Coronavirus accessory protein ORF3 biology and its contribution to viral behavior and pathogenesis

iScience, Год журнала: 2023, Номер 26(4), С. 106280 - 106280

Опубликована: Фев. 28, 2023

Coronavirus porcine epidemic diarrhea virus (PEDV) is classified in the genus Alphacoronavirus, family Coronaviridae that encodes only accessory protein, ORF3 protein. However, how contributes to viral pathogenicity, adaptability, and replication obscure. In this review, we summarize current knowledge identify gaps many aspects of protein PEDV, with emphasis on its unique biological features, including membrane topology, Golgi retention mechanism, potential intrinsic disordered property, functional motifs, glycosylation, codon usage phenotypes related genetic evolution gene expression. addition, propose intriguing questions hope stimulate further studies encourage collaboration among virologists worldwide provide constructive about characteristics functions by which their role clarifying behavior pathogenesis can be possible.

Язык: Английский

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Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation

Poultry Science, Год журнала: 2023, Номер 102(11), С. 103029 - 103029

Опубликована: Авг. 23, 2023

Goose astroviruses (GoAstVs) are causative agents that account for fatal infection of goslings characterized by visceral urate deposition, resulting in severe economic losses major goose-producing regions China since 2017. In this study, we sought to unravel the intrinsic properties associated with adaptation and evolution host environment GoAstVs. Consistent results from phylogenetic analysis correspondence performed on codon usage patterns (CUPs) reveal 2 clusters GoAstVs, namely, GoAstV-1 GoAstV-2. However, multiple similar compositional characteristics were found, despite high divergence between Studies base composition GoAstVs an A/U bias, indicating a constraint, while natural selection prevailed determining CUPs virus genome based our neutrality plot analysis, reflecting adaptive pressure fit environment. Codon index (CAI) revealed higher degree fitness corresponding than avian influenza betacoronaviruses, which may be favorable factor contributing pathogenicity wide distribution goslings. addition, less adapted ducks chickens, significantly lower CAI values geese, reason different prevalence among these species. Extensive investigations dinucleotide significant suppression CpG UpA motifs genome, facilitate host's innate immune system evading surveillance. study reported trends increasing microenvironment through ongoing reduction genome. The present deepens understanding basic biology, pathogenesis, evolutionary pattern contributes development novel antiviral strategies.

Язык: Английский

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Evolutionary dynamics and adaptive analysis of Seneca Valley virus

Infection Genetics and Evolution, Год журнала: 2023, Номер 113, С. 105488 - 105488

Опубликована: Авг. 7, 2023

Over the past 20 years, Seneca Valley virus (SVV) has emerged in various countries and regions around world. Infected pigs display symptoms similar to foot-and-mouth disease other vesicular diseases, causing severe economic losses affected countries. In recent number of SVV infections been increasing Brazil, China, United States. this study, we comprehensively analyzed genomic sequence data from perspectives evolutionary dynamics, phylogeography, codon usage bias. We aimed gain further insights into SVV's genetic diversity, spatiotemporal distribution patterns, adaptations. Phylogenetic analysis revealed that evolved eight distinct lineages. Based on results phylogeographic analysis, it is speculated States might have source SVV, where subsequently spread different regions. Moreover, our positive selection sites capsid proteins suggests their potential importance process receptor recognition. Finally, preference indicates natural a primary driver influencing conclusion, in-depth investigation origin, dissemination, evolution, adaptation emphasizes significance surveillance control measures.

Язык: Английский

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Reverse Genetics Systems for Emerging and Re-Emerging Swine Coronaviruses and Applications

Viruses, Год журнала: 2023, Номер 15(10), С. 2003 - 2003

Опубликована: Сен. 26, 2023

Emerging and re-emerging swine coronaviruses (CoVs), including porcine epidemic diarrhea virus (PEDV), deltacoronavirus (PDCoV), acute syndrome-CoV (SADS-CoV), cause severe in neonatal piglets, CoV infection is associated with significant economic losses for the industry worldwide. Reverse genetics systems realize manipulation of RNA genome facilitate development new vaccines. Thus far, five reverse approaches have been successfully applied to engineer genome: targeted recombination, vitro ligation, bacterial artificial chromosome-based vaccinia -based yeast-based method. This review summarizes advantages limitations these approaches; it also discusses latest research progress terms their use virus-related pathogenesis elucidation, vaccine candidate development, antiviral drug screening, replication mechanism determination.

Язык: Английский

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Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission

Animals, Год журнала: 2023, Номер 13(16), С. 2617 - 2617

Опубликована: Авг. 14, 2023

Chaphamaparvoviruses (ChPVs) are ancient viruses that have been detected in a variety of hosts. In this study, through phylogenetic analysis and the adaptability ChPV to multiple hosts, we evaluated basis for ability feline (FeChPV) canine (CaChPV) cross-species transmission. Phylogenetic showed FeChPV CaChPV were closely related. Notably, two strains ChPVs isolated from domestic cats dogs clustered together with CaChPVs FeChPVs, respectively, suggesting stringent boundaries between may be broken. Further revealed more adapted than cats. Mutation identified several shared mutations cross-species-transmissible strains. Furthermore, VP structures exhibited high degree similarity across both non-cross-species-transmissible However, it is crucial note these results largely computational, limitations exist terms number diversity samples analyzed; capacity transmission should approached caution elucidated further studies.

Язык: Английский

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Natural selection shapes codon usage and host adaptation of NS1 in mosquito-borne pathogenic flaviviruses

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 292, С. 139187 - 139187

Опубликована: Дек. 28, 2024

Язык: Английский

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Attenuation of a Highly Pathogenic Porcine Deltacoronavirus Strain CZ2020 by a Serial Passage In Vitro

Transboundary and Emerging Diseases, Год журнала: 2023, Номер 2023, С. 1 - 12

Опубликована: Март 31, 2023

Porcine deltacoronavirus (PDCoV) is an emerging swine coronavirus that causes severe diarrhea to pigs of all ages, especially the suckling piglets under one-week-old. We previously isolated a highly pathogenic PDCoV strain, CZ2020, from diarrheal piglet and have passaged it for over 100 passages. The adaptability CZ2020 increased gradually in vitro as passage increased. Amino acid mutations were observed pp1a, pp1ab, spike, envelop, membrane proteins, spike protein accounts 66.7% amino mutations. Then, high strains, CZ2020-F80 CZ2020-F100, selected evaluation pathogenicity three-day-old examine whether these changes affected their virulence. At 2 days postchallenge (DPC), 2/5 started show typical diarrhea, at 4 DPC, was CZ2020-challenged piglets. Viral RNA could be detected 1 DPC rectal swabs reached its highest group. CZ2020-F80- CZ2020-F100-challenged groups one exhibiting mild 6 respectively. Compared with group, F100-challenged had lower viral loads swabs, intestines, other organs. No obvious histopathological lesions intestines Virulent infection also induce strong interferons proinflammatory cytokines vivo. These data indicate significantly attenuated via serial passaging potential developing vaccine candidates.

Язык: Английский

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Phylogenetic Analysis and Codon Usage Bias Reveal the Potential of Feline and Canine Chaphamaparvovirus for Cross-species Transmission

Опубликована: Июнь 1, 2023

Chaphamaparvovirus (ChPV) is an ancient virus that has been detected in a variety of hosts. In this study, based on the phylogenetic analysis and adaptability ChPV to multiple hosts, we evaluated potential feline (FeChPV) canine (CaChPV) for cross-species transmis-sion. Phylogenetic showed FeChPV CaChPV were closely related. Notably, two strains ChPVs isolated from domestic cats 2 dogs clustered together with CaChPVs FeChPVs, respectively, suggesting stringent boundaries between may be broken. Further revealed more adapted than cats, strongly possibility unidirectional or bidirectional transmission be-tween cats. Mutation identified several shared mutations cross-species-transmissible not located within immune epitopes. Furthermore, VP struc-tures exhibited high degree similarity across both non-cross-species-transmissible strains. However, definitive experimental evi-dence lacking, its capacity should approached cau-tion elucidated further studies.

Язык: Английский

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Analyzing the Evolution and Host Adaptation of the Rabies Virus from the Perspective of Codon Usage Bias

Transboundary and Emerging Diseases, Год журнала: 2023, Номер 2023, С. 1 - 17

Опубликована: Окт. 10, 2023

Rabies virus (RABV) is a highly pathogenic that causes fatal disease in humans and other mammals, but the mechanism of its evolution, spread, spillover remains unknown. In this study, we analyzed codon usage pattern 2,018 RABV full-length genome sequences from 79 countries collected between 1931 2021 to provide an insight into molecular evolution unravel unknown host-adapted pattern. We found exhibited weak bias, with preference for codons ending A (28.10 ± 0.01) or U (26.43 0.02). Moreover, natural selection plays major role shaping bias RABV. Notably, nearly half 18 were best matched hosts’ most abundant isoacceptor tRNAs, which might account wide range hosts. Furthermore, significant differences observed patterns different host species, suggesting may be influenced by host-specific factors. conclusion, our study reveals help development control strategies effective vaccines therapies against deadly virus.

Язык: Английский

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Analysis of codon usage patterns of porcine enteric alphacoronavirus and its host adaptability

Virology, Год журнала: 2023, Номер 587, С. 109879 - 109879

Опубликована: Сен. 1, 2023

Язык: Английский

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