Potential Novel N-Glycosylation Patterns Associated with the Emergence of New Genetic Variants of PRRSV-2 in the U.S

Vaccines, Journal Year: 2022, Volume and Issue: 10(12), P. 2021 - 2021

Published: Nov. 26, 2022

Glycosylation of proteins is a post-translational process where oligosaccharides are attached to proteins, potentially altering their folding, epitope availability, and immune recognition. In Porcine reproductive respiratory syndrome virus-type 2 (PRRSV-2), positive selection pressure acts on amino acid sites associated with escape through glycan shielding. Here, we describe the patterns potential N-glycosylation over time across different phylogenetic lineages PRRSV-2 better understand how these may contribute coexistence emergence lineages. We screened 19,179 PRRSV GP5 sequences (2004−2021) in silico for N-glycosylated sites. The novel combinations coincided past epidemics U.S. For lineage L1A, glycosylation at residues 32, 33, 44, 51, 57 first appeared 2012, but represented >62% all L1A by 2015, coinciding 1-7-4 strain that increased prevalence from 8 86% 2012 2015. L1C 1-4-4 emerged 2020 also had distinct pattern (residues 51). From 2021, this was responsible 44−47% sequences, contrasting <5% years prior. Our findings support hypothesis antigenic evolution contributes sequential dominance strains partially account differences amongst strains. Further studies its effect folding needed further shape occurrence.

Language: Английский

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Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets

Nutrients, Journal Year: 2023, Volume and Issue: 15(7), P. 1616 - 1616

Published: March 27, 2023

Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality growth faltering. Gut microbiome-related studies mostly focus on relationship between bacteria neonatal onset, no research study has investigated role gut virome diarrhea. Here, using metagenomic sequencing, we characterized fecal viral community diarrheal healthy piglets. We found that piglets showed higher individual heterogeneity elevated abundance Myoviridae. By predicting bacterial host identified genomes, phages infecting Proteobacteria, especially E. coli, were dominant taxa Consistent with this, antibiotic resistance gene coli origin was also enriched Finally, established a random forest model accurately discriminate controls genus coli- listeria-infecting bacteriophages, including psa C5 viruses, as key biomarkers. In conclusion, provide first glance function characteristics These findings expand our understanding among phages, diarrhea, may facilitate development therapeutics for prevention treatment

Language: Английский

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Predicting Antigenic Distance from Genetic Data for PRRSV-Type 1: Applications of Machine Learning

Microbiology Spectrum, Journal Year: 2022, Volume and Issue: 11(1)

Published: Dec. 13, 2022

The control of porcine reproductive and respiratory syndrome (PRRS) remains a significant challenge due to the genetic antigenic variability causative virus (PRRSV). Predominantly, PRRSV management includes using vaccines live inoculations confer immunity against on farms. While understanding cross-protection among strains is crucial for continued success these interventions, how diversity translates elusive. We developed machine learning algorithms estimate distance in silico, based sequence data, identify differences specific amino acid sites associated with between viruses. First, we obtained estimates derived from serum neutralization assays cross-reacting monospecific antisera isolates 27 PRRSV1 viruses circulating Europe. Antigenic distances were weakly moderately ectodomain open reading frames (ORFs) 2 4 (ρ < 0.2) ORF5 = 0.3), respectively. Dividing values at median, then categorized sera-virus pairs into two levels: low high (dissimilarity). In models, used ectodomains ORFs 5 site-wise as potential predictors dissimilarity. Using mixed-effect gradient boosting estimated (high versus low) serum-virus an accuracy 81% (95% confidence interval, 76 85%); sensitivity specificity 86% 75%, demonstrate that data can strains. IMPORTANCE Understanding cocirculating reducing losses PRRS outbreaks experimental studies determine are instrumental, vivo not always practical or timely many emerging this study, ability rapidly immunologic cross-reaction different silico routinely collected by production systems. These models provide fast turn-around information improving decisions such selecting vaccines/live inoculation be farms assessing risk previously exposed certain vaccine development others.

Language: Английский

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Analysis of Virus-Derived siRNAs in Strawberry Plants Co-Infected with Multiple Viruses and Their Genotypes

Plants, Journal Year: 2023, Volume and Issue: 12(13), P. 2564 - 2564

Published: July 6, 2023

Plants can be infected with multiple viruses. High-throughput sequencing tools have enabled numerous discoveries of multi-strain infections, when more than one viral strain or divergent genomic variant infects a single plant. Here, we investigated small interfering RNAs (siRNAs) in strawberry plant co-infected several strains mottle virus (SMoV), crinkle (SCV) and 1 (StrV-1). A range plants subsets the initial species that were obtained by aphid-mediated transmission also evaluated. Using high-throughput sequencing, characterized RNA fractions associated different genotypes these three viruses determined hotspot regions genomes. comparison virus-specific siRNA (vsiRNA) abundance relative concentrations did not reveal any consistent agreement. Strawberry exhibiting considerable variations found to comparable quantities vsiRNAs. Additionally, estimating specificity siRNAs strains, observed substantial pool vsiRNAs could target all SMoV while strain-specific predominantly targeted rhabdoviruses, SCV StrV-1. This highlights intricate nature potential interference antiviral response within are present.

Language: Английский

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

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

Published: March 2, 2024

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

Language: Английский

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Dynamics of a multi-strain HIV/AIDS epidemic model with treatment and its adherence

The European Physical Journal Plus, Journal Year: 2024, Volume and Issue: 139(8)

Published: Aug. 30, 2024

Language: Английский

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Modelling COVID-19 mutant dynamics: understanding the interplay between viral evolution and disease transmission dynamics

Royal Society Open Science, Journal Year: 2024, Volume and Issue: 11(10)

Published: Oct. 1, 2024

Understanding virus mutations is critical for shaping public health interventions. These lead to complex multi-strain dynamics often under-represented in models. Aiming understand the factors influencing variants' fitness and evolution, we explore several scenarios of spreading gain qualitative insight into dictating which variants ultimately predominate at population level. To this end, propose a two-strain stochastic model that accounts asymptomatic transmission, possibility disease import. We find with milder symptoms are likely spread faster than those severe symptoms. This because can prompt affected individuals seek medical help earlier, potentially leading quicker identification isolation cases. However, or cases may more widely, making it harder control spread. Therefore, increased transmissibility still result higher hospitalizations fatalities due widespread infection. The proposed highlights interplay between viral evolution transmission dynamics. Offering nuanced view variant spread, provides foundation further investigation mitigating strategies

Language: Английский

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Features of the teaching of evolutionary theory and fundamentals of ecology in the medical university at the department of medical biology

Faktori eksperimental noi evolucii organizmiv, Journal Year: 2023, Volume and Issue: 32, P. 171 - 175

Published: Sept. 1, 2023

Aim. To justify the peculiarities of teaching basics evolution and ecology in a medical university to ensure high level general biological training achieve orientation first-year students. Methods. Study analysis typical working programs, monographs, textbooks, didactic materials methodical recommendations from discipline "Medical Biology" universities. Results. In conditions reforming modern education, biology teachers are paying more attention formation scientific picture world, that is, worldview future doctors, which corresponds approaches integration content theoretical clinical education need for its continuity further practical activities doctor-specialist any field medicine. Teaching involves conveying students three possible regimes evolution: Lamarck’s, environmental factors influence development (epigenesis); Darwinian, when random mutations selected by progressive (biogenesis); Rait's, there only coincidences. Conclusions. During personality doctor, should combine material classical with latest information on achievements fields natural sciences.

Language: Английский

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