Endogenous viral elements in animal genomes

Cryptic infection of a giant virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. In this work, we describe a 617-kilo-base pairs integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolved the integrated viral genome using long-read sequencing, identified a putative polintovirus-like integrase, and show that viral particles accumulate primarily during the stationary growth phase. A diverse array of viral-encoded selfish genetic elements is expressed during viral activity, including several Fanzor nuclease-encoding transposable elements. In addition, we show that field isolates of Chlamydomonas spp. harbor signatures of endogenous giant viruses related to the C. reinhardtii virus that exhibit similar infection dynamics, suggesting that giant virus latency is prevalent in natural host communities. Our work describes an unusually large temperate virus of a unicellular eukaryote, substantially expanding the scope of cryptic viral infections in the virosphere.

detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data

Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.

Evolution of KoRV-A transcriptional silencing in wild koalas

Koala retrovirus-A (KoRV-A) is spreading through wild koalas in a north-to-south wave while transducing the germ line, modifying the inherited genome as it transitions to an endogenous retrovirus. Previously, we found that KoRV-A is expressed in the germ line, but unspliced genomic transcripts are processed into sense-strand PIWI-interacting RNAs (piRNAs), which may provide an initial "innate" form of post-transcriptional silencing. Here, we show that this initial post-transcriptional response is prevalent south of the Brisbane River, whereas KoRV-A expression is suppressed, promoters are methylated, and sense and antisense piRNAs are equally abundant in a subpopulation of animals north of the river. These animals share a KoRV-A provirus in the MAP4K4 gene's 3' UTR that is spreading through northern koalas and produces hybrid transcripts that are processed into antisense piRNAs, which guide transcriptional silencing. We speculate that this provirus triggers adaptive transcriptional silencing of KoRV-A and is sweeping to fixation.

Diversity and evolution analysis of RNA viruses in three wheat aphid species

BACKGROUND

Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.

RESULTS

We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.

CONCLUSIONS

This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.

Genomic and Epidemiological Investigations Reveal Chromosomal Integration of the Acipenserid Herpesvirus 3 Genome in Lake Sturgeon Acipenser fulvescens

DNA sequence from a new alloherpesvirus named acipenserid herpesvirus 3 (AciHV-3) was found in sturgeon species that are vulnerable to decline globally. A study was undertaken to develop a better understanding of the virus genome and to develop diagnostic tools to support an epidemiological investigation. A 184,426 bp genome was assembled from PacBio HiFi sequences generated with DNA from a Lake Sturgeon Acipenser fulvescens gonad cell line. The AciHV-3 genome was contiguous with host chromosomal DNA and was structured with telomere-like terminal direct repeat regions, five internal direct repeat regions and a U region that included intact open reading frames encoding alloherpesvirus core proteins. Diagnostic testing conducted with a newly developed and analytically validated qPCR assay established the ubiquitous presence and high titer of AciHV-3 DNA in somatic and germline tissues from wild Lake Sturgeon in the Hudson Bay drainage basin. Phylogenetic reconstructions confirm that the monophyletic AciHV-3 lineage shares a common ancestor with AciHV-1 and that AciHV-3 taxa cluster according to their sturgeon host. The same genotype of AciHV-3 is found in disjunctive Lake Sturgeon populations within and among drainage basins. The results support the hypotheses that AciHV-3 has established latency through germline chromosomal integration, is vertically transmitted via a Mendelian pattern of inheritance, is evolving in a manner consistent with a replication competent virus and has co-evolved with its host reaching genetic fixation in Lake Sturgeon populations in central Canada.

Molecular antiviral responses, immune priming and inheritance in insects

Viral diseases transmitted by insects to plants cause severe agricultural damage and arboviruses transmitted to humans cause severe disease outbreaks. The interaction between viruses and the insect defences is complex and has evolved into acting-counteracting molecular interplays. Viruses depict complex molecular mechanisms to ensure invasion, replication and exit the insect host cell, to invade other cells. On the other hand, insect cells use molecular strategies to recognize, halt replication and eliminate the invaders. In turn, virus counteract with evasive strategies. The main antiviral defence mechanism RNA interference (RNAi) recognizes and degrades viral RNA, thereby inhibiting viral replication. These in conjunction with other canonical immune pathways, Toll, IMD, JAK/STAT and Akt-ERK developed mainly to combat bacteria, fungi and protozoa, along with mechanisms to eliminate infected cells like apoptosis and phagocytosis comprise a multifactorial system. Insects exposed to an attenuated or sublethal viral infection could respond with faster and enhanced immune responses to the same pathogen (priming), which is like immunological memory in vertebrates. Several mechanisms have been proposed to explain priming, including endoreplication, epigenetic gene modifications by DNA methylation and histone acetylation. Priming could be inherited by the offspring (transgenerational immune priming, TGIP). However, the precise molecular mechanisms underlying TGIP remain to be elucidated. This article reviews the molecular mechanisms employed by insects to combat viral infections, discusses the current information and the outstanding research questions in the area.

Aberrant expression of human endogenous retrovirus K9-derived elements is associated with better clinical outcome of acute myelocytic leukemia

BACKGROUND

Acute myelocytic leukemia (AML) is a common hematological malignancy in adults. Although several risk stratifications based on cytogenetic and molecular abnormalities are available to guide the indications for allogeneic hematopoietic cell transplantation (allo-HCT), determining optimal treatment strategies for AML remains challenging. In this study, using transcriptome datasets, we investigated the association between event-free survival (EFS) in intensively treated AML patients and the aberrant expression of endogenous viral element (EVE)-derived open reading frames (ORFs), which have been reported to be associated with the pathophysiology of various malignancies and have the potential to serve as neoantigens in specific cancers.

RESULTS

The expression levels of human endogenous retrovirus family K9 (HERVK9) ORFs were associated with EFS, independent of conventional risk stratification. Furthermore, AML cells with higher levels of HERVK9 expression exhibited enhanced antigen processing and presentation, along with increased expression of genes associated with adaptive immune responses and apoptosis, indicating that aberrant HERVK9 expression may initiate an anti-neoplastic immune response via increased antigen presentation.

CONCLUSIONS

HERVK9 expression may have serve as a crucial prognostic indicator that could aid in determining the indications for upfront allo-HCT in AML patients.

Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element

BACKGROUND

Advancing our knowledge of vector species genomes is a key step in our battle against the spread of diseases. Biting midges of the genus Culicoides are vectors of arboviruses that significantly affect livestock worldwide. Culicoides stellifer is a suspected vector with a wide range distribution in North America, for which cryptic diversity has been described.

RESULTS

With just one specimen of C. stellifer, we assembled and annotated the nuclear and mitochondrial genome using the ultra-low input DNA PacBio protocol. The genome assembly is 119 Mb in length with a contig N50 value of 479.3 kb, contains 11% repeat sequences and 18,895 annotated protein-coding genes. To further elucidate the role of this species as a vector, we provide genomic evidence of a non-retroviral endogenous viral element integrated into the genome that corresponds to rhabdovirus nucleocapsid proteins, the same family as the vesicular stomatitis virus.

CONCLUSIONS

This genomic information will pave the way for future investigations into this species's putative vector role. We also demonstrate the practicability of completing genomic studies in small dipterans using single specimens preserved in ethanol as well as introduce a workflow for data analysis that considers the challenges of insect genome assembly.

Microbial Nanoparticles in Biological Plant Protection

Nanoparticles are small structures that differ in terms of their shape and composition; their high surface-to-volume ratio is responsible for their unique properties that make them perfect mediators for the delivery of substances. Nanoparticles do not only include metallic spheres but also complex polysaccharides capsule viruses or bacterial protein complexes (which can be considered bionanoparticles), which are 1-100 nm in size. Although nanoparticles are most widely studied from medical perspectives, their potential applications are almost limitless. One such promising use of functional nanoparticles is for plant protection against diseases. Although the precise use of nanoparticles decreases the need for the use of other chemical compounds, thanks to their increased product stability and delivery to a target site, the production of nanoparticles is often burdened by large quantities of toxic wastes. This problem can be limited if we apply the bioreactor green synthesis method, which includes the production of nanoparticles with the use of microorganisms. Bacteria can produce nanoparticles internally, externally, by only producing metabolites used for nanoparticle production directly, e.g., polysaccharides or surfactants, or indirectly as reducing agents for metal nanoparticle production. Regardless of the source of the nanoparticles, they can be widely used in processes from plant disease/pathogen detection to disease suppression. The endless variety of materials for nanoparticle production and the possible modifications that nanoparticles can be subjected to makes it impossible to predict how their structures will be used in the future. Nevertheless, in this study, we would like to turn attention to the fact that although nanoparticles are viewed as synthetic structures, they are ever-present in the microbial world and play an important part in intermicrobial interactions. As nanoparticle usefulness has been tested over years of co-evolution, it may be useful to look for potential future directions for this fascinating technology.

Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions

Background

Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.

Methods

In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.

Results

Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.

Conclusion

These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.

EVE-X: Software to Identify Novel Viral Insertions in Wild-Caught Arthropod Hosts From Next-Generation Short Read Data

Eukaryotic genomes harbour sequences derived from non-retroviral RNA viruses, known as endogenous viral elements (EVEs) or non-retroviral integrated RNA virus sequences (NIRVS). These sequences represent a record of past infections and have been implicated in host anti-viral response. We have created a program to identify viral sequences integrated in a host genome. It begins with a specimen BAM file and outputs candidate NIRVS, along with putative host insertion sites and overlapping genomic features of the host genome in XML and visual formats, with minimal intermediary intervention. We ran through this software short-read data derived from the genomes of 222 wild-caught A. aegypti mosquitoes, from a dozen geographical regions, and located putative NIRVS from seven virus families. This program is as accurate as currently available software for NIRVS detection, and represents a significant improvement in adaptability and user-friendliness. Furthermore, the flexibility of this pipeline allows the user to search for sequence integrations across the genome of any organism, as long as a query sequence database and a reference genome is provided. Potential extended applications include identification of integrated transgenic sequences used for research or vector control strategies.

EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes

Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.

Evidence of endogenous non-retroviral RNA virus sequences into the genome and transcriptome of the malaria vector Anopheles darlingi

The characterization of non-retroviral integrated RNA virus sequences (NIRVS) in mosquitoes has emerged as a significant area of research that could yield insight into virus-host interactions. This study aimed to characterize NIRVS in the Anopheles darlingi reference genome and identify putative transcribed NIRVS in field-collected mosquitoes from Colombia. The An. darlingi reference genome was analyzed to identify and characterize NIRVS by conducting a BLAST query with all the virus sequences previously identified in arthropods available in the NCBI-virus repository. In addition, An. darlingi field-collected mosquitoes were examined for NIRVS using a metatranscriptomic approach. As a result, 44 NIRVS were identified in the An. darlingi genome, constituting integrations of negative single-stranded RNA viruses (ssRNA-) from the families Rhabdoviridae, Chuviridae and Phasmaviridae, and integrations of double-stranded RNA viruses (dsRNA) from the families Partitiviridae and Sedoreoviridae. These NIRVS were not randomly distributed but clustered in specific regions of the genome enriched with BEL/Pao and Ty3/Gypsy long terminal repeat elements. Furthermore, putative NIRVS-like sequences were present in the transcriptomic data from all the Colombian An. darlingi natural populations. This study is significant as it represents the first identification of NIRVS in the most important malaria vector of the Neotropics. The findings help in understanding the intricate relationship between the mosquito and its virome, and the regulation of viruses' mechanisms in the Anopheles genus.

Endogenous viral elements: insights into data availability and accessibility

Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.

Impact of endogenous viral elements on glioma clinical phenotypes by inducing OCT4 in the host

Introduction

Endogenous viral elements (EVEs) are viral sequences integrated within the host genome that can influence gene regulation and tumor development. While EVEs have been implicated in cancer, their role in regulating key transcription factors in glioblastoma (GBM) remains underexplored. This study investigates the relationship between EVEs and the activation of OCT4, a critical transcription factor in GBM progression.

Methods

We utilized CancerHERVdb and HervD Atlas databases to identify potential interactions between EVEs and key genes involved in GBM. Data from 273 GBM patient samples in the TCGA database were analyzed to examine the correlation between OCT4 expression and mutations in glioma-related genes. Furthermore, glioblastoma stem cells (GSCs) were assessed for the expression levels of OCT4 and SOX2, and Pearson correlation analysis was performed.

Results

Our analysis revealed that OCT4 is a pivotal gene activated by EVEs in GBM. OCT4 expression was significantly correlated with mutations in key glioma-associated genes. Higher OCT4 levels were associated with poorer patient prognosis, higher tumor grades, and older age. Additionally, GSCs exhibited elevated expression of both OCT4 and SOX2, with a positive correlation observed between these two genes in GBM patients.

Discussion

This study highlights the potential role of EVEs in driving GBM progression through the activation of OCT4. The findings emphasize the importance of OCT4 in GBM malignancy and suggest that targeting EVE-mediated pathways may provide new therapeutic approaches for GBM treatment.

Deep mining reveals the diversity of endogenous viral elements in vertebrate genomes

Integration of viruses into host genomes can give rise to endogenous viral elements (EVEs), which provide insights into viral diversity, host range and evolution. A systematic search for EVEs is becoming computationally challenging given the available genomic data. We used a cloud-computing approach to perform a comprehensive search for EVEs in the kingdoms Shotokuvirae and Orthornavirae across vertebrates. We identified 2,040 EVEs in 295 vertebrate genomes and provide evidence for EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. In addition, our analyses revealed that reptarenaviruses and filoviruses probably acquired their glycoprotein ectodomains three times independently from retroviral elements. Taken together, these findings encourage the addition of 4 virus families and the Hepacivirus genus to the growing virus fossil record of vertebrates, providing key insights into their natural history and evolution.

Endogenous nege-like viral elements in arthropod genomes reveal virus-host coevolution and ancient history of two plant virus families

Negevirus is a recently proposed taxon of arthropod-infecting virus, which is associated with plant viruses of two families (Virgaviridae and Kitaviridae). Nevertheless, the evolutionary history of negevirus-host and its relationship with plant viruses remain poorly understood. Endogenous nege-like viral elements (ENVEs) are ancient nege-like viral sequences integrated into the arthropod genomes, which can serve as the molecular fossil records of previous viral infection. In this study, 292 ENVEs were identified in 150 published arthropod genomes, revealing the evolutionary history of nege-like viruses and two related plant virus families. We discovered three novel and eight strains of nege-like viruses in 11 aphid species. Further analysis indicated that 10 ENVEs were detected in six aphid genomes, and they were divided into four types (ENVE1-ENVE4). Orthologous integration and phylogenetic analyses revealed that nege-like viruses had a history of infection of over 60 My and coexisted with aphid ancestors throughout the Cenozoic Era. Moreover, two nege-like viral proteins (CP and SP24) were highly homologous to those of plant viruses in the families Virgaviridae and Kitaviridae. CP- and SP24-derived ENVEs were widely integrated into numerous arthropod genomes. These results demonstrate that nege-like viruses have a long-term coexistence with arthropod hosts and plant viruses of the two families, Virgaviridae and Kitaviridae, which may have evolved from the nege-like virus ancestor through horizontal virus transfer events. These findings broaden our perspective on the history of viral infection in arthropods and the origins of plant viruses.

IMPORTANCE

Although negevirus is phylogenetically related to plant virus, the evolutionary history of negevirus-host and its relationship with plant virus remain largely unknown. In this study, we used endogenous nege-like viral elements (ENVEs) as the molecular fossil records to investigate the history of nege-like viral infection in arthropod hosts and the evolution of two related plant virus families (Virgaviridae and Kitaviridae). Our results showed the infection of nege-like viruses for over 60 My during the arthropod evolution. ENVEs highly homologous to viral sequences in Virgaviridae and Kitaviridae were present in a wide range of arthropod genomes but were absent in plant genomes, indicating that plant viruses in these two families possibly evolved from the nege-like virus ancestor through cross-species horizontal virus transmission. Our findings provide a new perspective on the virus-host coevolution and the origins of plant viruses.

Crosstalk between human endogenous retroviruses and exogenous viruses

Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections of human germ-line cells, which are mostly silenced during evolution, but could be de-repressed and play a pathological role. Infection with some exogenous viruses, including herpesviruses, HIV-1 and SARS-CoV-2, was demonstrated to induce the expression of HERV RNAs and proteins.

Latent infection of an active giant endogenous virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe the activity and viral production from a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral region using long-read sequencing and show that viral particles are produced and released in otherwise healthy cultures. A diverse array of viral-encoded selfish genetic elements are expressed during GEVE reactivation and produce proteins that are packaged in virions. In addition, we show that field isolates of Chlamydomonas sp. harbor latent giant viruses related to the C. reinhardtii GEVE that exhibit similar infection dynamics, demonstrating that giant virus latency is prevalent in natural host communities. Our work reports the largest temperate virus documented to date and the first active GEVE identified in a unicellular eukaryote, substantially expanding the known limits of viral latency.

Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China

BACKGROUND

Hainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies.

METHODS

In this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed.

RESULTS

The results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene.

CONCLUSION

The EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

Several coronaviruses infect humans, with three, including the SARS-CoV2, causing diseases. While coronaviruses are especially prone to induce pandemics, we know little about their evolutionary history, host-to-host transmissions, and biogeography. One of the difficulties lies in dating the origination of the family, a particularly challenging task for RNA viruses in general. Previous cophylogenetic tests of virus-host associations, including in the Coronaviridae family, have suggested a virus-host codiversification history stretching many millions of years. Here, we establish a framework for robustly testing scenarios of ancient origination and codiversification versus recent origination and diversification by host switches. Applied to coronaviruses and their mammalian hosts, our results support a scenario of recent origination of coronaviruses in bats and diversification by host switches, with preferential host switches within mammalian orders. Hotspots of coronavirus diversity, concentrated in East Asia and Europe, are consistent with this scenario of relatively recent origination and localized host switches. Spillovers from bats to other species are rare, but have the highest probability to be towards humans than to any other mammal species, implicating humans as the evolutionary intermediate host. The high host-switching rates within orders, as well as between humans, domesticated mammals, and non-flying wild mammals, indicates the potential for rapid additional spreading of coronaviruses across the world. Our results suggest that the evolutionary history of extant mammalian coronaviruses is recent, and that cases of long-term virus-host codiversification have been largely over-estimated.

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil

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.

Intra- and inter-host origin, evolution dynamics and spatial-temporal transmission characteristics of circoviruses

Introduction

Since their identification in 1974, circoviruses have caused clinicopathological diseases in various animal species, including humans. However, their origin, transmission, and genetic evolution remain poorly understood.

Methods

In this study, the genome sequences of circovirus were obtained from GenBank, and the Bayesian stochastic search variable selection algorithm was employed to analyzed the evolution and origin of circovirus.

Results

Here, the evolutionary origin, mode of transmission, and genetic recombination of the circovirus were determined based on the available circovirus genome sequences. The origin of circoviruses can be traced back to fish circovirus, which might derive from fish genome, and human contributes to transmission of fish circovirus to other species. Furthermore, mosquitos, ticks, bats, and/or rodents might play a role as intermediate hosts in circovirus intra- and inter-species transmission. Two major lineages (A and B) of circoviruses are identified, and frequent recombination events accelerate their variation and spread. The time to the most recent common ancestor of circoviruses can be traced back to around A.D. 600 and has been evolving at a rate of 10-4 substitutions site-1 year-1 for a long time.

Discussion

These comprehensive findings shed light on the evolutionary origin, population dynamics, transmission model, and genetic recombination of the circovirus providing valuable insights for the development of prevention and control strategies against circovirus infections.

Characterization of Caulimovirid-like Sequences from Upland Cotton (Gossypium hirsutum L.) Exhibiting Terminal Abortion in Georgia, USA

In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant tissue samples revealed near-complete EVE-Georgia (EVE-GA) sequences closely related to caulimoviruses. The analysis of EVE-GA's putative open reading frames (ORFs) compared to cotton virus A and endogenous cotton pararetroviral elements (eCPRVE) revealed their similarity in putative ORFs 1-4. However, in the ORF 5 and ORF 6 encoding putative coat protein and reverse transcriptase, respectively, the sequences from EVE-GA have stop codons similar to eCPRVE sequences from Mississippi. In silico mining of the cotton genome database using EVE-GA as a query uncovered near-complete viral sequence insertions in the genomes of G. hirsutum species (~7 kb) but partial in G. tomentosum (~5.3 kb) and G. mustelinum (~5.1 kb) species. Furthermore, cotton EVEs' episomal forms and messenger RNA (mRNA) transcripts were detected in both symptomatic and asymptomatic plants collected from cotton fields. No significant yield difference was observed between symptomatic and asymptomatic plants of the two varieties evaluated in the experimental plot. Additionally, EVEs were also detected in cotton seeds and seedlings. This study emphasizes the need for future research on EVE sequences, their coding capacity, and any potential role in host immunity or pathogenicity.

Eukaryotic genomic data uncover an extensive host range of mirusviruses

A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses, Varidnaviria and Duplodnaviria. Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in 1,901 publicly available eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 915 assemblies spanning 227 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, suggesting that mirusviral infection contributes to the alteration of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil-producing thraustochytrid Schizochytrium sp. and the endolithic green alga Ostreobium quekettii. Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.

Innate and germline immune memory: specificity and heritability of the ancient immune mechanisms for adaptation and survival

The immune memory is one of the defensive strategies developed by both unicellular and multicellular organisms for ensuring their integrity and functionality. While the immune memory of the vertebrate adaptive immune system (based on somatic recombination) is antigen-specific, encompassing the generation of memory T and B cells that only recognize/react to a specific antigen epitope, the capacity of vertebrate innate cells to remember past events is a mostly non-specific mechanism of adaptation. This "innate memory" can be considered as germline-encoded because its effector tools (such as innate receptors) do not need somatic recombination for being active. Also, in several organisms the memory-related information is integrated in the genome of germline cells and can be transmitted to the progeny for several generations, but it can also be erased depending on the environmental conditions. Overall, depending on the organism, its environment and its living habits, innate immune memory appears to be a mechanism for achieving better protection and survival against repeated exposure to microbes/stressful agents present in the same environment or occurring in the same anatomical district, able to adapt to changes in the environmental cues. The anatomical and functional complexity of the organism and its lifespan drive the generation of different immune memory mechanisms, for optimal adaptation to changes in the living/environmental conditions. The concept of innate immunity being non-specific needs to be revisited, as a wealth of evidence suggests a significant degree of specificity both in the primary immune reaction and in the ensuing memory-like responses. This is clearly evident in invertebrate metazoans, in which distinct scenarios can be observed, with both non-specific (immune enhancement) or specific (immune priming) memory-like responses. In the case of mammals, there is evidence that some degree of specificity can be attained in different situations, for instance as organ-specific protection rather than microorganism-specific reaction. Thus, depending on the challenges and conditions, innate memory can be non-specific or specific, can be integrated in the germline and transmitted to the progeny or be short-lived, thereby representing an exceptionally plastic mechanism of defensive adaptation for ensuring individual and species survival.

Symbionts of Ciliates and Ciliates as Symbionts

Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.

Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals

Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.

A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

BACKGROUND

Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes.

RESULTS

Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.

CONCLUSIONS

We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.

Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles

During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.

High-Throughput Sequencing Reveals Three Rhabdoviruses Persisting in the IRE/CTVM19 Cell Line

Cell cultures derived from ticks have become a commonly used tool for the isolation and study of tick-borne pathogens and tick biology. The IRE/CTVM19 cell line, originating from embryos of Ixodes ricinus, is one such line. Previously, reovirus-like particles, as well as sequences with similarity to rhabdoviruses and iflaviruses, were detected in the IRE/CTVM19 cell line, suggesting the presence of multiple persisting viruses. Subsequently, the full genome of an IRE/CTVM19-associated rhabdovirus was recovered from a cell culture during the isolation of the Alongshan virus. In the current work, we used high-throughput sequencing to describe a virome of the IRE/CTVM19 cell line. In addition to the previously detected IRE/CTVM19-associated rhabdovirus, two rhabdoviruses were detected: Chimay rhabdovirus and Norway mononegavirus 1. In the follow-up experiments, we were able to detect both positive and negative RNA strands of the IRE/CTVM19-associated rhabdovirus and Norway mononegavirus 1 in the IRE/CTVM19 cells, suggesting their active replication in the cell line. Passaging attempts in cell lines of mammalian origin failed for all three discovered rhabdoviruses.

Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps

Thousands of endoparasitoid wasp species in the families Braconidae and Ichneumonidae harbor "domesticated endogenous viruses" (DEVs) in their genomes. This study focuses on ichneumonid DEVs, named ichnoviruses (IVs). Large quantities of DNA-containing IV virions are produced in ovary calyx cells during the pupal and adult stages of female wasps. Females parasitize host insects by injecting eggs and virions into the body cavity. After injection, virions rapidly infect host cells which is followed by expression of IV genes that promote the successful development of wasp offspring. IV genomes consist of two components: proviral segment loci that serve as templates for circular dsDNAs that are packaged into capsids, and genes from an ancestral virus that produce virions. In this study, we generated a chromosome-scale genome assembly for Hyposoter didymator that harbors H. didymator ichnovirus (HdIV). We identified a total of 67 HdIV loci that are amplified in calyx cells during the wasp pupal stage. We then focused on an HdIV gene, U16, which is transcribed in calyx cells during the initial stages of replication. Sequence analysis indicated that U16 contains a conserved domain in primases from select other viruses. Knockdown of U16 by RNA interference inhibited virion morphogenesis in calyx cells. Genome-wide analysis indicated U16 knockdown also inhibited amplification of HdIV loci in calyx cells. Altogether, our results identified several previously unknown HdIV loci, demonstrated that all HdIV loci are amplified in calyx cells during the pupal stage, and showed that U16 is required for amplification and virion morphogenesis.

Potential of Viruses as Environmental Etiological Factors for Non-Syndromic Orofacial Clefts

In this study, we analyzed the potential of viral infections in the species Homo sapiens as environmental causes of orofacial clefts (OFCs). A scoring system was adapted for qualitatively assessing the potential of viruses to cause cleft lip and/or palate (CL/P). This assessment considered factors such as information from the literature, nucleotide and amino acid similarities, and the presence of Endogenous Viral Elements (EVEs). The analysis involved various algorithm packages within Basic Local Alignment Search Tool 2.13.0 software and databases from the National Center for Biotechnology Information and the International Committee on Taxonomy of Viruses. Twenty significant viral species using different biosynthesis strategies were identified: Human coronavirus NL63, Rio Negro virus, Alphatorquevirus homin9, Brisavirus, Cosavirus B, Torque teno mini virus 4, Bocaparvovirus primate2, Human coronavirus HKU1, Monkeypox virus, Mammarenavirus machupoense, Volepox virus, Souris mammarenavirus, Gammapapillomavirus 7, Betainfluenzavirus influenzae, Lymphocytic choriomeningitis mammarenavirus, Ledantevirus kern, Gammainfluenzavirus influenzae, Betapolyomavirus hominis, Vesiculovirus perinet, and Cytomegalovirus humanbeta5. The evident viral etiological potential in relation to CL/P varies depending on the Baltimore class to which the viral species belongs. Given the multifactorial nature of CL/P, this relationship appears to be dynamic.

Rhabdoviral Endogenous Sequences Identified in the Leishmaniasis Vector Lutzomyia longipalpis Are Widespread in Sandflies from South America

Sandflies are known vectors of leishmaniasis. In the Old World, sandflies are also vectors of viruses while little is known about the capacity of New World insects to transmit viruses to humans. Here, we relate the identification of RNA sequences with homology to rhabdovirus nucleocapsids (NcPs) genes, initially in the Lutzomyia longipalpis LL5 cell lineage, named NcP1.1 and NcP2. The Rhabdoviridae family never retrotranscribes its RNA genome to DNA. The sequences here described were identified in cDNA and DNA from LL-5 cells and in adult insects indicating that they are transcribed endogenous viral elements (EVEs). The presence of NcP1.1 and NcP2 in the L. longipalpis genome was confirmed in silico. In addition to showing the genomic location of NcP1.1 and NcP2, we identified another rhabdoviral insertion named NcP1.2. Analysis of small RNA molecules derived from these sequences showed that NcP1.1 and NcP1.2 present a profile consistent with elements targeted by primary piRNAs, while NcP2 was restricted to the degradation profile. The presence of NcP1.1 and NcP2 was investigated in sandfly populations from South America and the Old World. These EVEs are shared by different sandfly populations in South America while none of the Old World species studied presented the insertions.

In vitro characterization of cell-fusing agent virus DNA forms in Aedes aegypti mosquitoes

How non-retroviral endogenous viral elements (EVEs) are established is a long-standing question. Viral DNA (vDNA) forms of RNA viruses are likely to be EVE precursors. Cell-fusing agent virus (CFAV) is a major insect-specific virus (ISV) in the Aedes aegypti mosquitoes and one of the few existing non-retroviral RNA viruses found as EVEs. We characterized CFAV-derived vDNA in the cell line to understand the mechanism of why current viruses are rarely endogenized. vDNA production was affected by cell culture media independent of CFAV replication. vDNAs that correspond to different regions covering the entire viral genome were detected, implying multiple initiation sites exist. A considerable proportion of vDNAs corresponded to ssDNA. Higher vDNA copies were detected in the cytoplasm than the nucleus. Our findings provide valuable insights into the intracellular characteristics of ISV-derived vDNAs, which will aid in understanding the underlying mechanisms of non-retroviral EVE formation.

Eukaryotic genomic data uncover an extensive host range of mirusviruses

A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses, Varidnaviria and Duplodnaviria. Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in publicly available 1,901 eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 1,348 assemblies spanning 284 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, underscoring the impact of mirusviral infection on the evolution of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil producing thraustochytrid Schizochytrium sp. and the endolithic green alga Ostreobium quekettii. Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.

Mosquito transgenerational antiviral immunity is mediated by vertical transfer of virus DNA sequences and RNAi

Mosquitoes are important vectors for transmission of many viruses of public and veterinary health concern. These viruses most commonly have an RNA genome and infect mosquitoes for life. The principal mosquito antiviral response is the RNAi system which destroys virus RNA. Here, we confirm an earlier study that Aedes aegypti mosquitoes infected with positive-stranded RNA arboviruses can transmit specific immunity to their offspring. We show that this trans-generational immunity requires replication of virus RNA and reverse transcription of vRNA to vDNA in the infected parents and intergenerational transfer of vDNA. This vDNA is both genome-integrated and episomal. The episomal vDNA sequences are flanked by retrotransposon long-terminal repeats, predominantly Copia-like. Integrated vDNA sequences are propagated along several generations but specific immunity is effective only for a few generations and correlates with the presence of vRNA and episomal vDNA. This understanding raises new possibilities for the control of important mosquito-borne virus diseases.

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans

IMPORTANCE

Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.

Intrinsic factors driving mosquito vector competence and viral evolution: a review

Mosquitoes are responsible for the transmission of numerous viruses of global health significance. The term "vector competence" describes the intrinsic ability of an arthropod vector to transmit an infectious agent. Prior to transmission, the mosquito itself presents a complex and hostile environment through which a virus must transit to ensure propagation and transmission to the next host. Viruses imbibed in an infectious blood meal must pass in and out of the mosquito midgut, traffic through the body cavity or hemocoel, invade the salivary glands, and be expelled with the saliva when the vector takes a subsequent blood meal. Viruses encounter physical, cellular, microbial, and immunological barriers, which are influenced by the genetic background of the mosquito vector as well as environmental conditions. Collectively, these factors place significant selective pressure on the virus that impact its evolution and transmission. Here, we provide an overview of the current state of the field in understanding the mosquito-specific factors that underpin vector competence and how each of these mechanisms may influence virus evolution.

Functional characterization of Microplitis demolitor bracovirus genes that encode nucleocapsid components

IMPORTANCE

Understanding how bracoviruses (BVs) function in wasps is of broad interest in the study of virus evolution. This study characterizes most of the Microplitis demolitor bracovirus (MdBV) genes whose products are nucleocapsid components. Results indicate several genes unknown outside of nudiviruses and BVs are essential for normal capsid assembly. Results also indicate most MdBV tyrosine recombinase family members and the DNA binding protein p6.9-1 are required for DNA processing and packaging into nucleocapsids.

Co-option of a non-retroviral endogenous viral element in planthoppers

Non-retroviral endogenous viral elements (nrEVEs) are widely dispersed throughout the genomes of eukaryotes. Although nrEVEs are known to be involved in host antiviral immunity, it remains an open question whether they can be domesticated as functional proteins to serve cellular innovations in arthropods. In this study, we found that endogenous toti-like viral elements (ToEVEs) are ubiquitously integrated into the genomes of three planthopper species, with highly variable distributions and polymorphism levels in planthopper populations. Three ToEVEs display exon‒intron structures and active transcription, suggesting that they might have been domesticated by planthoppers. CRISPR/Cas9 experiments revealed that one ToEVE in Nilaparvata lugens, NlToEVE14, has been co-opted by its host and plays essential roles in planthopper development and fecundity. Large-scale analysis of ToEVEs in arthropod genomes indicated that the number of arthropod nrEVEs is currently underestimated and that they may contribute to the functional diversity of arthropod genes.

Mosquito community composition shapes virus prevalence patterns along anthropogenic disturbance gradients

Previously unknown pathogens often emerge from primary ecosystems, but there is little knowledge on the mechanisms of emergence. Most studies analyzing the influence of land-use change on pathogen emergence focus on a single host-pathogen system and often observe contradictory effects. Here, we studied virus diversity and prevalence patterns in natural and disturbed ecosystems using a multi-host and multi-taxa approach. Mosquitoes sampled along a disturbance gradient in Côte d'Ivoire were tested by generic RT-PCR assays established for all major arbovirus and insect-specific virus taxa including novel viruses previously discovered in these samples based on cell culture isolates enabling an unbiased and comprehensive approach. The taxonomic composition of detected viruses was characterized and viral infection rates according to habitat and host were analyzed. We detected 331 viral sequences pertaining to 34 novel and 15 previously identified viruses of the families Flavi-, Rhabdo-, Reo-, Toga-, Mesoni- and Iflaviridae and the order Bunyavirales. Highest host and virus diversity was observed in pristine and intermediately disturbed habitats. The majority of the 49 viruses was detected with low prevalence. However, nine viruses were found frequently across different habitats of which five viruses increased in prevalence towards disturbed habitats, in congruence with the dilution effect hypothesis. These viruses were mainly associated with one specific mosquito species (Culex nebulosus), which increased in relative abundance from pristine (3%) to disturbed habitats (38%). Interestingly, the observed increased prevalence of these five viruses in disturbed habitats was not caused by higher host infection rates but by increased host abundance, an effect tentatively named abundance effect. Our data show that host species composition is critical for virus abundance. Environmental changes that lead to an uneven host community composition and to more individuals of a single species are a key driver of virus emergence.

Deciphering the Origin of DNA Viruses (Replication-Associated Parvo-NS1) That Infect Vertebrates from Invertebrate-Infecting Viruses

DNA replication is a standard and essential function among DNA viruses; however, this functional domain's common ancestor, origin, and evolutionary path in invertebrate- and vertebrate-infecting viruses are not yet fully understood. Here, we present evidence, using a combination of phylogenetic relationships, coevolution, and CLANS (cluster analysis of sequences) analysis, that the parvo-NS1 domain (nonstructural protein NS1, DNA helicase domain) of these DNA viruses that infect vertebrates potentially originated from the invertebrate (Platyhelminthes) parvo-NS1 domain of parvovirus-related sequences (PRSs). Our results suggest that papillomaviruses and the parvovirus subfamilies Densovirinae and Hamaparvovirinae DNA helicase evolved directly from the Platyhelminthes NS1 domain (PRSs). Similarly, the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the PRSs through Hamaparvovirinae. Further, our analysis also clarified that herpesviruses and adenoviruses independently obtained the parvo-NS1 domain from Dependoparvovirus (Parvovirinae). Furthermore, virus-host coevolution analysis revealed that the parvovirus NS1 domain has coevolved with hosts, from flatworms to humans, and it appears that the papillomavirus may have obtained the DNA helicase during the early stages of parvovirus evolution and later led to the development of the DNA helicase of adomavirus and polyomavirus. Finally, herpesviruses and adenoviruses likely inherited the parvo-NS1 domain from Dependoparvovirus in the later stages of evolution. To the best of our knowledge, this is the first evolutionary evidence to suggest that the DNA helicase of viruses that infect vertebrates originated from the invertebrate PRSs. IMPORTANCE DNA replication of DNA viruses is an essential function. This allows DNA replication of viruses to form virus particles. The DNA helicase domain is responsible for this primary function. This domain is present in parvoviruses, papillomaviruses, polyomaviruses, herpesviruses, and adenoviruses. But little is known about the common ancestor, origin, and evolutionary path of DNA helicase in invertebrate- and vertebrate-infecting viruses. Here, we report the possibility of the origin of DNA viruses (DNA helicase) infecting vertebrates from Platyhelminthes (invertebrate) PRSs. Our study established that the parvovirus subfamily Parvovirinae NS1 domain displayed evolutionary heritage from the Platyhelminthes PRSs through Hamaparvovirinae. Furthermore, our study suggests that the papillomavirus DNA helicase may have evolved in the early stages of parvovirus evolution and then led to the development of the adomavirus and polyomavirus. Our study suggests that the herpesviruses and adenoviruses likely inherited the parvo-NS1 domain through gene capture from Dependoparvovirus in the later stages of parvovirus evolution in their hosts.

Antiviral Activity of an Endogenous Parvoviral Element

Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses. Some EVEs have open reading frames (ORFs) that can express proteins with physiological roles in their host. Furthermore, some EVEs exhibit a protective role against exogenous viral infection in their host. Endogenous parvoviral elements (EPVs) are highly represented in mammalian genomes, and although some of them contain ORFs, their function is unknown. We have shown that the locus EPV-Dependo.43-ODegus, an EPV with an intact ORF, is transcribed in Octodon degus (degu). Here we examine the antiviral activity of the protein encoded in this EPV, named DeRep. DeRep was produced in bacteria and used to generate antibodies that recognize DeRep in western blots of degu tissue. To test if DeRep could protect against exogenous parvovirus, we challenged cells with the minute virus of mice (MVM), a model autonomous parvovirus. We observed that MVM protein expression, DNA damage induced by replication, viral DNA, and cytopathic effects are reduced when DeRep is expressed in cells. The results of this study demonstrate that DeRep is expressed in degu and can inhibit parvovirus replication. This is the first time that an EPV has been shown to have antiviral activity against an exogenous virus.

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.

The hidden diversity of ancient bornaviral sequences from X and P genes in vertebrate genomes

Endogenous bornavirus-like elements (EBLs) are heritable sequences derived from bornaviruses in vertebrate genomes that originate from transcripts of ancient bornaviruses. EBLs have been detected using sequence similarity searches such as tBLASTn, whose technical limitations may hinder the detection of EBLs derived from small and/or rapidly evolving viral X and P genes. Indeed, no EBLs derived from the X and P genes of orthobornaviruses have been detected to date in vertebrate genomes. Here, we aimed to develop a novel strategy to detect such 'hidden' EBLs. To this aim, we focused on the 1.9-kb read-through transcript of orthobornaviruses, which encodes a well-conserved N gene and small and rapidly evolving X and P genes. We show a series of evidence supporting the existence of EBLs derived from orthobornaviral X and P genes (EBLX/Ps) in mammalian genomes. Furthermore, we found that an EBLX/P is expressed as a fusion transcript with the cellular gene, ZNF451, which potentially encodes the ZNF451/EBLP fusion protein in miniopterid bat cells. This study contributes to a deeper understanding of ancient bornaviruses and co-evolution between bornaviruses and their hosts. Furthermore, our data suggest that endogenous viral elements are more abundant than those previously appreciated using BLAST searches alone, and further studies are required to understand ancient viruses more accurately.

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Bioinformatic, genetic and molecular analysis of several badnavirus sequences integrated in the genomes of diverse cocoa (Theobroma cacao L.) germplasm

Endogenous viral elements (EVEs) are integrations of whole or partial viral genomes into the host genome, where they act as host alleles. They exist in a wide range of plant species including Theobroma cacao, the source of chocolate. Because of the international transfer of cacao germplasm, it is important to discriminate between the presence of these inserts and any episomal viruses that may be present in the material. This study was designed to survey a wide range of cacao germplasm, to assess the number, length, orientation, and precise location of the inserts and to identify any effect on the transcription of the gene into which they are inserted. Using a combination of bioinformatic, genetic and molecular approaches, we cloned and sequenced a series of different inserts, including one full-length virus sequence. We also identified, for the first time, an inhibitory effect of the insert on the expression of host genes. Such information is of practical importance in determining the regulation of germplasm transfer and of fundamental relevance to aiding an understanding of the role that such inserts may have on the performance of the host plant.