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1.
Braz. j. biol ; 83: e247237, 2023. tab, graf
Artículo en Inglés | MEDLINE, LILACS, VETINDEX | ID: biblio-1339386

RESUMEN

Abstract Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.


Resumo O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.


Asunto(s)
Humanos , Animales , Quirópteros , COVID-19 , Filogenia , Simulación por Computador , Genoma Viral/genética , SARS-CoV-2
2.
Nat Commun ; 13(1): 2314, 2022 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-35538057

RESUMEN

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.


Asunto(s)
Subtipo H1N1 del Virus de la Influenza A , Virus de la Influenza A , Gripe Humana , Genoma Viral/genética , Genómica , Humanos , Subtipo H1N1 del Virus de la Influenza A/genética , Virus de la Influenza A/genética , Gripe Humana/epidemiología , Gripe Humana/genética
3.
Arch Microbiol ; 204(6): 304, 2022 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-35524836

RESUMEN

Phage-derived therapies are promising treatments in the fight against bacterial diseases as an alternative strategy nowadays. Species of Aeromonas veronii is an important pathogen causing freshwater fish diseases, the findings on genomic sequences of their bacteriophages are limited. In this work, a lytic bacteriophage capable of specifically infecting A. veronii strain AEv1810 was characterized at the gene level and was designated as pAEv1810. Transmission electron microscopic observation revealed that pAEv1810 belongs to the family of Myoviridae. The genome of phage pAEv1810 consists of 235,066 bp with 38.4% G + C content. Twenty-three of 249 putative proteins encoded by this phage have known functions, and four tRNA genes were found in phage genome. Phylogenetic analyses of RNA polymerase and Terminase large subunit revealed that phage pAEv1810 is closing to those phages classified to the genus Petsuvirus.


Asunto(s)
Bacteriófagos , Myoviridae , Aeromonas veronii , Animales , Bacteriófagos/genética , Genoma Viral , Genómica , Myoviridae/genética , Filogenia
4.
Sci Adv ; 8(18): eabj9670, 2022 05 06.
Artículo en Inglés | MEDLINE | ID: mdl-35507660

RESUMEN

Many eukaryotic viruses assemble mature particles within distinct subcellular compartments, but bacteriophages are generally assumed to assemble randomly throughout the host cell cytoplasm. Here, we show that viral particles of Pseudomonas nucleus-forming jumbo phage PhiPA3 assemble into a unique structure inside cells we term phage bouquets. We show that after capsids complete DNA packaging at the surface of the phage nucleus, tails assemble and attach to capsids, and these particles accumulate over time in a spherical pattern, with tails oriented inward and the heads outward to form bouquets at specific subcellular locations. Bouquets localize at the same fixed distance from the phage nucleus even when it is mispositioned, suggesting an active mechanism for positioning. These results mark the discovery of a pathway for organizing mature viral particles inside bacteria and demonstrate that nucleus-forming jumbo phages, like most eukaryotic viruses, are highly spatially organized during all stages of their lytic cycle.


Asunto(s)
Bacteriófagos , Bacteriófagos/genética , Cápside/ultraestructura , Núcleo Celular , Genoma Viral , Virión
5.
J Gen Virol ; 103(5)2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35506996

RESUMEN

The family Potyviridae includes plant viruses with single-stranded, positive-sense RNA genomes of 8-11 kb and flexuous filamentous particles 650-950 nm long and 11-20 nm wide. Genera in the family are distinguished by the host range, genomic features and phylogeny of the member viruses. Most genomes are monopartite, but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Potyviridae, which is available at ictv.global/report/potyviridae.


Asunto(s)
Virus de Plantas , Potyviridae , Genoma Viral , Especificidad del Huésped , Filogenia , Virus de Plantas/genética , Plantas , Potyviridae/genética , Virión/genética , Replicación Viral
6.
Nat Commun ; 13(1): 2494, 2022 May 06.
Artículo en Inglés | MEDLINE | ID: mdl-35523782

RESUMEN

The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.


Asunto(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiología , Genoma Viral/genética , Ghana/epidemiología , Humanos , Mutación , Pandemias , Filogenia , SARS-CoV-2/genética , Glicoproteína de la Espiga del Coronavirus/genética
7.
J Virol Methods ; 305: 114537, 2022 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-35526667

RESUMEN

Due to strictly cell-associated growth, experiments requiring cell-free virus are not applicable to recent clinical HCMV isolates to date. On the other hand, adaptation to cell-free growth is associated with undesirable changes in the viral gene regions RL13 and UL128. We had previously found that siRNA-mediated reduction of UL128 expression allowed transient release of cell-free virus by clinical isolates, and now hypothesized that virus yield could be further increased by additional knockdown of RL13. Despite the extensive polymorphism of RL13, effective RL13-specific siRNAs could be designed for three recent isolates and the Merlin strain. Knockdown efficiency was demonstrated at the protein level with a Merlin variant expressing V5-tagged pRL13. Knockdown of RL13 alone did not result in measurable release of cell-free virus, but combined knockdown of RL13 and UL128 increased infectivity in cell-free supernatants by a factor of 10-2000 compared to knockdown of UL128 alone. These supernatants could be used in dose-response assays to compare the effect of a neutralizing antibody on the various HCMV isolates. In summary, combined knockdown of RL13 and UL128 by specific siRNAs allows reliable release of cell-free infectivity from otherwise strictly cell-associated HCMV isolates without the need to modify the viral genome.


Asunto(s)
Citomegalovirus , Neurofibromina 2 , Línea Celular , Citomegalovirus/genética , Genes Virales , Genoma Viral , Neurofibromina 2/genética , Neurofibromina 2/metabolismo , Proteínas del Envoltorio Viral/genética
8.
PLoS One ; 17(5): e0266683, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35507581

RESUMEN

Foodborne diseases have become a serious havoc, where antimicrobial resistance is throwing significant challenges on daily basis. With the increase of drug-resistant bacteria and food-borne infection associated with Vibrio parahaemolyticus, new and effective strategies were needed to control the emergence of vibriosis. Lytic bacteriophages come up as a promising way to resist the pathogenic population in various applications. In this study, a V. parahaemolyticus specific phage vB_VpS_PG28 was isolated from sewage in the seafood market. Results showed vB_VpS_PG28, is strictly a lytic bacteriophage and has a relatively large burst size of 103 plaque-forming units per infected cell. Comparative genomic and bioinformatic analyses proved that vB_VpS_PG28 is a new bacteriophage that had a homologous relation with Vibrio phages of family Siphoviridae, especially with phage VH2_2019, but transmission electron microscopy of vB_VpS_PG28 morphology characterized its morphology is similar to that of Myoviridae family. In silico analysis indicated that the vB_VpS_PG28 genome consists of 82712 bp (48.08% GC content) encoding 114 putative ORFs without tRNA,and any gene associated with resistance or virulence factors has not been found. The bacteriophage in the present study has shown significant outcomes in order to control bacterial growth under in vitro conditions. Thus, we are suggesting a beneficiary agent against foodborne pathogens. Further, to ensure the safe usage of phage oral toxicity testing is recommended.


Asunto(s)
Bacteriófagos , Vibrio parahaemolyticus , Animales , Crustáceos/genética , Genoma Viral , Filogenia , Alimentos Marinos , Análisis de Secuencia , Vibrio parahaemolyticus/genética
9.
Front Cell Infect Microbiol ; 12: 809407, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35480235

RESUMEN

Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11th 2020 to September 23rd 2021, were used to identify patients with two or more positive results. A total of 3,650 samples collected from 1,529 patients who had between 2 and 20 positive results were identified in a time frame that extended up to 403 days from the first positive. Cycle threshold values (Ct) were available for 1,622 samples, the median of which was over 30 by 11 days after the first positive. Extended recovery of infectious virus on cell culture was notable for up to 70 days after the first positive in immunocompromised patients. Whole genome sequencing data generated as a part of our SARS-CoV-2 genomic surveillance was available for 1,027 samples from patients that had multiple positive tests. Positive samples collected more than 10 days after initial positive with high quality sequences (coverage >90% and mean depth >100), were more likely to be from unvaccinated, or immunosuppressed patients. Reinfections with viral variants of concern were found in 3 patients more than 130 days from prior infections with a different viral clade. In 75 patients that had 2 or more high quality sequences, the acquisition of more substitutions or deletions was associated with lack of vaccination and longer time between the recovered viruses. Our study highlights the value of integrating genomic, laboratory, and clinical data for understanding the biology of SARS-CoV-2 as well as for setting a precedent for future epidemics and pandemics.


Asunto(s)
COVID-19 , Reinfección , COVID-19/diagnóstico , Genoma Viral/genética , Genómica , Humanos , Técnicas de Diagnóstico Molecular , ARN Viral/genética , SARS-CoV-2/genética
10.
Viruses ; 14(4)2022 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-35458406

RESUMEN

Clostridium perfringens is an important pathogen for both humans and animals, causing human foodborne disease and necrotic enteritis in poultry. In the present study, a C. perfringens-specific phage, vB_CpeS_BG3P (designated as BG3P hereafter), was isolated from chicken farm sewage. Both electron microscopy and phylogenetic analysis suggested that phage BG3P is a novel phage belonging to Siphoviridae family. Phage BG3P exhibited a broad host range against different C. perfringens isolates (90.63% of strains were infected). Sequencing of the complete genome revealed a linear double-stranded DNA (43,528 bp) with 28.65% GC content. After sequence analysis, 73 open reading frames (orfs) were predicted, of which only 13 were annotated with known functions. No tRNA and virulence encoding genes were detected. It should be noted that the protein of orf 15 has 97.92% homology to C. perfringens-specific chloramphenicol resistance protein, which has not been reported for any C. perfringens phage. Phylogenetic analysis of the ssDNA binding protein demonstrated that this phage is closely related to C. perfringens phages phiSM101 and phi3626. In considering future use as an antimicrobial agent, some biological characteristics were observed, such as a good pH (3-11) stability and moderate temperature tolerance (<60 °C). Moreover, bacteriophage BG3P showed a good antimicrobial effect against C. perfringens liquid cultures. Thus, phage treatment with MOI ≥ 100 completely inhibited bacterial growth compared to untreated cultures. Although phage BG3P shows good lytic efficiency and broad host range in vitro, future development and application may need to consider removal of the chloramphenicol-like resistance gene or exploring its lysin for future antibacterial applications.


Asunto(s)
Bacteriófagos , Siphoviridae , Animales , Clostridium perfringens/genética , Genoma Viral , Especificidad del Huésped , Filogenia , Siphoviridae/genética
11.
Viruses ; 14(4)2022 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-35458432

RESUMEN

Massive amounts of data from nucleic acid sequencing have changed our perspective about diversity and dynamics of marine viral communities. Here, we summarize recent metatranscriptomic and metaviromic studies targeting predominantly RNA viral communities. The analysis of RNA viromes reaffirms the abundance of lytic (+) ssRNA viruses of the order Picornavirales, but also reveals other (+) ssRNA viruses, including RNA bacteriophages, as important constituents of extracellular RNA viral communities. Sequencing of dsRNA suggests unknown diversity of dsRNA viruses. Environmental metatranscriptomes capture the dynamics of ssDNA, dsDNA, ssRNA, and dsRNA viruses simultaneously, unravelling the full complexity of viral dynamics in the marine environment. RNA viruses are prevalent in large size fractions of environmental metatranscriptomes, actively infect marine unicellular eukaryotes larger than 3 µm, and can outnumber bacteriophages during phytoplankton blooms. DNA and RNA viruses change abundance on hourly timescales, implying viral control on a daily temporal basis. Metatranscriptomes of cultured protists host a diverse community of ssRNA and dsRNA viruses, often with multipartite genomes and possibly persistent intracellular lifestyles. We posit that RNA viral communities might be more diverse and complex than formerly anticipated and that the influence they exert on community composition and global carbon flows in aquatic ecosystems may be underestimated.


Asunto(s)
Ecosistema , Virus ARN , Eucariontes/genética , Genoma Viral , Genómica , Filogenia , Virus ARN/genética , ARN Bicatenario , Transcriptoma
12.
Viruses ; 14(4)2022 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-35458433

RESUMEN

Dengue is an arboviral disease caused by dengue virus (DENV), leading to approximately 25,000 deaths/year and with over 40% of the world's population at risk. Increased international travel and trade, poorly regulated urban expansion, and warming global temperatures have expanded the geographic range and incidence of the virus in recent decades. This study used phylogenetic and selection pressure analyses to investigate trends in DENV evolution, using whole genome coding sequences from publicly available databases alongside newly sequenced isolates collected between 1963-1997 from Southeast Asia and the Pacific. Results revealed very similar phylogenetic relationships when using the envelope gene and the whole genome coding sequences. Although DENV evolution is predominantly driven by negative selection, a number of amino acid sites undergoing positive selection were found across the genome, with the majority located in the envelope and NS5 genes. Some genotypes appear to be diversifying faster than others within each serotype. The results from this research improve our understanding of DENV evolution, with implications for disease control efforts such as Wolbachia-based biocontrol and vaccine design.


Asunto(s)
Virus del Dengue , Dengue , Wolbachia , Evolución Molecular , Genoma Viral , Genotipo , Humanos , Filogenia
13.
Viruses ; 14(4)2022 03 29.
Artículo en Inglés | MEDLINE | ID: mdl-35458438

RESUMEN

Recent acknowledgment that multidrug resistant Stenotrophomonas maltophilia strains can cause severe infections has led to increasing global interest in addressing its pathogenicity. While being primarily associated with hospital-acquired respiratory tract infections, this bacterial species is also relevant to ophthalmology, particularly to contact lens-related diseases. In the current study, the capacity of Stenotrophomonas phage vB_SmaM_Ps15 to infect ocular S. maltophilia strains was investigated to explore its future potential as a phage therapeutic. The phage proved to be lytic to a range of clinical isolates collected in Australia from eye swabs, contact lenses and contact lens cases that had previously shown to be resistant to several antibiotics and multipurpose contact lenses disinfectant solutions. Morphological analysis by transmission electron microscopy placed the phage into the Myoviridae family. Its genome size was 161,350 bp with a G + C content of 54.2%, containing 276 putative protein-encoding genes and 24 tRNAs. A detailed comparative genomic analysis positioned vB_SmaM_Ps15 as a new species of the Menderavirus genus, which currently contains six very similar globally distributed members. It was confirmed as a virulent phage, free of known lysogenic and pathogenicity determinants, which supports its potential use for the treatment of S. maltophilia eye infections.


Asunto(s)
Bacteriófagos , Stenotrophomonas maltophilia , Australia , Bacteriófagos/genética , Genoma Viral , Myoviridae/genética , Stenotrophomonas maltophilia/genética
14.
Viruses ; 14(4)2022 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-35458461

RESUMEN

Lytic and lysogenic infections are the main strategies used by viruses to interact with microbial hosts. The genetic information of prophages provides insights into the nature of phages and their potential influences on hosts. Here, the siphovirus vB_MoxS-R1 was induced from a Microbacterium strain isolated from an estuarine Synechococcus culture. vB_MoxS-R1 has a high replication capability, with an estimated burst size of 2000 virions per cell. vB_MoxS-R1 represents a novel phage genus-based genomic analysis. Six transcriptional regulator (TR) genes were predicted in the vB_MoxS-R1 genome. Four of these TR genes are involved in stress responses, virulence and amino acid transportation in bacteria, suggesting that they may play roles in regulating the host cell metabolism in response to external environmental changes. A glycerophosphodiester phosphodiesterase gene related to phosphorus acquisition was also identified in the vB_MoxS-R1 genome. The presence of six TR genes and the phosphorus-acquisition gene suggests that prophage vB_MoxS-R1 has the potential to influence survival and adaptation of its host during lysogeny. Possession of four endonuclease genes in the prophage genome suggests that vB_MoxS-R1 is likely involved in DNA recombination or gene conversion and further influences host evolution.


Asunto(s)
Bacteriófagos , Profagos , Bacteriófagos/genética , Genoma Viral , Lisogenia , Microbacterium , Fósforo , Profagos/genética
15.
Viruses ; 14(4)2022 04 09.
Artículo en Inglés | MEDLINE | ID: mdl-35458511

RESUMEN

BACKGROUND: Studies have linked bats to outbreaks of viral diseases in human populations such as SARS-CoV-1 and MERS-CoV and the ongoing SARS-CoV-2 pandemic. METHODS: We carried out a longitudinal survey from August 2020 to July 2021 at two sites in Zimbabwe with bat-human interactions: Magweto cave and Chirundu farm. A total of 1732 and 1866 individual bat fecal samples were collected, respectively. Coronaviruses and bat species were amplified using PCR systems. RESULTS: Analysis of the coronavirus sequences revealed a high genetic diversity, and we identified different sub-viral groups in the Alphacoronavirus and Betacoronavirus genus. The established sub-viral groups fell within the described Alphacoronavirus sub-genera: Decacovirus, Duvinacovirus, Rhinacovirus, Setracovirus and Minunacovirus and for Betacoronavirus sub-genera: Sarbecoviruses, Merbecovirus and Hibecovirus. Our results showed an overall proportion for CoV positive PCR tests of 23.7% at Chirundu site and 16.5% and 38.9% at Magweto site for insectivorous bats and Macronycteris gigas, respectively. CONCLUSIONS: The higher risk of bat coronavirus exposure for humans was found in December to March in relation to higher viral shedding peaks of coronaviruses in the parturition, lactation and weaning months of the bat populations at both sites. We also highlight the need to further document viral infectious risk in human/domestic animal populations surrounding bat habitats in Zimbabwe.


Asunto(s)
Alphacoronavirus , COVID-19 , Quirópteros , Animales , COVID-19/epidemiología , Evolución Molecular , Femenino , Genoma Viral , Filogenia , SARS-CoV-2/genética , Zimbabwe/epidemiología
16.
Viruses ; 14(4)2022 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-35458529

RESUMEN

Reticuloendotheliosis virus (REV) is a retroviral pathogen capable of infecting several avian hosts and is associated with immunosuppression, anemia, proventriculitis, neoplasia, and runting-stunting syndrome. Its genome contains the three major genes, gag, pol, and env, and two flanking long terminal repeat (LTR) regions. Complete genome sequences of REV are limited in terms of geographical origin. The aim of this study was to characterize the complete genome of REV detected in Brazilian chickens with multiple viral coinfections and analyze the polymorphisms in the deduced amino acids sequences corresponding to its encoded proteins. We tested the presence and completeness of REV as well as other viral pathogens in samples from Brazilian poultry farms by qPCR. The complete genomes of two REV strains were sequenced by overlapping fragments through the dideoxy method. Phylogenetic analysis, pairwise identity matrix, polymorphism identification and protein modeling were performed along the entire genome. We detected REV in 65% (26/40) of the tested samples. Concomitant viral infections were detected in 82.5% (33/40) of the samples and in 90% (9/10) of the farms. Multiple infections included up to seven viruses. Phylogenetic analysis classified both Brazilian strains into REV subtype 3, and the pairwise comparison indicated that strains from the USA and fowlpox virus (FWPV)-related strains were the most identical. The subdomain p18 in gag, the reverse transcriptase/ribonuclease H in pol, and the surface (SU) in the env protein were the most polymorphic in genomic comparisons. The relevant motifs for each protein were highly conserved, with fewer polymorphisms in the fusion peptide, immunosuppression domain, and disulfide bonds on the surface (SU) and transmembrane (TM) of env. This is the first study to include complete genomes of REV in Brazil and South America detected in farms with multiple viral coinfections. Our findings suggest an involvement of REV as an immunosuppressor and active agent in the emergence and progression of multiple infectious diseases. We also found a possible etiological relationship between Brazilian strains and the USA and FWPV recombinant strains. This information highlights the need for epidemiological vigilance regarding REV in association with another pathogens.


Asunto(s)
Coinfección , Virus de la Viruela de las Aves de Corral , Enfermedades de las Aves de Corral , Virus de la Reticuloendoteliosis , Animales , Brasil/epidemiología , Pollos/genética , Coinfección/genética , Coinfección/veterinaria , Virus de la Viruela de las Aves de Corral/genética , Genoma Viral , Filogenia , Virus de la Reticuloendoteliosis/genética
17.
Viruses ; 14(4)2022 04 14.
Artículo en Inglés | MEDLINE | ID: mdl-35458543

RESUMEN

Six novel mycoviruses that collectively represent the mycovirome of Rhizoctonia solani anastomosis group (AG)-3 PT strain ZJ-2H, which causes potato black scurf, were identified through metatranscriptome sequencing and putatively designated as Rhizoctonia solani fusarivirus 4 [RsFV4, positive single-stranded RNA (+ssRNA)], Rhizoctonia solani fusarivirus 5 (RsFV5, +ssRNA), Rhizoctonia solani mitovirus 40 (RsMV40, +ssRNA), Rhizoctonia solani partitivirus 10 [RsPV10, double-stranded RNA (dsRNA)], Rhizoctonia solani partitivirus 11 (RsPV11, dsRNA), and Rhizoctonia solani RNA virus 11 (RsRV11, dsRNA). Whole genome sequences of RsFV4, RsMV40, RsPV10, RsPV11, and RsRV11, as well as a partial genome sequence of RsFV5, were obtained. The 3'- and 5'- untranslated regions of the five mycoviruses with complete genome sequences were folded into stable stem-loop or panhandle secondary structures. RsFV4 and RsFV5 are most closely related to Rhizoctonia solani fusarivirus 1 (RsFV1), however, the first open reading frame (ORF) of RsFV4 and RsFV5 encode a hypothetical protein that differs from the first ORF of RsFV1, which encodes a helicase. We confirmed that RsPV10 and RsPV11 assemble into the spherical virus particles (approximately 30 nm in diameter) that were extracted from strain ZJ-2H. This is the first report that +ssRNA and dsRNA viruses co-infect a single strain of R. solani AG-3 PT.


Asunto(s)
Virus Fúngicos , Virus ARN , Anastomosis Quirúrgica , Virus Fúngicos/genética , Genoma Viral , Filogenia , Virus ARN/genética , ARN Bicatenario/genética , ARN Viral/genética , Rhizoctonia
18.
Arch Virol ; 167(6): 1461-1466, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35469094

RESUMEN

A new potyvirus was found in Thevetia ahouai L. (Fam. Apocynaceae) plants exhibiting white spots on leaves and fruit discoloration in Ecuador. The complete genome sequences of two isolates of this virus, tentatively named "thevetia white spot virus" (ThWSV), were determined and found to be 9,912 (isolate 1) and 9,904 (isolate 2) nucleotides (nt) in length, each encoding a polyprotein of 363 kDa. Sequence comparisons between the two isolates showed 80 and 87% identity at the nt and amino acid (aa) level, respectively, whereas the overall sequence identity between ThWSV and its closest relative was 69% and 71% at the nt and aa level, respectively.


Asunto(s)
Potyvirus , Thevetia , Ecuador , Genoma Viral , Filogenia , Enfermedades de las Plantas , Potyvirus/genética , ARN Viral/genética
19.
Arch Virol ; 167(6): 1491-1494, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35474497

RESUMEN

The genome of a novel virus identified in Cnidium officinale is composed of a monopartite ssRNA of 16,755 nucleotides that shares 68.73% (query coverage, 20%) sequence identity with carrot yellow leaf virus (CYLV, accession no. FJ869862.1). It contains 11 putative open reading frames and has an organization typical of closteroviruses. It shares 30-50% nucleotide sequence identity with other closteroviruses. The heat shock protein 70-like protein (HSP70), putative RNA-dependent RNA polymerase (RdRp), and coat protein (CP) show 39-66%, 16-60%, and 24-41% amino acid sequence identity, respectively, to the homologous proteins of previously identified closteroviruses. Molecular and HSP70-based phylogenetic analysis of the genome and encoded protein sequences suggested that this virus is a novel member of the genus Closterovirus in the family Closteroviridae, which we have tentatively named "cnidium closterovirus 1" (CnClV1).


Asunto(s)
Closterovirus , Closterovirus/genética , Cnidium , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , ARN Viral/genética
20.
Arch Virol ; 167(6): 1495-1498, 2022 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-35482088

RESUMEN

In April 2011, a virus was isolated by single-lesion isolation on Chenopodium quinoa leaves from an amaryllis plant with chlorotic ringspots in a private garden in Changhua County, Taiwan. An Illumina MiSeq sequencing system was used to determine the genomic nucleotide (nt) sequence of the virus. A de novo-assembled contig with 9377 nt, containing an open reading frame encoding a putative potyviral polyprotein, was annotated as the potyvirus Amazon lily mosaic virus (ALiMV), sharing 95.5% nt sequence identity with a partial genomic sequence of ALiMV available in the GenBank database. Therefore, the amaryllis virus was designated as ALiMV-TW. Through 5´ and 3´ rapid amplification of cDNA ends (RACE), the complete 9618-nt genome sequence of ALiMV-TW was determined. Sequence comparisons indicated that the genome and polyprotein of ALiMV-TW share 52.3-65.1% nt and 30.1-64.2% aa sequence identity, respectively, with those of other potyviruses. This is the first report of a complete genome sequence of ALiMV.


Asunto(s)
Amaryllidaceae , Lilium , Potyvirus , Genoma Viral , Filogenia , Poliproteínas/genética , Potyvirus/genética
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