Forecasting contagion processes on heterogeneous complex networks DOI Open Access
Kunpeng Mu

Опубликована: Янв. 1, 2023

Real-time epidemic forecasting using mathematical and computational models of infectious disease transmission is increasingly used to provide scenario analysis forecasts help public health agencies the society react respond emergent outbreaks, such as most recent COVID-19 pandemic. In my thesis, I utilized Global Epidemic Mobility (GLEAM) model which combines real-world data on human mixing patterns short-range long-range mobility networks with elaborate stochastic analyze spatiotemporal spreading magnitude pandemic in United States proposed use energy score evaluate performance probabilistic that are provided format quantiles or intervals identify plausible best for each round Scenario Modeling Hub project. Chapter 1, introduced important role modeling plays during COVID- 19 why a collaborative hub needed make reliable robust projections policy makers integrating predictive into decision-making process. Besides, pointed out different goals short-term long-term forecasts. briefly research projects, summarized publications at end this chapter. 2, reported contributions development data-driven approach build age-stratified contact by highly detailed macro (census) micro (survey) from publicly available sources key socio-demographic features (such as: age structure, household composition members' gaps, employment rates, school community structures, etc.) studied importance heterogeneity modeling. The were then integrated traditional SLIR-like compartment GLEAM evolution 3, an machine learning algorithms socio-economic, demographic meteorological population size, distance, purchase power parity, language, currency, predict monthly air passenger flows reproduce analogous origin-destination network one obtained Official Airline Guide (OAG) database. predicted will be account travel instead purchasing OAG every year. 4, applied extended participate Multi-Model Outbreak Decision Support (MMODS) project launched Models Infectious Disease Agent Study (MIDAS) mid-May 2020 effectiveness study trade-offs between economic outcomes four reopening strategies generic mid-sized US county novel process designed fully express scientific uncertainty while reducing linguistic cognitive biases. Control populations helpful faced state local officials. 5, multi-scale two distinct work geographical resolutions (the Local (LEAM-US)) produce long- term based scenarios aimed enveloping future drivers trajectory (Vaccine delivery/administration, SARS-CoV-2 variants prevalence, relaxation non-pharmaceuticals interventions (NPIs), national level US. Then our results aggregated ensemble guidance decision-makers, experts, general response 6 reports last PhD research, focus evaluation performances all projection rounds score: generalization continuous ranked probability (CRPS). defined function distances quantifies both calibration sharpness distributions single value. also standardization normalization method overcome drawback original multivariate does not any distinction components forecast vector. illustrated thesis shows how we integrate about processes well utilizing score. frameworks approaches presented here flexible extendable they can contribute addressing challenges decision developing intervention fight against other epidemics.--Author's abstract

Язык: Английский

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic DOI

Alexander Crits‐Christoph,

Joshua I. Levy, Jonathan E. Pekar

и другие.

Cell, Год журнала: 2024, Номер 187(19), С. 5468 - 5482.e11

Опубликована: Сен. 1, 2024

Язык: Английский

Процитировано

26
COVID-origins study links raccoon dogs to Wuhan market: what scientists think DOI Open Access

Smriti Mallapaty

Nature, Год журнала: 2023, Номер 615(7954), С. 771 - 772

Опубликована: Март 21, 2023

Язык: Английский

Процитировано

15
A framework to predict zoonotic hosts under data uncertainty: A case study on betacoronaviruses DOI Creative Commons
Andrea Tonelli, Marcus S. C. Blagrove, Maya Wardeh

и другие.

Methods in Ecology and Evolution, Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

Abstract Modelling approaches aimed at identifying unknown hosts of zoonotic pathogens have the potential to make high‐impact contributions global strategies for risk surveillance. However, geographical and taxonomic biases in host–pathogen associations affect reliability models their predictions. Here, we propose a methodological framework mitigate effect data account uncertainty models' Our approach involves ‘pseudo‐negative’ species integrating sampling into modelling pipeline. We present an application on genus Betacoronavirus provide estimates mammal‐borne betacoronavirus hazard scale. show that inclusion pseudo‐negatives analysis improved overall validation performance our model when compared does not use pseudo‐negatives, especially reducing rate false positives. Results unveil currently unrecognised hotspots subequatorial Africa Americas. addresses crucial limitations association modelling, with important downstream implications assessments. The proposed is adaptable different multi‐host disease systems may be used identify surveillance priorities as well knowledge gaps pathogens' host‐range.

Язык: Английский

Процитировано

0
JN.1 variants circulating in Italy from October 2023 to April 2024: genetic diversity and immune recognition DOI Creative Commons
Emanuela Giombini, Ilaria Schiavoni, Luigina Ambrosio

и другие.

BMC Infectious Diseases, Год журнала: 2025, Номер 25(1)

Опубликована: Фев. 28, 2025

The continuous emergence of SARS-CoV-2 variants and subvariants poses significant public health challenges. latest designated subvariant JN.1, with all its descendants, shows more than 30 mutations in the spike gene. JN.1 has raised concerns due to genomic diversity potential enhance transmissibility immune evasion. This study aims analyse molecular characteristics JN.1-related lineages (JN.1*) identified Italy from October 2023 April 2024 evaluate neutralization activity against a subsample sera individuals vaccinated XBB.1.5 mRNA. gene 794 JN.1* strain was evaluated phylogenetic analysis conducted compare distance XBB.1.5. Moreover, serum assays were performed on 19 healthcare workers (HCWs) monovalent mRNA booster assess neutralizing capacity JN.1. Sequence displayed high variability between investigation confirmed substantial differentiation regions 29 shared mutations, which 17 located within RBD region. Pre-booster observed 42% HCWs sera, increasing significantly post-booster, showing three months after vaccination. A correlation found anti-trimeric Spike IgG levels titers highlights Italy. Results vaccine suggested enhanced

Язык: Английский

Процитировано

0
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic DOI Creative Commons

Alexander Crits‐Christoph,

Joshua I. Levy, Jonathan E. Pekar

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 14, 2023

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start COVID-19 pandemic was traced epidemiologically to Huanan Wholesale Seafood Market, site with most reported wildlife vendors in city Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected market early 2020. We demonstrate that SARS-CoV-2 genetic diversity linked this is consistent emergence, find increased positivity near within a particular stall. identify DNA all positive This includes species such as civets, bamboo rats, porcupines, hedgehogs, one species, raccoon dogs, known be capable transmission. also detect other infect rats. Combining metagenomic phylogenetic approaches, recover genotypes animals compare them those markets. analysis provides basis for short list potential intermediate hosts prioritize retrospective serological testing viral sampling.

Язык: Английский

Процитировано

8
Overview of diagnostic tools and nano-based therapy of SARS-CoV-2 infection DOI
Bedanta Bhattacharjee, Damanbhalang Rynjah, Abdul Baquee Ahmed

и другие.

Chemical Papers, Год журнала: 2024, Номер 78(4), С. 2123 - 2154

Опубликована: Янв. 17, 2024

Язык: Английский

Процитировано

2
Quercetin: A promising drug candidate against the potential SARS-CoV-2-Spike mutants with high viral infectivity DOI Creative Commons

Boyu Pan,

Senbiao Fang,

Liangjiao Wang

и другие.

Computational and Structural Biotechnology Journal, Год журнала: 2023, Номер 21, С. 5092 - 5098

Опубликована: Янв. 1, 2023

The emergence of SARS-CoV-2-Spike mutants not only enhances viral infectivity but also lead to treatment failure. Gaining a comprehensive understanding the molecular binding mode between mutant and human ACE2 receptor is crucial for therapeutic development against this virus. Building upon our previous predictions verifications regarding heightened six potential mutants, study aims further investigate disruption interaction these by quercetin, Chinese herbal compound. Molecular docking dynamics simulations results reveal that sites quercetin particularly enriched around specific "cavity" at interface Spike/ACE2 complex, indicating favorable region interfere with interaction. Virus infection assay confirms attenuates wild-type virus suppresses all tested mutants. Therefore, represents promising candidate both future variants SARS-CoV-2 exhibiting high infectivity.

Язык: Английский

Процитировано

4
A framework to predict zoonotic reservoirs under data uncertainty: a case study on betacoronaviruses DOI
Andrea Tonelli, Marcus S. C. Blagrove, Maya Wardeh

и другие.

Research Square (Research Square), Год журнала: 2024, Номер unknown

Опубликована: Апрель 26, 2024

Abstract 1. Modelling approaches aimed at identifying currently unknown hosts of zoonotic diseases have the potential to make high-impact contributions global strategies for risk surveillance. However, geographical and taxonomic biases in host-pathogen associations might influence reliability models their predictions. 2. Here we propose a methodological framework mitigate effect host–pathogen data account uncertainty models’ Our approach involves “pseudo-negative” species integrating sampling into modelling pipeline. We present an application on Betacoronavirus genus provide estimates mammal-borne betacoronavirus hazard scale. 3. show that inclusion pseudo-negatives analysis improves overall performance our model significantly (AUC = 0.82 PR-AUC 0.48, average) compared does not use 0.75 0.39, average), reducing rate false positives. Results unveil unrecognised hotspots subequatorial Africa, South America. 4. addresses crucial limitations host–virus association modelling, with important downstream implications assessments. The proposed is adaptable different multi-host disease systems may be used identify surveillance priorities as well knowledge gaps pathogens’ host-range.

Язык: Английский

Процитировано

1
Cell type dependent stability and virulence of a recombinant SARS-CoV-2, and engineering of a propagation deficient RNA replicon to analyze virus RNA synthesis DOI Creative Commons
Li Wang,

María Adelina Schlie Guzmán,

Diego Muñoz‐Santos

и другие.

Frontiers in Cellular and Infection Microbiology, Год журнала: 2023, Номер 13

Опубликована: Окт. 24, 2023

Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool the study virus life cycle, virus-host interactions and pathogenesis, as well development effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is emergent human that has caused disease (COVID-19) pandemic. The engineering a full-length infectious cDNA clone fluorescent replicon SARS-CoV-2 Wuhan-Hu-1, using bacterial artificial chromosome, reported. Viral growth genetic stability in eleven cell lines were analyzed, showing both VeroE6 cells overexpressing transmembrane serin protease (TMPRSS2) lung derived resulted optimization system to preserve stability. recombinant point mutant expressing D614G spike protein variant virulent mouse model. RNA was propagation-defective, allowing its use BSL-2 conditions analyze synthesis. developed constitute useful studying molecular biology virus, genetically defined vaccines establish compounds screening.

Язык: Английский

Процитировано

3
Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2 DOI Creative Commons

YeZhi Hu,

Arivizhivendhan Kannan Villalan, Xin Fan

и другие.

PLoS ONE, Год журнала: 2024, Номер 19(5), С. e0293441 - e0293441

Опубликована: Май 2, 2024

SARS-CoV-2 infections in animals have been reported globally. However, the understanding of complete spectrum susceptible to remains limited. The virus’s dynamic nature and its potential infect a wide range are crucial considerations for One Health approach that integrates both human animal health. This study introduces bioinformatic predict susceptibility domestic wild animals. By examining genomic sequencing, we establish phylogenetic relationships between virus hosts. We focus on interaction genome sequence specific regions host species’ ACE2 receptor. analyzed compared receptor sequences from 29 species known be infected, selecting 10 least common amino acid sites (LCAS) key binding domains based similarity patterns. Our analysis included 49 across primates, carnivores, rodents, artiodactyls, revealing consistency LCAS identifying them as potentially susceptible. employed pattern likelihood infection unexamined species. method serves valuable screening tool assessing risks animals, aiding prevention disease outbreaks.

Язык: Английский

Процитировано

0