Competition of SARS-CoV-2 variants on the pandemic transmission dynamics

Chaos Solitons & Fractals, Journal Year: 2023, Volume and Issue: 169, P. 113193 - 113193

Published: Feb. 10, 2023

Language: Английский

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Measures of Population Immunity Can Predict the Dominant Clade of Influenza A (H3N2) in the 2017–2018 Season and Reveal Age‐Associated Differences in Susceptibility and Antibody‐Binding Specificity

Influenza and Other Respiratory Viruses, Journal Year: 2024, Volume and Issue: 18(11)

Published: Nov. 1, 2024

For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that compared others. Antibodies hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate population susceptibility different clades A (H3N2) could predict success in following season.

Language: Английский

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Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(1), P. e0311555 - e0311555

Published: Jan. 14, 2025

Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context globalisation. When different co-occur same fields, they may be simultaneously present host plant (i.e. mixed infection), with potentially important consequences disease outcome. This case Burkina Faso rice yellow mottle virus (RYMV), which endemic to Africa and a major constraint on production. We aimed decipher distinct RYMV isolates that infect single sequence their genomes. To this end, we tested sequencing strategies, finally combined direct cDNA ONT (Oxford Nanopore Technology) bioinformatics tool RVhaplo. method was validated by successful reconstruction two viral genomes were less than hundred nucleotides apart (out genome 4450nt length, i.e. 2–3%), artificial mixes at ratio up 99/1. then used subsequently analyze infections from field samples, revealing three within one sample Faso. In most cases, complete sequences obtained, better estimation diversity detection recombination events. The described thus allows identify various haplotypes infecting plant, obtaining full-length sequences, as well rough estimate relative frequencies sample. It efficient, cost-effective, portable, so it could further implemented where endemic. Prospects include unravelling other RNA viruses threaten crop production worldwide.

Language: Английский

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Mathematical analysis of the COVID-19 pandemic dynamics in the emergence of resistant strains of SARS-CoV-2 in a vaccinated and non-vaccinated population: a real-world scenario in most countries

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 63 - 80

Published: Jan. 1, 2025

Language: Английский

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Repeat offenders: PRRSV-2 clinical re-breaks from a whole genome perspective

Veterinary Microbiology, Journal Year: 2025, Volume and Issue: 302, P. 110411 - 110411

Published: Jan. 29, 2025

Language: Английский

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A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus

iMetaOmics., Journal Year: 2025, Volume and Issue: unknown

Published: April 6, 2025

Abstract Porcine epidemic diarrhea virus (PEDV) is a lethal coronavirus in neonatal piglets characterized by rapid evolution both genotype and phenotype. However, the underlying genetic mechanism has not been completely elucidated. In this study, we investigated PEDV field strains circulating China between 2021 2022, which revealed significant divergence. To improve classification of PEDV, developed site‐polymorphism‐based genotyping system utilizing global sequences from public databases. While there are currently multiple genotypic classification‐based systems for our proposed approach could offer more stable considering characteristics evolutionary dynamics. Our analysis indicates that most prevalent lineages originated South Korea China, with G2c: L4 predominating L10 United States. Importantly, discrete phylogenetic potential pathways showing termini S gene prone to recombination, while adaptive selection evident middle region. Overall, findings provide complementary practical methodology novel insights into pathway coronaviruses.

Language: Английский

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Current Evolutionary Dynamics of Porcine Epidemic Diarrhea Virus (PEDV) in the U.S. a Decade After Introduction

Viruses, Journal Year: 2025, Volume and Issue: 17(5), P. 654 - 654

Published: April 30, 2025

Porcine Epidemic Diarrhea Virus (PEDV) was introduced in the United States (U.S.) 2013, spreading rapidly and leading to economic losses. Two strains, S-INDEL non-S-INDEL, are present U.S. We analyzed 313 genomes 556 Spike protein sequences generated since its introduction. PEDV case numbers were highest during first two years after introduction (epidemic phase), then declined stabilized following (endemic phase). Sequence surveillance higher initial epidemic phase. Our results suggest non-S-INDEL strain is predominant The exhibit pairwise nucleotide identity percentages above 97.6%. Most sampled 2017 clustered into sub-clades. No descendants derived from other clades period detected contemporary data, suggesting that these no longer circulating currently restricted respective geographic regions our limited inter-regional spread. This insight helps determine risk of re-introduction if it regionally eliminated. Ongoing molecular essential confirming some older circulate anymore U.S., mapping distribution spread recent clades, understanding PEDV’s evolutionary diversification.

Language: Английский

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Measures of population immunity can predict the dominant clade of influenza A (H3N2) in the 2017-2018 season and reveal age-associated differences in susceptibility and antibody-binding specificity

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

Published: Oct. 27, 2023

For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that compared others. Antibodies hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate population susceptibility different clades A (H3N2) could predict success in following season.

Language: Английский

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Evolutionary Invasion Analysis of Modern Epidemics Highlights the Context-Dependence of Virulence Evolution

Bulletin of Mathematical Biology, Journal Year: 2024, Volume and Issue: 86(8)

Published: June 14, 2024

Abstract Models are often employed to integrate knowledge about epidemics across scales and simulate disease dynamics. While these approaches have played a central role in studying the mechanics underlying epidemics, we lack ways reliably predict how relationship between virulence (the harm hosts caused by an infection) transmission will evolve certain virus-host contexts. In this study, invoke evolutionary invasion analysis—a method used identify evolution of uninvadable strategies dynamical systems—to examine virulence-transmission dichotomy can models virus infections defined different natural histories. We reveal peculiar patterns with histories (SARS-CoV-2 hepatitis C virus). discuss findings regards public health implications predicting evolution, broader theoretical canon involving host-parasite systems.

Language: Английский

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Machine learning approaches for estimating cross-neutralization potential among FMD serotype O viruses

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

Published: May 24, 2024

Abstract In this study, we aimed to develop an algorithm that uses sequence data estimate cross-neutralization between serotype O foot-and-mouth disease viruses (FMDV) based on r1 values, while identifying key genomic sites associated with high or low values. The ability potential among co-circulating FMDVs in silico is significant for vaccine developers, animal health agencies making herd immunization decisions, and preparedness. Using published virus neutralization titer (VNT) assays VP1 sequences from GenBank, applied machine learning algorithms (BORUTA random forest) predict cross-reaction serum/vaccine-virus pairs 73 distinct FMDV strains. Model optimization involved tenfold cross-validation sub-sampling address imbalance improve performance. predictors included amino acid distances, site-wise polymorphisms, differences N-glycosylation sites. dataset comprised 108 observations (serum-virus pairs) Observations were dichotomized using a 0.3 threshold, yielding putative non-cross-neutralizing (< values) cross-neutralizing groups (≥ values). best model had training accuracy, sensitivity, specificity of 0.96 (95% CI: 0.88-0.99), 0.93, 0.96, respectively, accuracy 0.94 0.71-1.00), sensitivity 1.00, positive, negative predictive values 0.60 one testing AUC, specificity, all approaching 1.00 second dataset. Additionally, positions 48, 100, 135, 150, 151 the region alongside distance found be important cross-neutralization. Our study highlights value genetic/genomic informing strategies management understanding immune-mediated competition amongst related endemic strains field. We also showcase leveraging routinely generated applying parsimonious expedite decision-making selection candidates application vaccines controlling FMD, particularly O. A similar approach can other serotypes.

Language: Английский

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