SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Май 11, 2021

Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding set, characterize evolutionary constraint, and prioritize functional mutations. select 44 Sarbecovirus genomes at ideally-suited distances, quantify signatures overlapping constraint. find strong for ORFs 3a, 6, 7a, 7b, 8, 9b, novel alternate-frame gene, ORF3c, whereas 2b, 3d/3d-2, 3b, 9c, 10 lack or convincing experimental evidence function. Furthermore, we show no other conserved genes remain be discovered. Mutation analysis suggests ORF8 contributes within-individual fitness but not person-to-person transmission. Cross-strain within-strain pressures agree, except fewer-than-expected mutations in nsp3 S1, more-than-expected nucleocapsid, which shows cluster predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories residues disrupted by spike-protein substitutions D614G, N501Y, E484K, K417N/T clues about their biology, catalog likely-functional co-inherited Previously reported RNA-modification sites enrichment conservation. Here report evolutionary-history annotations providing valuable resources insights on mutations, evolution.

Язык: Английский

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Possible Effects of Climate Change on Ixodid Ticks and the Pathogens They Transmit: Predictions and Observations

Journal of Medical Entomology, Год журнала: 2020, Номер 58(4), С. 1536 - 1545

Опубликована: Окт. 28, 2020

Abstract The global climate has been changing over the last century due to greenhouse gas emissions and will continue change this century, accelerating without effective efforts reduce emissions. Ticks tick-borne diseases (TTBDs) are inherently climate-sensitive sensitivity of tick lifecycles climate. Key direct weather sensitivities include survival individual ticks, duration development host-seeking activity ticks. These mean that in some regions a warming may increase survival, shorten life-cycles lengthen seasons. Indirect effects on host communities may, with changes abundance, facilitate enhanced transmission pathogens. High temperatures, extreme events (heat, cold, flooding) anticipated change, these pathogen locations. Studies possible TTBDs date generally project poleward range expansion geographical ranges (with contraction away from increasingly hot tropics), upslope elevational spread mountainous regions, increased abundance ticks many current endemic regions. However, relatively few studies, using long-term (multi-decade) observations, provide evidence recent populations could be attributed change. Further integrated ‘One Health’ observational modeling studies needed detect TTBD occurrence, attribute them develop predictive models public- animal-health needs plan for emergence.

Язык: Английский

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A high-quality Ixodes scapularis genome advances tick science

Nature Genetics, Год журнала: 2023, Номер 55(2), С. 301 - 311

Опубликована: Янв. 19, 2023

Язык: Английский

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Genome sequences of four Ixodes species expands understanding of tick evolution

BMC Biology, Год журнала: 2025, Номер 23(1)

Опубликована: Янв. 21, 2025

Язык: Английский

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The origin of the odorant receptor gene family in insects

eLife, Год журнала: 2018, Номер 7

Опубликована: Июль 31, 2018

The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with evolution terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved an ancestral OR co-receptor (Orco) after and OR/Orco system is adaptation winged flight We investigated genomes Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, Ephemeroptera, find present all but absent from lineages predating Orco only ancestrally wingless lineage Archaeognatha. Our new genome sequence zygentoman firebrat Thermobia domestica reveals a full system. conclude before flight, perhaps as terrestriality, representing key evolutionary novelty ancestor insects, hence molecular synapomorphy for Class Insecta.

Язык: Английский

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Strategies for new and improved vaccines against ticks and tick‐borne diseases

Parasite Immunology, Год журнала: 2016, Номер 38(12), С. 754 - 769

Опубликована: Май 21, 2016

Summary Ticks infest a variety of animal species and transmit pathogens causing disease in both humans animals worldwide. Tick–host–pathogen interactions have evolved through dynamic processes that accommodated the genetic traits hosts, transmitted vector tick mediate their development survival. New approaches for control are dependent on defining molecular between ticks to allow discovery key molecules could be tested vaccines or new generation therapeutics intervention tick–pathogen cycles. Currently, constitute an effective environmentally sound approach transmission associated tick‐borne diseases. candidate protective antigens will most likely identified by focusing proteins with relevant biological function feeding, reproduction, development, immune response, subversion host immunity and/or vital pathogen infection transmission. This review addresses different strategies used antigens, including functions proteins, reverse genetics, vaccinomics protein evolution interactomics. improved contain multiple infestations

Язык: Английский

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Genome Sequencing of the Phytoseiid Predatory MiteMetaseiulus occidentalisReveals Completely AtomizedHoxGenes and Superdynamic Intron Evolution

Genome Biology and Evolution, Год журнала: 2016, Номер 8(6), С. 1762 - 1775

Опубликована: Март 6, 2016

Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr evolution radically different lifestyles. We present a 152-Mb draft assembly M. genome: Larger than that its favored prey, Tetranychus urticae, but considerably smaller those many other chelicerates, enabling extremely contiguous complete to be built-the best arachnid date. Aided transcriptome data, genome annotation cataloged 18,338 protein-coding genes identified large numbers Helitron transposable elements. Comparisons with arthropods revealed particularly dynamic turbulent genomic evolutionary history. Its exhibit elevated molecular evolution, strikingly high intron gains losses, in stark contrast deer tick Ixodes scapularis Uniquely among examined arthropods, this mite's Hox completely atomized, dispersed across genome, it encodes five copies normally single-copy RNA processing Dicer-2 gene. Examining gene families linked characteristic traits tiny provides initial insights into processes sex determination, development, immune defense, how detects, disables, digests prey. As first reference Phytoseiidae, any species rare determination system parahaploidy, western orchard improves sampling chelicerates invaluable new resources functional analyses family agriculturally important

Язык: Английский

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Tick-Borne Viruses and Biological Processes at the Tick-Host-Virus Interface

Frontiers in Cellular and Infection Microbiology, Год журнала: 2017, Номер 7

Опубликована: Июль 26, 2017

Ticks are efficient vectors of arboviruses, although less than 10% tick species known to be virus vectors. Most tick-borne viruses (TBV) RNA some which cause serious diseases in humans and animals world-wide. Several TBV impacting human or domesticated animal health have been found emerge re-emerge recently. In order survive nature, must infect replicate both vertebrate cells, representing very different physiological environments. Information on molecular mechanisms that allow switch between infecting replicating cells is scarce. general, ticks succeed completing their blood meal thanks a plethora biologically active molecules saliva counteract modulate arms the host defence responses (haemostasis, inflammation, innate acquired immunity, wound healing). The transmission occurs primarily during feeding complex process, promoted by constituents. However, underlying poorly understood. Immunomodulatory properties helping overcome first line injury early interactions at tick-host skin interface appear essential successful infection susceptible hosts. local site attachment, modulated saliva, an important focus replication. Immunomodulation attachment also promotes co-feeding from infected non-infected absence viraemia (non-viraemic transmission). Future research should aimed identification key salivary promoting transmission, description tick-host-virus tick-mediated immunomodulation. Such insights will enable rationale design anti-tick vaccines protect against disease caused viruses.

Язык: Английский

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Infection-derived lipids elicit an immune deficiency circuit in arthropods

Nature Communications, Год журнала: 2017, Номер 8(1)

Опубликована: Фев. 14, 2017

Abstract The insect immune deficiency (IMD) pathway resembles the tumour necrosis factor receptor network in mammals and senses diaminopimelic-type peptidoglycans present Gram-negative bacteria. Whether unidentified chemical moieties activate IMD signalling cascade remains unknown. Here, we show that infection-derived lipids 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphoglycerol (POPG) 1-palmitoyl-2-oleoyl diacylglycerol (PODAG) stimulate of ticks. tick protects against colonization by three distinct bacteria, is Lyme disease spirochete Borrelia burgdorferi rickettsial agents Anaplasma phagocytophilum A. marginale . Cell ensues absence transmembrane peptidoglycan recognition proteins adaptor molecules Fas-associated protein with a death domain (FADD) IMD. Conversely, biochemical interactions occur between x-linked inhibitor apoptosis (XIAP), an E3 ubiquitin ligase, E2 conjugating enzyme Bendless. We propose existence two functionally networks, one insects another

Язык: Английский

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Tick–Host–Pathogen Interactions: Conflict and Cooperation

PLoS Pathogens, Год журнала: 2016, Номер 12(4), С. e1005488 - e1005488

Опубликована: Апрель 21, 2016

The Model Ticks are blood-feeding arthropod ectoparasites that transmit pathogens constitute a growing burden for human and animal health worldwide [1][2][3].Only second to mosquitoes as vector of diseases the first diseases, ticks bacterial, parasitic, viral [1].One these is intracellular bacterium Anaplasma phagocytophilum, which vectored primarily by Ixodes tick species causative agent granulocytic anaplasmosis (HGA), equine canine anaplasmosis, tick-borne fever ruminants [1].This pathogen good model because recent analysis molecular interactions between vectors, A. host cells showed pathogenic effects both but also revealed mutual beneficial tick-host-pathogen [4][5][6][7].

Язык: Английский

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