RESUMEN
The worldwide dispersal of the ectoparasitic mite Varroa destructor from its Asian origins has fundamentally transformed the relationship of the honey bee (Apis mellifera) with several of its viruses, via changes in transmission and/or host immunosuppression. The extent to which honey bee-virus relationships change after Varroa invasion is poorly understood for most viruses, in part because there are few places in the world with several geographically close but completely isolated honey bee populations that either have, or have not, been exposed long-term to Varroa, allowing for separate ecological, epidemiological, and adaptive relationships to develop between honey bees and their viruses, in relation to the mite's presence or absence. The Azores is one such place, as it contains islands with and without the mite. Here, we combined qPCR with meta-amplicon deep sequencing to uncover the relationship between Varroa presence, and the prevalence, load, diversity, and phylogeographic structure of eight honey bee viruses screened across the archipelago. Four viruses were not detected on any island (ABPV-Acute bee paralysis virus, KBV-Kashmir bee virus, IAPV-Israeli acute bee paralysis virus, BeeMLV-Bee macula-like virus); one (SBV-Sacbrood virus) was detected only on mite-infested islands; one (CBPV-Chronic bee paralysis virus) occurred on some islands, and two (BQCV-Black queen cell virus, LSV-Lake Sinai virus,) were present on every single island. This multi-virus screening builds upon a parallel survey of Deformed wing virus (DWV) strains that uncovered a remarkably heterogeneous viral landscape featuring Varroa-infested islands dominated by DWV-A and -B, Varroa-free islands naïve to DWV, and a refuge of the rare DWV-C dominating the easternmost Varroa-free islands. While all four detected viruses investigated here were affected by Varroa for one or two parameters (usually prevalence and/or the Richness component of ASV diversity), the strongest effect was observed for the multi-strain LSV. Varroa unambiguously led to elevated prevalence, load, and diversity (Richness and Shannon Index) of LSV, with these results largely shaped by LSV-2, a major LSV strain. Unprecedented insights into the mite-virus relationship were further gained from implementing a phylogeographic approach. In addition to enabling the identification of a novel LSV strain that dominated the unique viral landscape of the easternmost islands, this approach, in combination with the recovered diversity patterns, strongly suggests that Varroa is driving the evolutionary change of LSV in the Azores. This study greatly advances the current understanding of the effect of Varroa on the epidemiology and adaptive evolution of these less-studied viruses, whose relationship with Varroa has thus far been poorly defined.
Asunto(s)
Varroidae , Animales , Abejas/virología , Abejas/parasitología , Varroidae/virología , Azores , Virus de Insectos/genética , Virus de Insectos/aislamiento & purificación , Virus de Insectos/clasificación , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificaciónRESUMEN
Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments. IMPORTANCE: Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.
Asunto(s)
Culicidae , Filogenia , Viroma , Animales , Brasil , Viroma/genética , Culicidae/virología , Mosquitos Vectores/virología , Genoma Viral , ARN Viral/genética , Virus de Insectos/genética , Virus de Insectos/clasificación , Virus de Insectos/aislamiento & purificación , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificaciónRESUMEN
Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as 'ambiviruses,' were described. 'Ambiviruses' have single-stranded RNA genomes of about 4-5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known 'ambiviruses,' and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae. However, 'ambivirus' genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations-features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as 'epsilonviruses,' 'zetaviruses,' and some 'obelisks'). As a first step toward the formal classification of 'ambiviruses,' the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota, to accommodate an initial set of 20 members with well-annotated genome sequences.
Asunto(s)
Genoma Viral , Sistemas de Lectura Abierta , Viroides , Viroides/genética , Viroides/clasificación , Filogenia , ARN Viral/genética , Virus ARN/genética , Virus ARN/clasificación , Hongos/genética , Hongos/virología , ARN Polimerasa Dependiente del ARN/genética , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificaciónRESUMEN
BACKGROUND: Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples. METHODS: The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools. RESULTS: The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242). CONCLUSION: The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
Asunto(s)
Pollos , Heces , Metagenómica , ARN Viral , Viroma , Animales , Pollos/virología , Sudáfrica/epidemiología , Heces/virología , Viroma/genética , Metagenómica/métodos , ARN Viral/genética , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Granjas , Metagenoma , Estaciones del AñoRESUMEN
BACKGROUND: Like all other species, fungi are susceptible to infection by viruses. The diversity of fungal viruses has been rapidly expanding in recent years due to the availability of advanced sequencing technologies. However, compared to other virome studies, the research on fungi-associated viruses remains limited. RESULTS: In this study, we downloaded and analyzed over 200 public datasets from approximately 40 different Bioprojects to explore potential fungal-associated viral dark matter. A total of 12 novel viral sequences were identified, all of which are RNA viruses, with lengths ranging from 1,769 to 9,516 nucleotides. The amino acid sequence identity of all these viruses with any known virus is below 70%. Through phylogenetic analysis, these RNA viruses were classified into different orders or families, such as Mitoviridae, Benyviridae, Botourmiaviridae, Deltaflexiviridae, Mymonaviridae, Bunyavirales, and Partitiviridae. It is possible that these sequences represent new taxa at the level of family, genus, or species. Furthermore, a co-evolution analysis indicated that the evolutionary history of these viruses within their groups is largely driven by cross-species transmission events. CONCLUSIONS: These findings are of significant importance for understanding the diversity, evolution, and relationships between genome structure and function of fungal viruses. However, further investigation is needed to study their interactions.
Asunto(s)
Virus Fúngicos , Hongos , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia , Virus ARN , Virus ARN/genética , Virus ARN/clasificación , Hongos/genética , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Evolución MolecularRESUMEN
A new fusagra-like virus infecting papaya (Carica papaya L.) was genetically characterized. The genome of the virus, provisionally named "papaya sticky fruit-associated virus" (PSFaV), is a single molecule of double-stranded RNA, 9,199 nucleotides (nt) in length, containing two discontinuous open reading frames. Pairwise sequence comparisons based on complete RNA-dependent-RNA-polymerase (RdRp) sequences revealed identity of 79.4% and 83.3% at the nt and amino acid (aa) level, respectively, to babaco meleira-like virus (BabMelV), an uncharacterized virus sequence discovered in babaco (Vasconcellea x heilbornii) in Ecuador. Additional plant-associated viruses with sequence identity in the 50% range included papaya meleira virus (PMeV) isolates from Brazil. Phylogenetic analysis based on the amino acid sequences of the capsid protein (CP), RdRp, and CP-RdRp fusion protein genes placed PSFaV in a group within a well-supported clade that shares a recent ancestor with Sclerotium rolfsii RNA virus 2 and Phlebiopsis gigantea mycovirus dsRNA 2, two fungus-associated fusagraviruses. Genomic features and phylogenetic relatedness suggest that PSFaV, along with its closest relative BabMelV, represent a species of novel plant-associated virus classified within the recently established family Fusagraviridae.
Asunto(s)
Carica , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Enfermedades de las Plantas , ARN Viral , Carica/virología , Genoma Viral/genética , Ecuador , Enfermedades de las Plantas/virología , ARN Viral/genética , Secuenciación Completa del Genoma , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , ARN Polimerasa Dependiente del ARN/genética , Proteínas de la Cápside/genéticaRESUMEN
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.
Asunto(s)
Genoma Viral , Micorrizas , Filogenia , Virus ARN , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Micorrizas/genética , Micorrizas/virología , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , ARN Viral/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Proteínas Virales/genética , Sistemas de Lectura Abierta , Secuencia de BasesRESUMEN
A novel negative-sense single-stranded RNA mycovirus, designated as "Magnaporthe oryzae mymonavirus 1" (MoMNV1), was identified in the rice blast fungus Magnaporthe oryzae isolate NJ39. MoMNV1 has a single genomic RNA segment consisting of 10,515 nucleotides, which contains six open reading frames. The largest open reading frame contains 5837 bases and encodes an RNA replicase. The six open reading frames have no overlap and are arranged linearly on the genome, but the spacing of the genes is small, with a maximum of 315 bases and a minimum of 80 bases. Genome comparison and phylogenetic analysis indicated that MoMNV1 is a new member of the genus Penicillimonavirus of the family Mymonaviridae.
Asunto(s)
Virus Fúngicos , Genoma Viral , Sistemas de Lectura Abierta , Oryza , Filogenia , Enfermedades de las Plantas , Virus ARN , ARN Viral , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , Virus Fúngicos/genética , Virus Fúngicos/aislamiento & purificación , Virus Fúngicos/clasificación , Oryza/microbiología , Oryza/virología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , ARN Viral/genética , Ascomicetos/virología , Ascomicetos/genética , Proteínas Virales/genética , Magnaporthe/virología , Magnaporthe/genéticaRESUMEN
The virus family Phenuiviridae (order Hareavirales, comprising segmented negative-sense single stranded RNA viruses) has highly diverse members that are known to infect animals, plants, protozoans, and fungi. In this study, we identified a novel phenuivirus infecting a strain of the entomopathogenic fungus Cordyceps javanica isolated from a small brown plant hopper (Laodelphax striatellus), and this virus was tentatively named "Cordyceps javanica negative-strand RNA virus 1" (CjNRSV1). The CjNRSV1 genome consists of three negative-sense single stranded RNA segments (RNA1-3) with lengths of 7252, 2401, and 1117 nt, respectively. The 3'- and 5'-terminal regions of the RNA1, 2, and 3 segments have identical sequences, and the termini of the RNA segments are complementary to each other, reflecting a common characteristic of viruses in the order Hareavirales. RNA1 encodes a large protein (â¼274 kDa) containing a conserved domain for the bunyavirus RNA-dependent RNA polymerase (RdRP) superfamily, with 57-80% identity to the RdRP encoded by phenuiviruses in the genus Laulavirus. RNA2 encodes a protein (â¼79 kDa) showing sequence similarity (47-63% identity) to the movement protein (MP, a plant viral cell-to-cell movement protein)-like protein (MP-L) encoded by RNA2 of laulaviruses. RNA3 encodes a protein (â¼28 kDa) with a conserved domain of the phenuivirid nucleocapsid protein superfamily. Phylogenetic analysis using the RdRPs of various phenuiviruses and other unclassified phenuiviruses showed CjNRSV1 to be grouped with established members of the genus Laulavirus. Our results suggest that CjNRSV1 is a novel fungus-infecting member of the genus Laulavirus in the family Phenuiviridae.
Asunto(s)
Cordyceps , Genoma Viral , Filogenia , ARN Viral , Cordyceps/genética , ARN Viral/genética , Virus Fúngicos/clasificación , Virus Fúngicos/genética , Virus Fúngicos/aislamiento & purificación , Proteínas Virales/genética , Virus ARN de Sentido Negativo/genética , Virus ARN de Sentido Negativo/clasificación , ARN Polimerasa Dependiente del ARN/genética , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Secuencia de Aminoácidos , Sistemas de Lectura AbiertaRESUMEN
In this study, we identified a novel partitivirus, named "Cordyceps militaris partitivirus 1" (CmPV1), in Cordyceps militaris strain RCEF7506. The complete genome of CmPV1 comprises two segments, dsRNA1 and dsRNA2, each encoding a single protein. dsRNA1 (2,206 bp) encodes an RNA-dependent RNA polymerase (RdRp), and dsRNA2 (2,256 bp) encodes a coat protein (CP). Sequence analysis revealed that dsRNA1 has the highest similarity to that of Bipolaris maydis partitivirus 2 (BmPV2), whereas dsRNA2 shows the highest similarity to human blood-associated partitivirus (HuBPV). Phylogenetic analysis based on RdRp sequences suggests that CmPV1 is a new member of the genus Betapartitivirus of the family Partitiviridae. This is the first documentation of a betapartitivirus infecting the entomopathogenic fungus C. militaris.
Asunto(s)
Cordyceps , Virus Fúngicos , Genoma Viral , Filogenia , Virus ARN , Cordyceps/genética , Cordyceps/virología , Cordyceps/aislamiento & purificación , Genoma Viral/genética , Virus Fúngicos/genética , Virus Fúngicos/aislamiento & purificación , Virus Fúngicos/clasificación , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , ARN Viral/genética , ARN Polimerasa Dependiente del ARN/genética , Sistemas de Lectura Abierta , Proteínas Virales/genética , Proteínas de la Cápside/genéticaRESUMEN
Here, we report a novel ourmia-like mycovirus, named "Phomopsis asparagi magoulivirus 1" (PaMV1), derived from the phytopathogenic fungus Phomopsis asparagi. The genome of PaMV1 consists of a positive-sense single-stranded RNA (+ ssRNA) that is 2,639 nucleotides in length, with a GC content of 57.13%. It contains a single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) consisting of 686 amino acids with a molecular mass of 78.57 kDa. Phylogenetic analysis based on RdRp sequences revealed that PaMV1 grouped together with Diaporthe gulyae magoulivirus 1 (DgMV1) in a distinct clade. Sequence comparisons and phylogenetic analysis suggest that PaMV1 is a novel member of the genus Magoulivirus, family Botourmiaviridae.
Asunto(s)
Virus Fúngicos , Genoma Viral , Sistemas de Lectura Abierta , Phomopsis , Filogenia , ARN Viral , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Phomopsis/virología , ARN Viral/genética , Secuenciación Completa del Genoma , ARN Polimerasa Dependiente del ARN/genética , Composición de Base , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Proteínas Virales/genética , Secuencia de Bases , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificaciónRESUMEN
Monilinia fructicola is one of the most devastating fungal diseases of rosaceous fruit crops, both in the field and postharvest, causing significant yield losses. Here, we report the discovery of a novel positive single-stranded RNA virus, Monilinia fructicola hypovirus 3 (MfHV3), in a strain (hf-1) of the phytopathogenic fungus Monilinia fructicola. The complete genome of MfHV3 is 9259 nucleotides (nt) in length and contains a single large open reading frame (ORF) from nt position 462 to 8411. This ORF encodes a polyprotein with three conserved domains, namely UDP-glycosyltransferase, RNA-dependent RNA polymerase (RdRp), and DEAD-like helicase. The MfHV3 polyprotein shares the highest similarity with Colletotrichum camelliae hypovirus 1. Phylogenetic analysis indicated that MfHV3 clustered with members of the genus Betahypovirus within the family Hypoviridae. Taken together, the results of genomic organization comparisons, amino acid sequence alignments, and phylogenetic analysis convincingly show that MfHV3 is a new member of the genus Betahypovirus, family Hypoviridae.
Asunto(s)
Ascomicetos , Virus Fúngicos , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Enfermedades de las Plantas , Ascomicetos/virología , Ascomicetos/genética , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , ARN Viral/genética , Proteínas Virales/genética , Secuenciación Completa del Genoma , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , ARN Polimerasa Dependiente del ARN/genética , Secuencia de AminoácidosRESUMEN
The brown planthopper (BPH), Nilaparvata lugens, is a significant agricultural pest capable of long-distance migration and transmission of viruses that cause severe disease in rice. In this study, we identified a novel segmented RNA virus in a BPH, and this virus exhibited a close relationship to members of a recently discovered virus lineage known as "quenyaviruses" within the viral kingdom Orthornavirae. This newly identified virus was named "Nilaparvata lugens quenyavirus 1" (NLQV1). NLQV1 consists of five positive-sense, single-stranded RNAs, with each segment containing a single open reading frame (ORF). The genomic characteristics and phylogenetic analysis support the classification of NLQV1 as a novel quenyavirus. Notably, all of the genome segments of NLRV contained the 5'-terminal sequence AUCUG. The characteristic virus-derived small interfering RNA (vsiRNA) profile of NLQV1 suggests that the antiviral RNAi pathway of the host BPH was activated in response to virus infection. These findings represent the first documented report of quenyaviruses in planthoppers, contributing to our understanding of quenyaviruses and expanding our knowledge of insect-specific viruses in planthoppers.
Asunto(s)
Genoma Viral , Hemípteros , Sistemas de Lectura Abierta , Filogenia , Virus ARN , ARN Viral , Animales , Hemípteros/virología , Genoma Viral/genética , ARN Viral/genética , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Enfermedades de las Plantas/virología , Oryza/virología , Secuenciación Completa del Genoma , ARN Interferente Pequeño/genéticaRESUMEN
In this study, seven bee viruses of significant importance for bee health in Türkiye were investigated using one-step RT-PCR. For this purpose, larvae from 1183 hives and adult bees from 1196 hives were sampled from 400 apiaries in 40 provinces. The prevalence of viral infections in hives was as follows: acute bee paralysis virus (ABPV), 6.4%; black queen cell virus (BQCV), 77%; chronic bee paralysis virus (CBPV), 3.2%; deformed wing virus (DWV), 63.8%; Israel acute bee paralysis virus (IAPV), 7%; Kashmir bee virus (KBV), 2.7%; sacbrood virus (SBV), 49.7%. Moreover, 50 different combinations of viral infections were identified in the hives. While dual infections (36.1%) were the most common in hives, triple infections with BQCV, DWV, and SBV were found to have the highest prevalence (22.1%). At least one viral infection was detected in all of the apiaries tested. Phylogenetic analysis showed that the isolates from this study generally exhibited the highest similarity to previously reported Turkish isolates. When similarity ratios and the locations and types of amino acid mutations were analyzed, it was observed that the isolates from our study exhibited high similarity to isolates from various countries, including China, the United Kingdom, Syria, and Germany.
Asunto(s)
Virus de Insectos , Filogenia , Virus ARN , Animales , Abejas/virología , Virus de Insectos/genética , Virus de Insectos/aislamiento & purificación , Virus de Insectos/clasificación , Prevalencia , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , Larva/virología , Coinfección/virología , Coinfección/epidemiología , Dicistroviridae/genética , Dicistroviridae/aislamiento & purificación , Dicistroviridae/clasificaciónRESUMEN
A novel mitovirus was identified in Fusarium oxysporum f. sp. melonis strain T-SD3 and designated as "Fusarium oxysporum mitovirus 3" (FoMV3). The virus was isolated from diseased muskmelon plants with the typical symptom of fusarium wilt. The complete genome of FoMV3 is 2269 nt in length with a predicted AU content of 61.40% and contains a single open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF was predicted to encode a polypeptide of 679 amino acids (aa) containing a conserved RNA-dependent RNA polymerase (RdRp) domain with a molecular mass of 77.39 kDa, which contains six conserved motifs with the highly conserved GDD tripeptide in motif IV. The 5'-untranslated region (UTR) and 3'-UTR of FoMV3 were predicted to fold into stem-loop structures. BLASTp analysis revealed that the RdRp of FoMV3 shared the highest aa sequence identity (83.85%) with that of Fusarium asiaticum mitovirus 5 (FaMV5, a member of the family Mitoviridae) infecting F. asiaticum, the causal agent of wheat fusarium head blight. Phylogenetic analysis further suggested that FoMV3 is a new member of the genus Unuamitovirus within the family Mitoviridae. This is the first report of a new mitovirus associated with F. oxysporum f. sp. melonis.
Asunto(s)
Virus Fúngicos , Fusarium , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Enfermedades de las Plantas , Fusarium/virología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Virus Fúngicos/genética , Virus Fúngicos/aislamiento & purificación , Virus Fúngicos/clasificación , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , Secuenciación Completa del Genoma , ARN Viral/genética , ARN Polimerasa Dependiente del ARN/genética , Proteínas Virales/genética , Cucumis melo/virología , Cucumis melo/microbiología , Secuencia de Aminoácidos , Regiones no Traducidas 5' , Regiones no Traducidas 3' , Secuencia de BasesRESUMEN
Here, we characterized a novel mitovirus from the fungus Nigrospora oryzae, which was named "Nigrospora oryzae mitovirus 3" (NoMV3). The NoMV3 genome is 2,492 nt in length with a G + C content of 33%, containing a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 775 amino acids with a molecular mass of 88.75 kDa. BLASTp analysis revealed that the RdRp of NoMV3 had 68.6%, 50.6%, and 48.6% sequence identity to those of Nigrospora oryzae mitovirus 2, Suillus luteus mitovirus 6, and Fusarium proliferatum mitovirus 3, respectively, which belong to the genus Unuamitovirus within the family Mitoviridae. Phylogenetic analysis based on amino acid sequences supported the classification of NoMV3 as a member of a new species in the genus Unuamitovirus within the family Mitoviridae.
Asunto(s)
Ascomicetos , Virus Fúngicos , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Enfermedades de las Plantas , Virus ARN , ARN Polimerasa Dependiente del ARN , Genoma Viral/genética , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , ARN Polimerasa Dependiente del ARN/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Ascomicetos/virología , Ascomicetos/genética , ARN Viral/genética , Proteínas Virales/genética , Composición de Base , Secuencia de AminoácidosRESUMEN
The extensive use of high-throughput sequencing (HTS) has significantly advanced and transformed our comprehension of virus diversity, especially in intricate settings like soil and biological specimens. In this study, we delved into mycovirus sequence surveys within mycorrhizal fungus species Terfezia claveryi, through employing HTS with total double-stranded RNA (dsRNA) extracts. Our findings revealed the presence of four distinct members from the Alsuviricetes class, one flexivirus designated as Terfezia claveryi flexivirus 1 (TcFV1) and three endornaviruses (TcEV1, TcEV2, and TcEV3) in two different T. claveryi isolates. TcFV1, a member of the order Tymovirales, exhibits a unique genome structure and sequence features. Through in-depth analyses, we found that it shares sequence similarities with other deltaflexiviruses and challenges existing Deltaflexiviridae classification. The discovery of TcFV1 adds to the genomic plasticity of mycoviruses within the Tymovirales order, shedding light on their evolutionary adaptations. Additionally, the three newly discovered endornaviruses (TcEV1, TcEV2, and TcEV3) in T. claveryi exhibited limited sequence similarities with other endornaviruses and distinctive features, including conserved domains like DEAD-like helicase, ATPases Associated with Diverse Cellular Activities (AAA ATPase), and RNA dependent RNA polymerase (RdRp), indicating their classification as members of new species within the Alphaendornavirus genus. In conclusion, this research emphasizes the importance of exploring viral diversity in uncultivated fungi, bridging knowledge gaps in mycovirus ecology. The discoveries of a novel flexivirus with unique genome organization and endornaviruses in T. claveryi broaden our comprehension of mycovirus diversity and evolution, highlighting the need for continued investigations into viral populations in wild fungi.
Asunto(s)
Virus Fúngicos , Genoma Viral , Micorrizas , Filogenia , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Micorrizas/genética , Micorrizas/virología , Micorrizas/clasificación , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , ARN Viral/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Basidiomycota/virología , Basidiomycota/genéticaRESUMEN
Negeviruses are insect-specific enveloped RNA viruses that exhibit a wide geographic distribution. A novel nege-like virus, tentatively named Aphis gossypii nege-like virus (AGNLV, GenBank: OR880429.1), was isolated from aphids (Aphis gossypii) in Lijiang City, Yunnan, China. AGNLV has a genome sequence of 9258 nt (excluding the polyA tail) encoding three open reading frames (ORFs). ORF1 (7149 nt) encodes a viral methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase. ORF2 (1422 nt) encodes a DiSB-ORF2_chro domain and ORF3 encodes an SP24 domain. The genome sequence of AGNLV shares the highest nucleotide identity of 60.0% and 59.5% with Wuhan house centipede virus 1 (WHCV1) and Astegopteryx formosana nege-like virus (AFNLV), respectively. Phylogenetic analysis based on the RNA-dependent RNA polymerase shows that AGNLV is clustered with other negeviruses and nege-like viruses discovered in aphids, forming a distinct "unclassified clade". Interestingly, AGNLV only encodes three ORFs, whereas AFNLV and WHCV1 have four ORFs. Structure and transmembrane domain predictions show the presence of eight alpha helices and five transmembrane helices in the AGNLV ORF3. Translational enhancement of the AGNLV 5' UTR was similar to that of the 5' UTR of plant viruses. Our findings provide evidence of the diversity and structure of nege-like viruses and are the first record of such a virus from a member of the genus Aphis.
Asunto(s)
Áfidos , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Animales , Áfidos/virología , China , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , ARN Polimerasa Dependiente del ARN/genética , Proteínas Virales/genética , Proteínas Virales/química , Virus de Insectos/genética , Virus de Insectos/aislamiento & purificación , Virus de Insectos/clasificación , ARN Viral/genéticaRESUMEN
Genome sequence analysis and classification play critical roles in properly understanding an organism's main characteristics, functionalities, and changing (evolving) nature. However, the rapid expansion of genomic data makes genome sequence analysis and classification a challenging task due to the high computational requirements, proper management, and understanding of genomic data. Recently proposed models yielded promising results for the task of genome sequence classification. Nevertheless, these models often ignore the sequential nature of nucleotides, which is crucial for revealing their underlying structure and function. To address this limitation, we present SPM4GAC, a sequential pattern mining (SPM)-based framework to analyze and classify the macromolecule genome sequences of viruses. First, a large dataset containing the genome sequences of various RNA viruses is developed and transformed into a suitable format. On the transformed dataset, algorithms for SPM are used to identify frequent sequential patterns of nucleotide bases. The obtained frequent sequential patterns of bases are then used as features to classify different viruses. Ten classifiers are employed, and their performance is assessed by using several evaluation measures. Finally, a performance comparison of SPM4GAC with state-of-the-art methods for genome sequence classification/detection reveals that SPM4GAC performs better than those methods.
Asunto(s)
Algoritmos , Genoma Viral , Genómica/métodos , Biología Computacional/métodos , Sustancias Macromoleculares/química , Minería de Datos , Virus ARN/genética , Virus ARN/clasificaciónRESUMEN
RNA viruses quickly evolve subtle genotypic changes that can have major impacts on viral fitness and host range, with potential consequences for human health. It is therefore important to understand the evolutionary fitness of novel viral variants relative to well-studied genotypes of epidemic viruses. Competition assays are an effective and rigorous system with which to assess the relative fitness of viral genotypes. However, it is challenging to quickly and cheaply distinguish and quantify fitness differences between very similar viral genotypes. Here, we describe a protocol for using reverse transcription PCR in combination with commercial nanopore sequencing services to perform competition assays on untagged RNA viruses. Our assay, called the Universal Competition Assay by Nanopore Sequencing (U-CAN-seq), is relatively cheap and highly sensitive. We used a well-studied N24A mutation in the chikungunya virus (CHIKV) nsp3 gene to confirm that we could detect a competitive disadvantage using U-CAN-seq. We also used this approach to show that mutations to the CHIKV 5' conserved sequence element that disrupt sequence but not structure did not affect the fitness of CHIKV. However, similar mutations to an adjacent CHIKV stem loop (SL3) did cause a fitness disadvantage compared to wild-type CHIKV, suggesting that structure-independent, primary sequence determinants in this loop play an important role in CHIKV biology. Our novel findings illustrate the utility of the U-CAN-seq competition assay.