Inferring temporal trends of multiple pathogens, variants, subtypes or serotypes from routine surveillance data DOI Creative Commons
Oliver Eales, Saras M. Windecker, James M. McCaw

et al.

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

Published: Nov. 4, 2024

Abstract Estimating the temporal trends in infectious disease activity is crucial for monitoring spread and impact of interventions. Surveillance indicators routinely collected to monitor these are often a composite multiple pathogens. For example, ‘influenza-like illness’ — monitored as proxy influenza infections symptom definition that could be caused by wide range pathogens, including subtypes influenza, SARS-CoV-2, RSV. Inferred from such time series may not reflect any one component each which can exhibit distinct dynamics. Although many surveillance systems test subset individuals contributing indicator providing information on relative contribution pathogens obscured time-varying testing rates or substantial noise observation process. Here we develop general statistical framework inferring data. We demonstrate its application three different covering (influenza, dengue), locations (Australia, Singapore, USA, Taiwan, UK), scenarios (seasonal epidemics, non-seasonal pandemic emergence), reporting resolutions (weekly, daily). This methodology applicable systems.

Language: Английский

Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia DOI Creative Commons
Zhiyuan Chen, Joseph L.-H. Tsui, Jun Cai

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 8, 2025

East, South, and Southeast Asia (together referred to as Southeastern hereafter) have been recognized critical areas fuelling the global circulation of seasonal influenza. However, influenza migration network within remains unclear, including how pandemic-related disruptions altered this network. We leveraged genetic, epidemiological, airline travel data between 2007-2023 characterise dispersal patterns A/H3N2 B/Victoria viruses both out Asia, during perturbations by 2009 A/H1N1 COVID-19 pandemics. During pandemic, consistent autumn-winter movement waves from temperate regions were interrupted for subtype/lineages, however pandemic only disrupted spread. find a higher persistence than in identify distinct antigenic evolution two pandemics, compared interpandemic levels; similar are observed using genetic distance. The internal structure markedly diverged season, lesser extent, season. Our findings provide insights into heterogeneous impact on circulation, which can help anticipate effects future pandemics potential mitigation strategies dynamics. key dissemination viruses, but major (e.g., pandemics) may disrupt their role. Here, authors demonstrate H1N1 Asia.

Language: Английский

Citations

2
Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences DOI Creative Commons
Cécile Tran Kiem, Miguel I. Paredes, Amanda C. Perofsky

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Pathogen genomics can provide insights into underlying infectious disease transmission patterns1,2, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential3-5. In particular, genetically proximal viruses should be highly informative about events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences characterize fine-scale patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age residence location information between March 2021 December 2022. This corresponds 59,660 another sequence in the dataset. We find that is consistent expectations from mobility social contact data. Outliers relationship data explained by postcodes male prisons, prison facilities. groups vary across spatial scales. Finally, timing collection understand driving transmission. Overall, study improves our ability large determinants spread.

Language: Английский

Citations

1
Urban-EPR: a universal model for simulating individual human mobility within intra-urban areas DOI
Xin Jin, Kang Liu,

Zhongcai Cao

et al.

International Journal of Geographical Information Science, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 34

Published: Jan. 28, 2025

Language: Английский

Citations

0
Exploring long-term psychological effects of bronchiolitis and influenza in school-aged children DOI Creative Commons
Pankaj Soni,

Jenny Cheriathu

Frontiers in Pediatrics, Journal Year: 2025, Volume and Issue: 13

Published: March 10, 2025

Introduction This systematic review assessed the long-term psychological effects of severe respiratory infections—namely, bronchiolitis and influenza—in school-aged children (5–12 years). Methods PubMed, EMBASE, Cochrane Library were searched for randomized controlled trials, cohort longitudinal studies on years) with a history or influenza infection in early childhood published between 2014 2022. Studies evaluating outcomes at least 6 months post-infection included. Results Several that included this reported increased risks anxiety disorders, depression, attention deficit among those infections childhood. Additionally, prolonged follow-up periods often higher incidence morbidity children. However, some did not detect significant adverse effects, implying timely interventions supportive care may minimize negative outcomes. underscores necessity mental health support following children, highlights need further research biological psychosocial pathways linking illnesses to outcomes, emphasizes value multidisciplinary treatment strategies such comorbidities. Conclusions The findings provide insights healthcare practitioners, policymakers, researchers consider aimed improving affected

Language: Английский

Citations

0
Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City DOI Creative Commons
Renquan Zhang,

Jilei Tai,

Qing Yao

et al.

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(4), P. e1012979 - e1012979

Published: April 29, 2025

The COVID-19 pandemic in New York City (NYC) was characterized by marked disparities disease burdens across neighborhoods. Accurate neighborhood-level forecasts are critical for planning more equitable resource allocation to reduce health inequalities; however, such spatially high-resolution remain scarce operational use. In this study, we analyze aggregated foot traffic data derived from mobile devices measure the connectivity among 42 NYC neighborhoods driven various human activities as dining, shopping, and entertainment. Using real-world time-varying contact patterns different place categories, develop a parsimonious behavior-driven epidemic model that incorporates population mixing, indoor crowdedness, dwell time, seasonality of virus transmissibility. We fit case further couple with assimilation algorithm generate short-term cases 2020. find differential between activities. supports accurate modeling SARS-CoV-2 transmission throughout best-fitting model, estimate force infection (FOI) settings increases sublinearly crowdedness time. Retrospective forecasting demonstrates generates improved compared several baseline models. Our findings indicate foot-traffic routine can support NYC. This may be adapted use other respiratory pathogens sharing similar routes.

Language: Английский

Citations

0
Competition between transmission lineages mediated by human mobility shapes seasonal influenza epidemics in the US DOI Creative Commons
Simon P. J. de Jong, Andrew J. K. Conlan, Alvin X. Han

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: May 17, 2025

Due to its climatic variability, complex mobility networks and geographic expanse, the United States represents a compelling setting explore transmission processes that lead heterogeneous yearly seasonal influenza epidemics. By analyzing genomic epidemiological data collected in US from 2014 2023, we show epidemics consisted of multiple co-circulating lineages could emerge all regions often rapidly expanded. Lineage spread was characterized by strong spatiotemporal hierarchies lineage size correlated with timing establishment US. Mechanistic epidemic simulations, supported phylogeographic analyses, suggest competition between on network human consistent commuting flows drove dynamics. Our results disseminate viruses nationwide are highly structured, but variability short-term determine locations, timing, explosiveness initial sparks limits predictability regional national

Language: Английский

Citations

0
Development of Immunochromatographic and Homogeneous Assay Based on Quantum Dot-Functionalized Polystyrene Nanoprobes for the Qualitative and Quantitative Screening of Respiratory Viruses DOI

Shixiang Yang,

Wenjin Hu, Shengyang Wang

et al.

Biosensors and Bioelectronics, Journal Year: 2024, Volume and Issue: 267, P. 116716 - 116716

Published: Sept. 17, 2024

Language: Английский

Citations

2
Chemical inactivation of two non-enveloped viruses results in distinct thermal unfolding patterns and morphological alterations DOI Creative Commons

Pankhuri Narula,

Milan Kumar Lokshman,

Sandip B. Pathak

et al.

BMC Microbiology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Oct. 17, 2024

Non-enveloped viruses, which lack a lipid envelope, display higher resistance to disinfectants, soaps and sanitizers compared enveloped viruses. The capsids of these viruses are highly stable symmetric protein shells that resist inactivation by commonly employed virucidal agents. This group include transmissible human pathogens such as Rotavirus, Poliovirus, Foot Mouth Disease Virus, Norovirus Adenovirus; thus, devising appropriate strategies for chemical disinfection is essential.

Language: Английский

Citations

2
Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences DOI Creative Commons
Cécile Tran Kiem, Miguel I. Paredes, Amanda C. Perofsky

et al.

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

Published: May 25, 2024

Abstract Pathogen genomics can provide insights into underlying infectious disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential. In particular, genetically proximal viruses should be highly informative about events as genetic proximity indicates epidemiological linkage. Here, we leverage pairs of identical sequences characterise fine-scale patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age residence location information between March 2021 December 2022. This corresponds 59,660 another sequence in the dataset. We find that is consistent expectations from mobility social contact data. Outliers relationship data explained by postal codes male prisons, prison facilities. groups vary across spatial scales. Finally, use timing collection understand driving transmission. Overall, work improves our ability large determinants spread.

Language: Английский

Citations

1
Predictability of human mobility during the COVID-19 pandemic in the United States DOI Creative Commons

Michal Hajlasz,

Sen Pei

PNAS Nexus, Journal Year: 2024, Volume and Issue: 3(8)

Published: July 26, 2024

Abstract Human mobility is fundamental to a range of applications including epidemic control, urban planning, and traffic engineering. While laws governing individual movement trajectories population flows across locations have been extensively studied, the predictability population-level during COVID-19 pandemic driven by specific activities such as work, shopping, recreation remains elusive. Here we analyze data for six place categories at US county level from 2020 February 15 2021 November 23 measure how these metrics changed pandemic. We quantify time-varying in each category using an information-theoretic metric, permutation entropy. find disparate patterns over course pandemic, suggesting differential behavioral changes human perturbed disease outbreaks. Notably, change foot residential mostly opposite direction other categories. Specifically, visits residences had highest stay-at-home orders March 2020, while location types low this period. This pattern flipped after lifting restrictions summer 2020. identify four key factors, weather conditions, size, case growth, government policies, estimate their nonlinear effects on predictability. Our findings provide insights people behaviors public health emergencies may inform improved interventions future epidemics.

Language: Английский

Citations

1