An early warning indicator trained on stochastic disease-spreading models with different noises

Journal of The Royal Society Interface, Journal Year: 2024, Volume and Issue: 21(217)

Published: Aug. 1, 2024

The timely detection of disease outbreaks through reliable early warning signals (EWSs) is indispensable for effective public health mitigation strategies. Nevertheless, the intricate dynamics real-world spread, often influenced by diverse sources noise and limited data in stages outbreaks, pose a significant challenge developing EWSs, as performance existing indicators varies with extrinsic intrinsic noises. Here, we address modelling when measurements are corrupted additive white noise, multiplicative environmental demographic into standard epidemic mathematical model. To navigate complexities introduced these sources, employ deep learning algorithm that provides EWS infectious training on noise-induced disease-spreading models. indicator's effectiveness demonstrated its application to COVID-19 cases Edmonton simulated time series derived from spread models affected noise. Notably, indicator captures an impending transition outperforms indicators. This study contributes advancing capabilities addressing inherent presenting promising avenue enhancing preparedness response efforts.

Language: Английский

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Estimating SARS-CoV-2 transmission parameters between coinciding outbreaks in a university population and the surrounding community

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 11, 2024

Abstract Institutions of higher education faced a number challenges during the COVID-19 pandemic. Chief among them was whether or not to re-open second wave in fall 2020, which controversial because incidence young adults on rise. The migration students back campuses worried many that transmission within student populations would spread into surrounding communities. In light this, colleges and universities implemented mitigation strategies, with varied degrees success. Washington State University (WSU), located city Pullman Whitman County, WA, is an example this type university-community co-location, where role returning area for 2020 semester contentious. Using reported we retrospectively study dynamics occurred between community subpopulations 2020. We develop two-population ordinary differential equation mechanistic model infer rates across university subpopulations. use results from Bayesian parameter estimation determine if sustained County magnitude cross-transmission members. find these are consistent time-varying reproductive conclude WSU-Pullman did place at disproportionate risk when efforts were place.

Language: Английский

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Parametric analysis of the transmission dynamics during indigenous aggregated outbreaks caused by five SARS-CoV-2 strains in Nanjing, China

Frontiers in Public Health, Journal Year: 2024, Volume and Issue: 12

Published: March 8, 2024

Background SARS-CoV-2 strains have been of great concern due to their high infectivity and antibody evasion. Methods In this study, data were collected on indigenous aggregated outbreaks in Nanjing from January 2020 December 2022, caused by five including the original strain, Delta variant, Omicron variant (BA.2, BA.5.2, BF.7). The basic epidemiological characteristics infected individuals described then parametric analysis transmission dynamics was performed, calculation incubation period, serial interval (SI), reproductive number (R 0 ), household secondary attack rate (HSAR). Finally, we compared trends dynamic parameters different strains. Results period for BA.2, BF.7 6 d (95% CI: 3.5–7.5 d), 5 4.0–6.0 3 3.0–4.0 3.0–3.0 2 2.0–3.0 respectively; Also, SI 5.69 d, 4.79 2.7 2.12 2.43 respectively. Notably, had both a progressive shortening trend ( p < 0.001); Moreover, R 2.39 1.30–4.29), 3.73 2.66–5.15), 5.28 3.52–8.10), 5.54 2.69–11.17), 7.39 2.97–18.76), with an increasing gradually 0.01); HSAR 25.5% 20.1–31.7%), 27.4% 22.0–33.4%), 42.9% 34.3–51.8%), 53.1% 45.0–60.9%), 41.4% CI, 25.5–59.3%), also 0.001). Conclusion Compared decreased while increased, suggesting that population faster scope wider. Overall, it’s crucial keep implementing comprehensive measures like monitoring alert systems, herd immunization plans, outbreak control.

Language: Английский

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A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(11), P. e1012569 - e1012569

Published: Nov. 20, 2024

During pandemics, countries, regions, and communities develop various epidemic models to evaluate spread guide mitigation policies. However, model uncertainties caused by complex transmission behaviors, contact-tracing networks, time-varying parameters, human factors, limited data present significant challenges model-based approaches. To address these issues, we propose a novel framework that centers around reproduction number estimates perform counterfactual analysis, strategy evaluation, feedback control of epidemics. The 1) introduces mechanism quantify the impact testing-for-isolation intervention on basic number. Building this mechanism, 2) proposes method reverse engineer effective under different strengths strategy. In addition, based quantifies number, 3) closed-loop algorithm uses both as indicate severity goal adjustments in intensity intervention. We illustrate framework, along with its three core methods, addressing key questions validating effectiveness using collected during COVID-19 pandemic at University Illinois Urbana-Champaign (UIUC) Purdue University: How severe would an outbreak have been without implemented strategies? What varying strength had outbreak? can adjust current state

Language: Английский

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A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 13, 2023

Abstract Tracking pathogen transmissibility during infectious disease outbreaks is essential for assessing the effectiveness of public health measures and planning future control strategies. A key measure time-dependent reproduction number, which has been estimated in real-time a range pathogens from incidence time series data. While commonly used approaches estimating number can be reliable when recorded frequently, such data are often aggregated temporally (for example, numbers cases may reported weekly rather than daily). As we show, methods unreliable timescale transmission shorter recording. To address this, here develop simulation-based approach involving Approximate Bayesian Computation We first use simulated dataset representative situation daily unavailable only summary values reported, demonstrating that our method provides accurate estimates under those circumstances. then apply to two previous outbreak datasets consisting influenza case 2019-20 2022-23 Wales (in United Kingdom). Our simple-to-use allows more obtained outbreaks.

Language: Английский

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Association of School Instructional Mode with Community COVID-19 Incidence during August–December 2020 in Cuyahoga County, Ohio

International Journal of Environmental Research and Public Health, Journal Year: 2024, Volume and Issue: 21(5), P. 569 - 569

Published: April 29, 2024

Remote and hybrid modes of instruction were employed as alternatives to in-person part early mitigation efforts in response the COVID-19 pandemic. We investigated impact a public school district’s instructional mode on cumulative incidence transmission surrounding community by employing generalized estimating equations approach estimate association with weekly case counts zip code Cuyahoga County, Ohio, from August December 2020. only (RI) was 7 20 districts; 13 used some non-remote (NRI) (2–15 weeks). Weekly increased all codes peak late fall before declining. The within NRI districts higher than those offering RI (risk ratio = 1.12, p 0.01; risk difference 519 per 100,000, 95% confidence interval (123–519)). mean effect for emergent cases 2 weeks after exposure, controlling Social Vulnerability Index (SVI), significant high SVI 1.30, < 0.001. may be associated incidence, particularly communities SVI. Vulnerable need more resources open schools safely.

Language: Английский

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SARS-CoV-2 epidemiology, kinetics, and evolution: a narrative review

Published: May 6, 2024

Since winter 2019, SARS-CoV-2 emerged, spread, and evolved all around the globe. We explore four years of evolutionary epidemiology this virus, ranging from applied public health challenges to more conceptual biology perspectives. Through review, we revisit key episodes pandemic, highlighting important evolution notions they may raise, discuss how pandemic has transformed (or should transform) surveillance prevention viral respiratory infections.

Language: Английский

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Limited impact of lifting universal masks on SARS-CoV-2 transmission in schools: The crucial role of outcome measurements

PNAS Nexus, Journal Year: 2024, Volume and Issue: 3(6)

Published: May 31, 2024

Abstract Amid the COVID-19 pandemic, education systems globally implemented protective measures, notably mandatory mask wearing. As pandemic's dynamics changed, many municipalities lifted these mandates, warranting a critical examination of policy changes' implications. This study examines effects lifting mandates on transmission within Massachusetts school districts. We first replicated previous research that utilized difference-in-difference (DID) model for incidence. then repeated DID analysis by replacing outcome measurement with reproductive number (Rt), reflecting transmissibility. Due to data availability, Rt we estimated only measures transmission. found similar result in replication using incidence an average treatment effect treated (ATT) 39.1 (95% CI: 20.4 57.4) cases per 1,000 students associated masking mandates. However, when Rt, our findings suggest no significant association between and reduced (ATT: 0.04, 95% −0.09 0.18), except 2 weeks postintervention. Moreover, below 1 at 4 before across all types, suggesting nonsustainable implementation. Our reanalysis suggested evidence schools impacted long term. highlights importance examining transmissibility evaluating interventions against

Language: Английский

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Joint estimation of the effective reproduction number and daily incidence in the presence of aggregated and missing data

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 7, 2024

Abstract Disease surveillance is an integral component of government policy, allowing public health professionals to monitor transmission infectious diseases and appropriately apply interventions. To aid with efforts, there has been extensive development mathematical models help inform policy decisions, However, these rely upon data streams that are expensive often only practical for high income countries. With a growing focus on equitable tools dire need equipped handle the stream challenges prevalent in low middle countries, where incomplete subject aggregation. address this need, we develop model joint estimation effective reproduction number daily incidence disease using aggregated data. Our investigation demonstrates novel robust across variety reduced streams, making it suitable application diverse regions. Author summary Monitoring important part hindered by limitations streams. This especially true countries sectors have less funding. In work enhance overcoming limitations, providing accurate inferences relevant epidemiological parameters.

Language: Английский

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Estimating time-varying transmission and oral cholera vaccine effectiveness in Haiti and Cameroon, 2021-2023

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract In 2023, cholera affected approximately 1 million people and caused more than 5000 deaths globally, predominantly in low-income conflict settings. recent years, the number of new outbreaks has grown rapidly. Further, ongoing have been exacerbated by conflict, climate change, poor infrastructure, resulting prolonged crises. As a result, demand for treatment intervention is quickly outpacing existing resource availability. Prior to improved water sanitation systems, cholera, disease primarily transmitted via contaminated sources, also routinely ravaged high-income countries. Crumbling infrastructure change are now putting locations at risk — even Thus, understanding transmission prevention critical. Combating requires multiple interventions, two most common being behavioral education treatment. Two-dose oral vaccination (OCV) often used as complement these interventions. Due limited supply, countries recently switched single-dose vaccines (OCV1). One challenge lies where allocate OCV1 timely manner, especially settings lacking well-resourced public health surveillance systems. occurs propagates such locations, timely, accurate, openly accessible outbreak data typically inaccessible modeling subsequent decision-making. this study, we demonstrated value open-access rapidly estimate vaccine effectiveness. Specifically, obtained non-machine readable (NMR) epidemic curves countries, Haiti Cameroon, from figures published situation news reports. We computational digitization techniques derive weekly counts cases, nominal differences when compared against reported cumulative case (i.e., relative error rate 5.67% 0.54% Cameroon). Given digitized time series, leveraged EpiEstim—an open-source platform—to rapid estimates time-varying effective reproduction ( R t ). To compare effectiveness considered additionally VaxEstim, extension EpiEstim that facilitates estimation relation among three inputs: basic 0 ), , coverage. Here, with Cameroon studies, first implementation VaxEstim low-resource Importantly, use rather traditional data. initial phase outbreak, rolling average were elevated both countries: 2.60 [95% credible interval: 2.42-2.79] 1.90 [1.14-2.95]. These values largely consistent previous Haiti, ranged 1.06 3.72, 1.10 3.50. period high preceded longer during which oscillated around critical threshold 1. Our results derived suggest had higher (75.32% [54.00-86.39%] vs. 54.88% [18.94-84.90%]). generally aligned those field studies conducted other our study reinforces validity an alternative costly, time-consuming Indeed, prior work South Sudan, Bangladesh, Democratic Republic Congo ranging 40% 80%. This underscores combining NMR sources utility rapid, inexpensive data-poor

Language: Английский

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