Archives of Virology

Cotton (Gossypium spp.) is a globally significant cash crop cultivated for its versatile fiber, widely used in the textile industry. Cotton, as other crops, is vulnerable to infectious pathogens. Several of them, including viruses, are a major threat to cotton production. Geminiviruses (family Geminiviridae) are insect transmitted, small non-enveloped viruses, with circular single-stranded DNA genomes, which are encapsidated in quasi-icosahedral geminated virions. Here we present evidence of a novel begomovirus (genus Begomovirus) infecting cotton from Argentina. Two circular ssDNA virus sequences were assembled from high-throughput sequencing data from Gossyipium hirsutum cotton samples showing mosaic symptoms from Argentina. Structural and functional annotation indicated that the virus sequences corresponded to complete DNA components A and B of a novel New World bipartite begomovirus. Genetic distance and evolutionary analyses support that the detected sequences correspond to a new virus, a tentative prototype member of a novel species which we propose the name "Cotton mosaic virus" (CoMV).

Mpox, formerly monkeypox, is a viral zoonotic disease caused by the mpox virus (MPXV). MPXV, which is phylogenetically divided into Clades I and II, was declared a Public Health Emergency of International Concern for the second time in August 2024 due to rapid geographic expansion of Clade I viruses including the newly identified subclade Ib. With a unique set of genomic mutations and sustained human-to-human transmission, subclade Ib has rapidly spread throughout the eastern Democratic Republic of the Congo as well as neighboring non-endemic regions and outside the African continent. Currently, there is a lack of comparative genomic data with which to address the potential zoonotic transmissibility and pathobiology of subclade Ib. Here we report 105 protein-coding genes that are shared by all the queried MPXV subclade Ia, Ib, and IIb genomes. Our comparative genomic analysis identified that the core Clade I gene pair, OPG032 and OPG033, is now a critical branching element for subclade Ia/Ib due to their loss in subclade Ib. These genes encode the complement control protein (a vaccinia virus ortholog associated with virulence), and a Kelch-like protein associated with pathogenesis, respectively, suggesting a functional evolution that might play an important role in the pathobiology of the new MPXV subclade Ib. Our results lay the groundwork to exploit the genomic elements of MPXV as potential targets for therapeutics development/repurposing, vaccine design, and molecular diagnostic expansion, as well as to uncover the viral diversity, and human-to-human transmission of MPXV.

The maize leafhopper (Dalbulus maidis) is a significant threat to maize crops in tropical and subtropical regions, causing extensive economic losses. While its ecological interactions and control strategies are well-studied, its associated viral diversity remains largely unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the D. maidis RNA virome, revealing novel and diverse RNA viruses. We characterized six new viral members belonging to distinct families, with evolutionary cues of beny-like viruses (Benyviridae), bunya-like viruses (Bunyaviridae) iflaviruses (Iflaviridae), orthomyxo-like viruses (Orthomyxoviridae), and rhabdoviruses (Rhabdoviridae). Phylogenetic analysis of the iflaviruses places them within the genus Iflavirus in affinity with other leafhoppers-associated iflaviruses. The five-segmented and highly divergent orthomyxo-like virus showed a relationship with other insect associated orthomyxo-like viruses. The rhabdo virus is related with a leafhopper associated rhabdo-like virus. Furthermore, the beny-like virus belonged to a cluster of insect-associated beny-like viruses, while the bi-segmented bunya-like virus was related with other bi-segmented insect-associated bunya-like viruses. These results highlight the existence of a complex virome linked to D. maidis and paves the way for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses on the D. maidis--maize pathosystem.

Viruses in the family Partitiviridae consist of non-enveloped viruses with bisegmented double-stranded RNA genomes. Viruses in this family have been identified from plants and fungi. In this study, we identified several viruses belonging to the family Partitiviridae using plant transcriptomes. From 11 different plant species, we identified a total of 74 RNA segments representing 23 partitiviruses. Of 74 RNA segments, 28 RNA segments encode RNA-dependent RNA polymerases (RdRp) while 46 RNA segments encode coat proteins (CPs). According to ICTV demarcation for the family Partitiviridae, 25 RNAs encoding RdRp and 41 RNAs encoding CP were novel RNA segments. In addition, we identified eight RNA segments (three for RdRp and five for CP) belonging to the known partitivruses. Taken together, this study provides the largest number of partitiviruses from plant transcriptomes in a single study.

The Colorado potato beetle is one of the most devastating potato pests widespread in the world. However, its viral pathogens remain highly unexplored. Here using SISPA high-throughput sequencing of Colorado potato beetle (CPB) samples derived from prepupal larvae that died from an unknown infection, we have identified two previously unknown viruses and assembled their full-length genomic sequences. The subsequent genetic and phylogenetic analysis of the obtained sequences demonstrated that the isolated viruses, named Leptinotarsa iflavirus 1 and Leptinotarsa solinvi-like virus 1, are the novel representatives of Iflaviridae and Solinviviridae viral families, respectively. To the best of our knowledge, these are the first sequencing-confirmed insect viruses derived directly from CPB samples. And we also propose that Leptinotarsa iflavirus 1 may be associated with lethal disease in CPB.

RNA-dependent RNA polymerases (RdRps) are crucial for replication of RNA viruses and serve as key marker genes for defining deep taxonomic ranks and for understanding viral evolutionary history. Despite shared functions and conserved amino acid motifs, the high genetic diversity of RdRps complicates precise sequence comparisons across viral families, hindering accurate taxonomic classification of new species - especially important at the age of metagenomics. When available, three-dimensional (3D) RdRp structures can help address these challenges through structure-based alignments. However, such structures are scarce for understudied viruses infecting fungi and plants, preventing the investigation of their ecological and evolutionary links. In this study, we focused on the highy divergent order Sobelivirales. Using deep{-}learning structural modeling, we generated highly reliable 3D models on 20 representative viral species. Multiple structural alignment enabled the reconstruction of a robust phylogeny with improved quality and length. Based on this phylogeny, we proposed revisions of existing viral families and reclassified genera. Clade divergence dates were then estimated using the Prisoner of War model, which has previously revealed the ancient origin of the genus Sobemovirus. We provided here the first divergence time estimation between these plant and fungal viruses, dating back to 26.6 million years before present - significantly more recent than the divergence between their respective hosts. Our amino acid conservation analysis, validated on 99 other viral species, also identified molecular signatures of sobeliviral families and genera, which could help in future taxonomic assignment and diagnostic tools development. This interdisciplinary approach integrating structure modeling and date estimations offers new insights into the evolutionary divergence between fungus and plant viruses, with potential applications to other viral orders and families. Author summaryRNA-dependent RNA polymerases (RdRps) are essential for RNA virus replication and serve as important markers for classifying viruses and understanding their evolution. However, with the rising popularity of metagenomics and discovery of viruses with high genetic diversity in RdRps, it is difficult to compare viral families and accurately classify new species. When available, 3D structures of RdRps can help overcome this challenge through structural alignments. In this study, we focused on the highly divergent order of the Sobelivirales, using deep{-}learning models to generate reliable 3D structures for 20 representative viral species. These structural alignments allowed us to build a more accurate viral phylogeny. Based on this finding, we proposed updates to existing viral families and genera within the Sobelivirales order. We also estimated divergence dates using a model that previously uncovered the ancient origins of Sobemovirus. Notably, we provided the first estimate of when these plant and fungal viruses diverged - around 26.6 million years ago, which is much more recent than the separation of their hosts. We also identified molecular signatures that are useful for future virus classification and diagnosis, with potential applications to other viral groups.

Most members of the genus Gammacoronavirus infect avian hosts, but far fewer viruses have been characterized than in the other coronavirus genera, leaving their diversity largely unclear. Pigeon gammacoronaviruses were previously detected by consensus PCR, but only partial sequences were determined. In this study, we comprehensively analyzed public RNA-seq datasets and reconstructed two nearly complete genomes of pigeon gammacoronaviruses. Molecular evolutionary analyses showed pigeon gammacoronaviruses belong to the subgenus Igacovirus, and their pairwise distances to the members of this subgenus meet the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria, supporting their designation as a novel species in this subgenus. Notably, although nucleotide sequences are highly conserved gammacoronaviruses, their 3'-genomic region exhibited differences in gene organization among pigeon coronavirus variants. These findings expand our knowledge of the diversity of gammacoronaviruses.

The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRp). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats () in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.

Avian pox disease is a highly contagious infection caused by pox virus and has serious consequences on avian species with regards to economic and conservation aspects. This viral genus named as Avipox virus (APV) that infects nearly 300 bird species and lack of enough complete genome information creates hindrance to infer this virus biology. Thus in this study, we have revealed the first complete genome of an Indian pigeon pox virus that belongs to the genus APV followed by comparative genomics analysis. The entire genome of present isolate (PPV/Pur-Od-4b/01/Ind) having 280058 bp nucleotide sequences with the GC content 29.51%. The unique feature of this complete genome revealed the presence of 270 open reading frames (ORFs) circumscribed by inverted terminal repeats (ITRs) of 4,689 bp at each end and lack of recombination events. The concatenated amino acid phylogenetic tree deciphered the present isolate closely related with Feral Pigeon pox virus derived from Africa. The molecular markers, such as microsatellites were ubiquitously distributed throughout the genome and more prevalent within the functional genes.

Rabies disease can be caused by several lyssaviruses, which are a group of bullet-shaped, enveloped viruses with single-stranded, negative-sense RNA as their genome. Lyssaviruses are known to produce a full complement of genomic RNA (cRNA or antigenome) during their lifecycle. The rabies virus (RABV) is the prototype of the genus and has a genome of 12 kilobases. The RABV genome is known to encode five proteins from the genomic strand. In this study, we examined the coding potential of RABV and identified 17 novel ORFs (nORFs): one on the genomic strand and sixteen on the antigenomic strand. Synteny analysis revealed that several of these nORFs were conserved across the RABV clades. Additionally, five of the nORFs possessed Kozak sequences, and trRosetta predicted well-folded three-dimensional domains in these nORFs. Using LC-MS data of rabies-infected canine brain samples, we identified high-confidence peptides corresponding to the two nORF-coded proteins, nORF9 and nORF12. Furthermore, the structural and sequence similarity analyses indicated that these domains share homology with proteins involved in signalling and transcription.

Rhizoctonia cerealis is the pathogen of wheat sharp eyespot, which occurs throughout temperate wheat growing regions of the world. In this project, the genomes of viruses from four strains of R. cerealis were analyzed based on Illumina high-throughput RNA-Seq data. Ribosomal RNA-depleted total RNA and purified dsRNA from cultivated mycelia of each isolate were used for cDNA library construction and sequencing. After filtering out reads that mapped to the fungal genome, viral genomes were assembled using the remaining reads from the rRNA-depleted and dsRNA-Seq data. In total, 131 viral genome sequences containing complete ORFs, belonging to 117 viruses, were obtained. Based on phylogenetic analysis, some of them were identified as novel members of the families Curvulaviridae, Endornaviridae, Hypoviridae, Mitoviridae, Mymonaviridae and Phenuiviridae, while others were unclassified viruses. We compared the integrity and reliability of the viral sequences obtained by the two sequencing methods and, for the first time, estimated the density of some viruses in host cells. Most of these viruses from R. cerealis were sufficiently different from those deposited in databases. We propose the establishment of a new family, Rhizoctobunyaviridae, and two new genera, Rhizoctobunyavirus and Iotahypovirus. We further clarified the distribution and co-infection of these viruses in the four R. cerealis strains. In conclusion, the diversity of mycoviruses in R. cerealis is extremely rich. We report a series of novel viruses and provide important insight into virus evolution.

Mpox virus (MPXV) has consistently caused human infections since the first reported case in 1970, with the initial outbreaks primarily attributed to sporadic zoonotic transmissions. In recent years, an increase in human-to-human transmission has been observed, particularly during the 2022 outbreak caused by Clade IIb, which was declared a public health emergency by WHO. In 2024, the emergence of Clade Ib from Africa raised global concern once again. While several studies have provided valuable insights into the differences among MPXV clades, research on Clade Ib remains limited. In this study, we have conducted a comprehensive comparative genome sequence analysis and identified unique features across MPXV clade sequences. We report a [~]1141 bp long novel deletion resulting in loss of the complement control protein (CCP) in Clade Ib sequences, a deletion earlier exclusively reported in Clade II sequences. Additionally, B22R, a crucial host receptor-binding protein involved in viral entry and known for its high immunogenicity, shows clade-specific amino acid changes across three MPXV clades. Moreover, multiple extragenic mutations were identified in the 5 UTR of several genes, which may impact gene transcription. Other frequently mutated proteins are linked to immune evasion, translation, and viral entry and exit. The above results and APOBEC signatures associated with sustained human-to-human transmission highlight the viruss potential for rapid adaptation, underscoring the need for vigilance against reverse zoonosis and the risk of spillover to new hosts.

The subfamily Orthoparamyxovirinae is a group of single-stranded, negative-sense RNA viruses that contains many human, animal and zoonotic pathogens. While there are currently only 34 recognized member species in this subfamily, recent research has revealed that much of its diversity remains to be characterized. Using a newly developed nested PCR-based screening assay, we report here the discovery of fifteen orthoparamyxoviruses in rodents and shrews from Belgium and Guinea, thirteen of which are believed to represent new species. Using nanopore sequencing, complete genomes could be determined for almost all of these viruses, enabling a detailed evaluation of their genome characteristics. While most viruses are thought to belong to the rapidly expanding genus Jeilongvirus, we also identify novel members of the genera Narmovirus, Henipavirus and Morbillivirus. Together with other recently discovered orthoparamyxoviruses, both the henipaviruses and the morbillivirus discovered here appear to form distinct rodent-/shrew-borne clades within their respective genera, clustering separately from all currently classified member species. In the case of the henipaviruses, a comparison of the different members of this clade revealed the presence of a secondary conserved open reading frame, encoding for a transmembrane protein, within the F gene, the biological relevance of which remains to be established. While the characteristics of the viruses described here shed further light on the complex evolutionary origin of paramyxoviruses, they also illustrate that the diversity of this group of viruses in terms of genome organization appears to be much larger than previously assumed. Data availabilityThe genome sequences generated in this study have been submitted to GenBank (accession numbers OK623353-OK623368).

Mesta yellow vein mosaic disease (MYVMD), one of the major diseases circulating mesta growing regions of Indian sub-continent, is responsible for serious yield loss in mesta crops. A complex of monopartite begomovirus, Mesta yellow vein mosaic virus (MYVMV) and associated betasatellite, is reported in several studies as the causal agent of MYVMD. However, all-inclusive molecular evolutionary analysis of so far available MYVMVs and associated betasatellites disseminating in this region is still lacking. In this study, by estimating and analyzing various indexes of population genetics and evolutionary parameters, we discussed the sources of genetic variations, population dynamics and different forces acting on the evolution of MYVMVs and associated betasatellites. The study finds recombination as a vital force in the evolution and diversification of begomovirus complexes in different geographic locations however, betasatellites were found to be exposed to more diverse recombination events compared to MYVMVs. Indian isolates are reported to have high frequency of polymorphism in this study which suggests a balancing selection or expansion occurring in Indian populations of begomoviruses. Higher degree of genetic differentiation and lower rate of gene flow calculated between the viral populations of Bangladesh and Pakistan is justified by the relatively far geographical distance between these two countries. Although the study detects overall purifying selection, the degrees of constraints acting on individual gene tested are found different. Coat protein (AV1) is estimated with very high nucleotide substitution rate which is very likely to result from the strongest purifying selection pressure (dN/dS = 0.131) calculated in this study on coat protein. The findings of this study on different evolutionary forces that shape the emergence and diversification of MYVMVs and associated betasatellites may provide directions towards future evolutionary trend analysis and development of comprehensive disease control strategies for begomoviruses.

The Citrus yellow vein clearing virus (CYVCV) causes a viral disease that has been reported in specific citrus-growing regions in Euro-Asia including countries of Pakistan, India, Turkiye, Iran, China and south Korea. Recently, CYVCV was detected in a localized urban area in a town in heart of Californias citrus-growing region and marks the first occurrence of the virus in North America. CYVCV is spread by aphid and whitefly vectors and is graft and mechanically transmitted. Hence, it is an invasive disease that presents a significant threat to the California citrus industry, especially lemons which are highly susceptible to CYVCV. To elucidate the origin of the CYVCV California strain, we used long-read sequencing technology and obtained the complete genomes of three California CYVCV isolates, CA1, CA2, and CA3. The sequences of these isolates exhibited intergenomic similarities ranging from 95.4% to 97.4% to 54 publicly available CYVCV genome sequences which indicated a relatively low level of heterogeneity. However, CYVCV CA isolates formed a distinct clade from the other isolates when aligned against other CYVCV genomes and coat protein gene sequences. Based on a rooted Maximum Likelihood phylogenetic tree, CYVCV CA isolates shared the most recent common ancestor with isolates from India. Further examination of 79 coat protein gene sequences collected over a 31-year period that spanned regions from East and South Asia to the Middle East and California, Bayesian evolutionary inferences resulted in a spatiotemporal reconstruction that placed the origin of all CYVCV to the 1930s, with South Asia as the most plausible geographic source. This analysis also suggested that CYVCV CA isolates diverged from Indian lineages, possibly around the 2010s. Moreover, the spatiotemporal phylogenetic analysis indicated two additional virus diffusion pathways: one from South Asia to East Asia and another from South Asia to the Middle East. Collectively, our phylogenetic inferences offer insights into the probable dynamics of global CYVCV dissemination, emphasizing the need for citrus industries and regulatory agencies to closely monitor citrus commodities crossing state and international borders. Author SummaryA localized outbreak of CYVCV was detected in a central California town, marking its first appearance in North America. The study sequenced the complete genomes of three CYVCV isolates from California and employed statistical algorithms to investigate the population dynamics and origin of CYVCV. Upon comparing coat protein gene sequences, the CYVCV isolates from California formed a distinct group separate from those found in other geological regions. The studys spatiotemporal phylogenetic analysis highlighted that CYVCV likely originated in the 1930s, with South Asia as the most plausible source. Notably, the CYVCV isolates from California diverged from Indian lineages, possibly around the 2010s. This study contributes to a better understanding of CYVCVs genetic and molecular diversity, shedding light on virus ecology, evolution, and biology.

Locusts and grasshoppers are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling locust outbreaks in fragile ecosystems. Here we use metagenomic sequencing to profile the rich viral communities in 34 grasshopper species and report 322 viruses, including 202 novel species. Most of the identified viruses are related to other insect viruses and some are targeted by antiviral RNAi pathway, indicating they infect grasshoppers. Some plant/fungi/vertebrate associated viruses are also abundant in our samples. Our analysis of relationships between host and virus phylogenies suggests that the composition of viromes is closely allied with host evolution, and there is significant phylogenetic relatedness between grasshoppers and viruses from Lispiviridae, Partitiviridae, Orthomyxoviridae, Virgaviridae and Flaviviridae. Overall, this study is a thorough exploration of viruses in grasshoppers and provide an essential evolutionary and ecological context for host-virus interaction in Acridoidea. Author SummaryLocusts are the most destructive migratory pest in the world and continue to cause massive damages that endanger food security and threaten millions of people in 21st century. While chemical pesticides are still heavily relied on, biological pesticides developed from natural pathogens offer a reliable, less harmful alternative for controlling locust outbreaks in fragile ecosystems. Unfortunately, little is known about natural pathogens infecting this pest. In this study, we profile the viral communities in 34 grasshopper species include some major swarming species. While we identified as many as 202 novel viral species associated with grasshoppers, some of them are of potential to be developed as biocontrol agents. Our analysis of relatedness of phylogenies of grasshoppers and associated viruses helps to shed light on the eco-evolutionary interactions between insects and viruses. This work provides a valuable dataset of both academic and applied interest.

BackgroundHerpesviruses are a group of double-stranded DNA viruses known to infect a wide range of vertebrates and establish life-long latent infections. While bats serve as natural reservoir hosts for numerous viral families, relatively few bat herpesviruses have been successfully isolated. In this study, we report the isolation and characterization of two novel alphaherpesvirus strains obtained from Rousettus aegyptiacus bats in Coastal Kenya. MethodsThe samples of oral and rectal swabs were collected from three different species of bats from coastal Kenya between October 2024 and April 2025; the bat species collected include Hipposideros spp., Coleura afra, and Rousettus aegyptiacus. Virus isolation was performed by inoculation of samples in Vero E6 cells and subsequent monitoring for cytopathic effects (CPE). Total nucleic acids were extracted from CPE positive cultures and subjected to library preparation to enable unbiased detection of both RNA and DNA viruses. The libraries were sequenced using next-generation sequencing with Illumina MiSeq platform. Subsequently, bioinformatic analysis was carried out to identify the virus, generate consensus genomes as well as phylogenetic analysis to determine the placement of identified viruses. ResultsTwo samples from R. aegyptiacus (KIK_460_O and KIK_465_O) induced typical CPE within five days. Sequencing and assembly yielded partial consensus sequences of approximately 60 kb (KIK_460_O) and 70 kb (KIK_465_O), representing extended genomic data for a bat-associated alphaherpesvirus. This virus has a genome of about 140kb, indicating that our partial assemblies account for about 43-50% of the total genome. Both isolates were found to be closely related to Dzifa herpesvirus, an alphaherpesvirus previously identified in Kilifi, Kenya. Alphaherpesvirus was identified based on partial sequencing of UL19 (3,787bp) and UL30 (2,846bp) genes. The two isolates were found to be identical at the UL19 gene, showing that they belonged to the same virus strain. Phylogenetic analysis showed that the novel alphaherpesvirus belongs to primate alphaherpesviruses under the subfamily Alphaherpesvirinae. ConclusionThis study reports the isolation and genomic characterization of a novel fruit bat alphaherpesvirus from Kenyan Rousettus aegyptiacus bats. The partial genome assembly (60-70 kb) represent the first extended genomic data for this virus, covering approximately 43-50% of the estimated 140 kb complete genome. The phylogenetic placement of this alphaherpesvirus near primate viruses, especially Pteropodid alphaherpesvirus 1, suggests bat-association and needs further investigation into its zoonotic potential.

The kingdom Bamfordvirae comprises the majority of the realm Varidnaviria and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla Nucleocytoviricota and Preplasmiviricota. There are several fundamental unresolved issues related to the evolution of Bamfordvirae. These are questions concerning Bamfordvirae taxonomy including the branching order of Nucleocytoviricota and the question of the monophyly of Preplasmiviricota. Here, based on the analyses of the individual core protein phylogenies, supertree, concatenated trees, dendrograms, as well as superdendrogram, we have refined the branching order of major groups within phylum Nucleocytoviricota using the rooting of the entire phylum on the cellular outgroups. These efforts resulted in several major changes in Bamfordvirae phylogeny. In particular, we showed that Nucleocytoviricota consists of two sister clades, consisting of Phycodnaviridae sensu lato on the one hand and Mimiviridae sensu lato, Iridoviridae/Ascoviridae, Marseilleviridae, pithoviruses including Cedratvirus, Solumvirus, Solivirus, and Orpheovirus, Mininucleoviridae, Asfarviridae sensu lato, and Poxviridae on the other hand. According to our data, Asfarviridae sensu lato and Poxviridae have likely originated from within the class Megaviricetes. We gave evidence for polyphyly of the phylum Preplasmiviricota and argued for a transfer of the families Lavidaviridae, Adintoviridae, and Adenoviridae from the phylum Preplasmiviricota into the phylum Nucleocytoviricota. We also argued for the origin of the Nucleocytoviricota from small prokaryotic viruses and gave arguments against the origin of Nucleocytoviricota from the Adintoviridae/Polinton-like viruses. ImportanceThe monophyly of Varidnaviria, consisting of the Bamfordvirae and Helvetiavirae kingdoms, remains a matter of debate. To confirm or refute the monophyly of Varidnaviria, it is important to identify the sources of origin and phylogenetic relationships common to all Varidnaviria genes, such as the FtsK-HerA superfamily ATPases, major and minor capsid proteins. However, such studies are relevant only if the direction of evolution of both kingdoms was firmly established. Thus, our work, by clarifying the phylogenetic relationships within the Bamfordvirae kingdom, provided a solid basis for studying the evolutionary relationships of this kingdom with a vast diversity of supposedly related viruses outside of Bamfordvirae, including Helvetiavirae (Varidnaviria).

Tomato brown rugose fruit virus (Tobamovirus fructirugosum) is an emerging virus that affects tomatoes, capsicum, and chili. Since its first detection in Jordan in 2015, the virus was reported in more than 40 countries across all the continents. In Morocco, the virus was reported for the first time in October 2021. However, its genetic diversity remains unexplored. In this work, we used a collection of tomato fruits from local markets to investigate the variability of the virus in the country. We explored the different pressures acting on the N-terminus of the RNA-dependent RNA polymerase, the movement protein, and the coat protein genes. Then, we used haplotype network analyses to reveal the population structure within the Moroccan isolates and studied their relationships with the ones from the world. We found that genetic diversity is low, which is consistent with the global situation. No signatures of diversifying selection were detected across the analyzed genes. However, the virus sequences from Morocco showed a clear geographic structure, suggesting that geographic factors probably combined with agricultural practices may contribute to shaping the population structure of ToBRFV in Morocco.

The mesnidoviruses are positive single-stranded viruses belonging to the order Nidovirales. They were mostly found in mosquitoes, and represent a link from small to large nidoviruses. In this study, we report 18 newly discovered nidoviruses in TSA database, most of them are from spiders (Order Arachnida). After reassembly, we got 9 nearly complete genomes with sizes ranged from [~]19,500 to 33,500 nt. Further phylogenetic analyses assigned these nidoviruses to Mesnidovirineae. Among them, the spider viruses represent a new clade. Pairwise evolutionary distance (PED) analysis showed these mesnidoviruses are highly divergent, with PED values from 2.2 to 4.9 with existing ones. Even among themselves the PED values are notable: with most exceeding the threshold of 0.32 that defines a new virus genus, suggesting these viruses are new species or belong to new higher-ranking taxa. In summary, we reported 18 mesnidoviruses in spiders, insects, plant and Anthozoa, the highly divergence suggested that spiders may harbor diverse mesnidoviruses. As the first nidovirus reported in Arachnida and Anthozoa, this discovery will contribute to the evolution study of Nidovirales.