the commentary and include details in the supplemental materials for interested readers.
| S-EPMC8764932 | biostudies-literature
Project description:This study aims to inform SARS-CoV-2 vaccine development/licensure/decision-making/implementation, using mathematical modeling, by determining key preferred vaccine product characteristics and associated population-level impacts of a vaccine eliciting long-term protection. A prophylactic vaccine with efficacy against acquisition (VES) ?70% can eliminate the infection. A vaccine with VES <70% may still control the infection if it reduces infectiousness or infection duration among those vaccinated who acquire the infection, if it is supplemented with <20% reduction in contact rate, or if it is complemented with herd-immunity. At VES of 50%, the number of vaccinated persons needed to avert one infection is 2.4, and the number is 25.5 to avert one severe disease case, 33.2 to avert one critical disease case, and 65.1 to avert one death. The probability of a major outbreak is zero at VES ?70% regardless of the number of virus introductions. However, an increase in social contact rate among those vaccinated (behavior compensation) can undermine vaccine impact. In addition to the reduction in infection acquisition, developers should assess the natural history and disease progression outcomes when evaluating vaccine impact.
| S-EPMC7712303 | biostudies-literature
Project description:In this study, we examined various forms of mathematical models that are relevant for the containment, risk analysis, and features of COVID-19. Greater emphasis was laid on the extension of the Susceptible-Infectious-Recovered (SIR) models for policy relevance in the time of COVID-19. These mathematical models play a significant role in the understanding of COVID-19 transmission mechanisms, structures, and features. Considering that the disease has spread sporadically around the world, causing large scale socioeconomic disruption unwitnessed in contemporary ages since World War II, researchers, stakeholders, government, and the society at large are actively engaged in finding ways to reduce the rate of infection until a cure or vaccination procedure is established. We advanced argument for the various forms of the mathematical model of epidemics and highlighted their relevance in the containment of COVID-19 at the present time. Mathematical models address the need for understanding the transmission dynamics and other significant factors of the disease that would aid policymakers to make accurate decisions and reduce the rate of transmission of the disease.
| S-EPMC7461001 | biostudies-literature