Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2 DOI Creative Commons
Sravani Nanduri, Allison Black, Trevor Bedford

et al.

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

Published: Feb. 8, 2024

Abstract Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions require more sophisticated methods. Even when are appropriate, they can be unnecessary difficult interpret without specialty knowledge. For example, pairwise distances between enough related samples assign new existing clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic cause substantial morbidity mortality frequently recombine, respectively: seasonal influenza A/H3N2 SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation projection (UMAP) with well-defined clades either reassortment (H3N2) recombination (SARS-CoV-2). each low-dimensional sequences, calculated the correlation Euclidean in a hierarchical clustering method embedding. measured accuracy compared previously defined clades, clusters, recombinant lineages. found MDS embeddings accurately represented including intermediate placement SARS-CoV-2 lineages parental Clusters t-SNE recapitulated H3N2 groups, show simple statistical biological model represent relationships for relevant viruses. Our open source implementation these easily inappropriate.

Language: Английский

Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic DOI Creative Commons
Miguel I. Paredes,

Nashwa Ahmed,

Marlin Figgins

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(6), P. 1374 - 1386.e13

Published: Feb. 29, 2024

The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global transmission and population-level changes associated with controlling spread, we built phylogeographic phylodynamic models to analyze MPXV genomes from five regions together air traffic epidemiological data. Our reveal community prior detection, case reporting throughout the epidemic, large degree heterogeneity. We find that viral introductions played limited role prolonging spread after initial dissemination, suggesting travel bans would have had only minor impact. North America began declining before more than 10% high-risk individuals USA vaccine-induced immunity. findings highlight importance broader routine specimen screening surveillance for emerging infectious diseases joint integration genomic information early outbreak control.

Language: Английский

Citations

30
SARS-CoV-2 Diversity and Transmission on a University Campus across Two Academic Years during the Pandemic DOI
Amanda M. Casto, Miguel I. Paredes, Julia C. Bennett

et al.

Clinical Chemistry, Journal Year: 2025, Volume and Issue: 71(1), P. 192 - 202

Published: Jan. 1, 2025

Institutions of higher education (IHE) have been a focus SARS-CoV-2 transmission studies but there is limited information on how viral diversity and at IHE changed as the pandemic progressed.

Language: Английский

Citations

0
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

0
Effect of time-varying validity of individual interaction on co-evolution of awareness and epidemics in a multiplex high-order network DOI
Ming Li, Liang’an Huo

Applied Mathematics and Computation, Journal Year: 2025, Volume and Issue: 499, P. 129396 - 129396

Published: March 18, 2025

Language: Английский

Citations

0
Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2 DOI Creative Commons
Emma B. Hodcroft, Martin Wohlfender, Richard A. Neher

et al.

PLoS Computational Biology, Journal Year: 2025, Volume and Issue: 21(4), P. e1012960 - e1012960

Published: April 15, 2025

The wealth of genomic data that was generated during the COVID-19 pandemic provides an exceptional opportunity to obtain information on transmission SARS-CoV-2. Specifically, there is great interest better understand how effective reproduction number Re and overdispersion secondary cases, which can be quantified by negative binomial dispersion parameter k , changed over time across regions viral variants. aim our study develop a Bayesian framework infer id="m7">Re from sequence data. First, we developed mathematical model for distribution size identical clusters, in integrated transmission, mutation rate virus, incomplete case-detection. Second, implemented this within inference framework, allowing estimation id="m8">Re only. We validated simulation study. Third, identified clusters sequences all SARS-CoV-2 2021 Switzerland, Denmark, Germany were available GISAID. obtained monthly estimates posterior id="m9">Re with resulting id="m10">Re slightly lower than other methods, comparable previous results. found comparatively higher Denmark suggests less opportunities superspreading more controlled compared countries 2021. Our included case detection sampling probability, but had large uncertainty, reflecting difficulty estimating these parameters simultaneously. presents novel method infectious diseases its heterogeneity using With increasing availability pathogens future, expect has potential provide new insights into cases pathogens.

Language: Английский

Citations

0
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
EstimatingReand overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2 DOI Creative Commons
Emma B. Hodcroft, Martin Wohlfender, Richard A. Neher

et al.

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

Published: May 27, 2024

Abstract The wealth of genomic data that was generated during the COVID-19 pandemic provides an exceptional opportunity to obtain information on transmission SARS-CoV-2. Specifically, there is great interest better understand how effective reproduction number R e and overdispersion secondary cases, which can be quantified by negative binomial dispersion parameter k , changed over time across regions viral variants. aim our study develop a Bayesian framework infer from sequence data. First, we developed mathematical model for distribution size identical clusters, in integrated transmission, mutation rate virus, incomplete case-detection. Second, implemented this within inference framework, allowing estimation only. We validated simulation study. Third, identified clusters sequences all SARS-CoV-2 2021 Switzerland, Denmark, Germany were available GISAID. obtained monthly estimates posterior with resulting slightly lower than other methods, comparable previous results. found comparatively higher Denmark suggests less opportunities superspreading more controlled compared countries 2021. Our included case detection sampling probability, but had large uncertainty, reflecting difficulty estimating these parameters simultaneously. presents novel method infectious diseases its heterogeneity using With increasing availability pathogens future, expect has potential provide new insights into cases pathogens. Author summary Pathogen stochastic process characterized two parameters: relates average per current conditions immunity, captures variability cases. While estimated well data, difficult quantify since detailed about who infected whom required. Here, took advantage enormous identify sequences, providing indirect chains at different times pandemic, thus epidemic parameters. then extended previously defined estimate probability approach simulated real three countries, compatible estimates. In future increased pathogen availability, believe will pave way absence contact tracing

Language: Английский

Citations

1
Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach DOI Creative Commons

Ruopeng Xie,

Dillon C. Adam, Hu Shu

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(11)

Published: Nov. 1, 2024

Abstract Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including application deep learning overcome computational limitations, significant challenges persist due data inadequacies statistical unidentifiability key parameters. These issues are particularly pronounced in poorly resolved phylogenies, commonly observed outbreaks such as SARS-CoV-2. In this study, we conducted a thorough evaluation PhyloDeep, inference tool for phylodynamics, assessing its performance on phylogenies. Our findings reveal limited predictive accuracy PhyloDeep (and other state-of-the-art approaches) these scenarios. However, models trained resolved, realistically simulated trees demonstrate improved power, despite not being infallible, especially scenarios with superspreading dynamics, whose parameters challenging capture accurately. Notably, observe markedly minimal contact tracing data, which refines trees. Applying approach sample SARS-CoV-2 sequences partially matched from Hong Kong yields informative estimates potential, extending beyond scope alone. potential enhancing phylodynamic analysis complementary integration, ultimately increasing precision predictions crucial public health decision-making outbreak control.

Language: Английский

Citations

1
Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic DOI Creative Commons
Miguel I. Paredes,

Nashwa Ahmed,

Marlin Figgins

et al.

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

Published: Aug. 2, 2023

Abstract The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global transmission and population-level changes associated with controlling spread, we built phylogeographic phylodynamic models to analyze MPXV genomes from five regions together air traffic epidemiological data. Our reveal community prior detection, case-reporting throughout the epidemic, large degree heterogeneity. We find that viral introductions played limited role prolonging spread after initial dissemination, suggesting travel bans would have had only minor impact. North America began declining before more than 10% high-risk individuals USA vaccine-induced immunity. findings highlight importance broader routine specimen screening surveillance for emerging infectious diseases joint integration genomic information early outbreak control.

Language: Английский

Citations

2
Deep learning of SARS-CoV-2 outbreak phylodynamics with contact tracing data DOI Creative Commons

Ruopeng Xie,

Dillon C. Adam, Hu Shu

et al.

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

Published: June 11, 2024

Abstract Deep learning has emerged as a powerful tool for phylodynamic analysis, addressing common computational limitations affecting existing methods. However, notable disparities exist between simulated phylogenetic trees used training deep models and those derived from real-world sequence data, necessitating thorough examination of their practicality. We conducted comprehensive evaluation model performance by assessing an inference phylodynamics, PhyloDeep, against realistic characterized SARS-CoV-2. Our study reveals the poor predictive accuracy PhyloDeep trained on when applied to data. Conversely, demonstrate improved predictions, despite not being infallible, especially in scenarios where superspreading dynamics are challenging capture accurately. Consequently, we find markedly through integration minimal contact tracing Applying this approach sample SARS-CoV-2 sequences partially matched Hong Kong yields informative estimates potential beyond scope data alone. findings enhancing processing low resolution complementary integration, ultimately increasing precision epidemiological predictions crucial public health decision making outbreak control.

Language: Английский

Citations

0