Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Июнь 11, 2021

Abstract Non-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling ongoing SARS-CoV-2 pandemic. We estimated weekly values of effective basic reproductive number (R eff ) using a mechanistic metapopulation model and associated these with county-level characteristics NPIs in United States (US). Interventions that included school leisure activities closure nursing home visiting bans were all median R below 1 when combined either stay at orders (median 0.97, 95% confidence interval (CI) 0.58–1.39) or face masks CI 0.58–1.39). While direct causal effects unclear, our results suggest relaxation some will need to be counterbalanced by continuation and/or implementation others.

Язык: Английский

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An evaluation of prospective COVID-19 modelling studies in the USA: from data to science translation

The Lancet Digital Health, Год журнала: 2022, Номер 4(10), С. e738 - e747

Опубликована: Сен. 20, 2022

Infectious disease modelling can serve as a powerful tool for situational awareness and decision support policy makers. However, COVID-19 efforts faced many challenges, from poor data quality to changing human behaviour. To extract practical insight the large body of literature available, we provide narrative review with systematic approach that quantitatively assessed prospective, data-driven studies in USA. We analysed 136 papers, focused on aspects models are essential have documented forecasting window, methodology, prediction target, datasets used, geographical resolution each study. also found fraction papers did not evaluate performance (25%), express uncertainty (50%), or state limitations (36%). remedy some these identified gaps, recommend adoption EPIFORGE 2020 model reporting guidelines creating an information-sharing system is suitable fast-paced infectious outbreak science.

Язык: Английский

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An expert judgment model to predict early stages of the COVID-19 pandemic in the United States

PLoS Computational Biology, Год журнала: 2022, Номер 18(9), С. e1010485 - e1010485

Опубликована: Сен. 23, 2022

From February to May 2020, experts in the modeling of infectious disease provided quantitative predictions and estimates trends emerging COVID-19 pandemic a series 13 surveys. Data on existing transmission patterns were sparse when began, but synthesized information available them provide quantitative, judgment-based assessments current future state pandemic. We aggregated expert into single "linear pool" by taking an equally weighted average their probabilistic statements. At time few computational models made public or about pandemic, judgment (a) falsifiable short- long-term outcomes related reported cases, hospitalizations, deaths, (b) latent viral transmission, (c) counterfactual trajectories under different scenarios. The linear pool approach aggregating more consistently accurate than any individual expert, although predictive accuracy rarely most prediction. This work highlights importance that could play flexibly assessing wide array risks early outbreaks, especially settings where data cannot yet support data-driven modeling.

Язык: Английский

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A random forest model for forecasting regional COVID-19 cases utilizing reproduction number estimates and demographic data

Chaos Solitons & Fractals, Год журнала: 2022, Номер 156, С. 111779 - 111779

Опубликована: Янв. 5, 2022

Язык: Английский

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flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic

Epidemics, Год журнала: 2024, Номер 47, С. 100753 - 100753

Опубликована: Март 2, 2024

The COVID-19 pandemic led to an unprecedented demand for projections of disease burden and healthcare utilization under scenarios ranging from unmitigated spread strict social distancing policies. In response, members the Johns Hopkins Infectious Disease Dynamics Group developed flepiMoP (formerly called COVID Scenario Modeling Pipeline), a comprehensive open-source software pipeline designed creating simulating compartmental models infectious transmission inferring parameters through these models. framework has been used extensively produce short-term forecasts longer-term scenario at state county level in US, other countries various geographic scales, more recently seasonal influenza. this paper, we highlight how evolved throughout address changing epidemiological dynamics, new interventions, shifts policy-relevant model outputs. As reached mature state, provide detailed overview flepiMoP's key features remaining limitations, thereby distributing its documentation as flexible powerful tool researchers public health professionals rapidly build deploy large-scale complex any pathogen demographic setup.

Язык: Английский

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Accuracy of US CDC COVID-19 forecasting models

Frontiers in Public Health, Год журнала: 2024, Номер 12

Опубликована: Июнь 26, 2024

Accurate predictive modeling of pandemics is essential for optimally distributing biomedical resources and setting policy. Dozens case prediction models have been proposed but their accuracy over time by model type remains unclear. In this study, we systematically analyze all US CDC COVID-19 forecasting models, first categorizing them then calculating mean absolute percent error, both wave-wise on the complete timeline. We compare estimates to government-reported numbers, one another, as well two baseline wherein counts remain static or follow a simple linear trend. The comparison reveals that around two-thirds fail outperform one-third trend forecast. A wave-by-wave revealed no overall approach was superior others, including ensemble errors in increased during pandemic. This study raises concerns about hosting these official public platforms health organizations which risks giving an imprimatur when utilized formulate By offering universal evaluation method pandemic expect serve starting point development more accurate models.

Язык: Английский

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The variations of SIkJalpha model for COVID-19 forecasting and scenario projections

Epidemics, Год журнала: 2023, Номер 45, С. 100729 - 100729

Опубликована: Ноя. 16, 2023

We proposed the SIkJalpha model at beginning of COVID-19 pandemic (early 2020). Since then, as evolved, more complexities were added to capture crucial factors and variables that can assist with projecting desired future scenarios. Throughout pandemic, multi-model collaborative efforts have been organized predict short-term outcomes (cases, deaths, hospitalizations) long-term scenario projections. participating in five such efforts. This paper presents evolution its many versions used submit these since pandemic. Specifically, we show is an approximation a class epidemiological models. demonstrate how be incorporate various complexities, including under-reporting, multiple variants, waning immunity, contact rates, generate probabilistic outputs.

Язык: Английский

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Trend estimation and short-term forecasting of COVID-19 cases and deaths worldwide

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(32)

Опубликована: Авг. 3, 2022

Since the beginning of COVID-19 pandemic, many dashboards have emerged as useful tools to monitor its evolution, inform public, and assist governments in decision-making. Here, we present a globally applicable method, integrated daily updated dashboard that provides an estimate trend evolution number cases deaths from reported data more than 200 countries territories, well 7-d forecasts. One significant difficulties managing quickly propagating epidemic is details dynamic needed forecast are obscured by delays identification irregular reporting. Our forecasting methodology substantially relies on estimating underlying observed time series using robust seasonal decomposition techniques. This allows us obtain forecasts with simple yet effective extrapolation methods linear or log scale. We results assessment our discuss application production global regional risk maps.

Язык: Английский

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High Resolution Spatio-Temporal Model for Room-Level Airborne Pandemic Spread

Mathematics, Год журнала: 2023, Номер 11(2), С. 426 - 426

Опубликована: Янв. 13, 2023

Airborne pandemics have caused millions of deaths worldwide, large-scale economic losses, and catastrophic sociological shifts in human history. Researchers developed multiple mathematical models computational frameworks to investigate predict pandemic spread on various levels scales such as countries, cities, large social events, even buildings. However, attempts modeling airborne dynamics the smallest scale, a single room, been mostly neglected. As time indoors increases due global urbanization processes, more infections occur shared rooms. In this study, high-resolution spatio-temporal epidemiological model with airflow evaluate is proposed. The implemented, using Python, 3D data obtained from light detection ranging (LiDAR) device computing based Computational Fluid Dynamics (CFD) for Susceptible–Exposed–Infected (SEI) dynamics. evaluated four types rooms, showing significant differences short exposure duration. We show that room’s topology individual distribution room define ability air ventilation reduce throughout breathing zone infection.

Язык: Английский

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Structural Virology: The Key Determinants in Development of Antiviral Therapeutics

Viruses, Год журнала: 2025, Номер 17(3), С. 417 - 417

Опубликована: Март 14, 2025

Structural virology has emerged as the foundation for development of effective antiviral therapeutics. It is pivotal in providing crucial insights into three-dimensional frame viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment components, including capsids, envelope proteins, replication machinery, host interaction interfaces, instrumental unraveling multiplex mechanisms infection, replication, pathogenesis. The structural elucidation enzymes, proteases, polymerases, integrases, been essential combating like HIV-1 HIV-2, SARS-CoV-2, influenza. Techniques X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, Tomography have revolutionized field significantly aided discovery ubiquity chronic infections, along with emergence reemergence new threats necessitate novel strategies agents, while extensive diversity their high mutation rates further underscore critical need analysis to aid development. This review highlights significance structure-based investigations bridging gap between structure function, thus facilitating therapeutics, vaccines, antibodies tackling emerging threats.

Язык: Английский

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