Biosensors and Bioelectronics, Journal Year: 2025, Volume and Issue: unknown, P. 117323 - 117323
Published: March 1, 2025
Language: Английский
Cell, Journal Year: 2023, Volume and Issue: 186(21), P. 4662 - 4675.e12
Published: Sept. 20, 2023
Language: Английский
Citations
59
Annual Review of Virology, Journal Year: 2022, Volume and Issue: 9(1), P. 173 - 192
Published: June 15, 2022
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes underpin emergence of COVID-19 other zoonotic diseases. Herein, I review mechanisms determine why how viruses emerge in new hosts, as well barriers process. show traditional studies virus have an inherent anthropocentric bias, with humans considered inevitable outcome emergence, when reality are integral components global ecosystem characterized by continual host jumping also transmitting their animals. illustrate these points using coronaviruses, including severe acute respiratory syndrome 2, case study. outline potential steps can be followed help mitigate prevent future pandemics, combating climate change central component.
Language: Английский
Citations
44
Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(2), P. 182 - 193
Published: Jan. 12, 2023
Language: Английский
Citations
36
Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(4)
Published: April 1, 2023
RNA viruses are abundant and highly diverse infect all or most eukaryotic organisms. However, only a tiny fraction of the number diversity virus species have been catalogued. To cost-effectively expand known sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for viral RNA-dependent polymerase (RdRp)-the universal "hallmark" gene viruses. By using these to search National Center Biotechnology Information Transcriptome Shotgun Assembly database, identified 5,867 contigs encoding RdRps fragments thereof analyzed their diversity, taxonomic classification, phylogeny, host associations. Our study expands viruses, curated RdRp Profile Models provide useful resource discovery community.
Language: Английский
Citations
34
Neural Regeneration Research, Journal Year: 2023, Volume and Issue: 19(4), P. 833 - 845
Published: Aug. 14, 2023
A growing body of evidence suggests that the gut microbiota contributes to development neurodegenerative diseases via microbiota-gut-brain axis. As a contributing factor, dysbiosis always occurs in pathological changes diseases, such as Alzheimer's disease, Parkinson's and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped reveal bidirectional communication between central nervous system enteric is facilitated by microbiota's diverse microorganisms, for both neuroimmune neuroendocrine systems. Here, we summarize bioinformatics analysis wet-biology validation metagenomics with an emphasis on multi-omics studies virome. The pathogen-associated signaling biomarkers identifying brain disorders potential therapeutic targets are also elucidated. Finally, discuss role diet, prebiotics, probiotics, postbiotics exercise interventions remodeling microbiome reducing symptoms diseases.
Language: Английский
Citations
29
Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(11), P. 1834 - 1843
Published: Sept. 7, 2023
Abstract Virus transmission between host species underpins disease emergence. Both phylogenetic relatedness and aspects of their ecology, such as interactions predator–prey relationships, may govern rates patterns cross-species virus hence zoonotic risk. To address the impact phylogeny ecology on diversity evolution, we characterized virome structure a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through food web. We show barriers inhibited occurred at level phyla (between Chordata, Arthropoda Streptophyta) well lower taxonomic levels. By contrast, manifest diet, had smaller influence composition, especially higher The virus–host comprised ‘small world’ network, which hosts with high viruses were more likely to acquire new viruses, generalist infect multiple additional compared specialist viruses. Such highly connected increases likelihood transmission, particularly among closely related species, suggests present greatest risk
Language: Английский
Citations
27
Current Biology, Journal Year: 2024, Volume and Issue: 34(6), P. 1247 - 1257.e3
Published: Feb. 29, 2024
Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive have been widely studied in the context animal plant evolution, little is known about how they impact evolution viruses that infect these hosts, which turn may provide insights into drivers cross-species transmission hence disease emergence. We examined rapid radiation cichlid fishes African Lake Tanganyika over last 10 million years has shaped diversity carry. Through metatranscriptomic analysis 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated among various tissue types fell 13 4 DNA virus groups. Host-switching was commonplace, particularly within Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, Hepacivirus groups, occurring more frequently than other fish communities. A time-calibrated phylogeny revealed hepacivirus diversification not constant throughout but accelerated 2–3 ago, coinciding with period niche packing Tanganyika, thereby providing closely related hosts for viral infection. These data depict dynamic ecosystem cichlids characterized by frequent host jumping, likely reflecting their close phylogenetic relationships lower barriers to transmission.
Language: Английский
Citations
14
Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(30)
Published: July 17, 2024
It is commonly held that there a fundamental relationship between genome size and error rate, manifest as notional “error threshold” sets an upper limit on sizes. The sizes of RNA viruses, which have intrinsically high mutation rates due to lack mechanisms for correction, must therefore be small avoid accumulating excessive number deleterious mutations will ultimately lead population extinction. proposed exceptions this evolutionary rule are viruses from the order Nidovirales (such coronaviruses) encode error-correcting exonucleases, enabling them reach lengths greater than 40 kb. recent discovery large-genome flavi-like ( Flaviviridae ), comprise genomes up 27 kb in length yet seemingly do not exonuclease domains, has led proposal proofreading mechanism required facilitate expansion nonsegmented virus above 30 Herein, we describe ~40 identified Haliclona sponge metatranscriptome does known exonuclease. Structural analysis revealed may instead captured cellular domains associated with nucleic acid metabolism been previously found viruses. Phylogenetic inference placed divergent pesti-like lineage, such provisionally termed it “Maximus virus.” This represents instance achieving comparable demonstrates evolved multiple solutions overcome threshold.
Language: Английский
Citations
12
Genome biology, Journal Year: 2024, Volume and Issue: 25(1)
Published: May 13, 2024
Abstract Background Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)—virus-derived sequences can dramatically impact host biology serve virus fossil record. In this study, we introduce database-integrated genome screening (DIGS) approach investigate in silico, focusing on EVEs found within vertebrate genomes. Results Using DIGS 874 genomes, uncover approximately 1.1 million EVE sequences, with over 99% originating from retroviruses or transposable DNA. We show remaining 6038 represent thousand distinct horizontal gene transfer events across 10 families, including some have not previously been reported EVEs. explore genomic phylogenetic characteristics non-retroviral determine their rates acquisition during evolution. Our study uncovers novel diversity, broadens knowledge distribution among hosts, provides new insights into ecology evolution viruses. Conclusions comprehensively catalog analyze shedding light distribution, long-term viruses reveal extensive results demonstrate power linking relational database management system similarity search-based pipeline for silico exploration genome.
Language: Английский
Citations
9
Journal of Infection, Journal Year: 2022, Volume and Issue: 85(5), P. e130 - e133
Published: Aug. 22, 2022
Language: Английский
Citations
29