scholarly journals Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5761 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A. Mettel ◽  
Bayleigh E. Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

scholarly journals Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

2018 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A Mettel ◽  
Bayleigh E Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling towards vertebrates and land plants has limited our understanding of their diversity and evolution. Here we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated virus genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

scholarly journals Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

2018 ◽  
Author(s):  
Karyna Rosario ◽  
Kaitlin A Mettel ◽  
Bayleigh E Benner ◽  
Ryan Johnson ◽  
Catherine Scott ◽  
...  
Keyword(s):  
Land Plants ◽  
Biased Sampling ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Terrestrial Arthropods ◽  
Eukaryotic Organisms ◽  
Virus Genomes ◽  
Viral Sequences

Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling towards vertebrates and land plants has limited our understanding of their diversity and evolution. Here we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated virus genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.

scholarly journals Virome of Bat Guano from Nine Northern California Roosts

2020 ◽  
Author(s):  
Yanpeng Li ◽  
Eda Altan ◽  
Gabriel Reyes ◽  
Brian Halstead ◽  
Xutao Deng ◽  
...  
Keyword(s):  
Animal Species ◽  
Amino Acid Identity ◽  
Wide Distribution ◽  
Mouse Kidney ◽  
Northern California ◽  
Dna Viruses ◽  
Viral Genomes ◽  
In The Wild ◽  
Close Relatives ◽  
Viral Sequences

Bats are hosts to a large variety of viruses, including many capable of cross species transmissions to other mammals or humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Near or complete genomes of a novel parvovirus, astrovirus, nodavirus, CRESS-DNA viruses and densoviruses and more partial genomes of a novel alphacoronavirus, and bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found likely reflecting their wide distribution among different bats. Unexpectedly a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR possibly originating from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent indicating that numerous viruses still remain to be characterized even from such a heavily investigated order as Chiroptera. IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected whose presence are likely the result of contamination from defecation and urination atop guano and reflect the close interaction of these mammals in the wild.

scholarly journals Genes for Membrane Transport Proteins: Not So Rare in Viruses

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 456 ◽  
Author(s):  
Timo Greiner ◽  
Anna Moroni ◽  
James Van Etten ◽  
Gerhard Thiel
Keyword(s):  
Membrane Transport ◽  
Evolutionary History ◽  
Viral Proteins ◽  
Transport Proteins ◽  
Viral Genomes ◽  
Membrane Transport Proteins ◽  
Different Types ◽  
Genes Encoding ◽  
Eukaryotic Organisms ◽  
Virus Genomes

Some viruses have genes encoding proteins with membrane transport functions. It is unknown if these types of proteins are rare or are common in viruses. In particular, the evolutionary origin of some of the viral genes is obscure, where other viral proteins have homologs in prokaryotic and eukaryotic organisms. We searched virus genomes in databases looking for transmembrane proteins with possible transport function. This effort led to the detection of 18 different types of putative membrane transport proteins indicating that they are not a rarity in viral genomes. The most abundant proteins are K+ channels. Their predicted structures vary between different viruses. With a few exceptions, the viral proteins differed significantly from homologs in their current hosts. In some cases the data provide evidence for a recent gene transfer between host and virus, but in other cases the evidence indicates a more complex evolutionary history.

scholarly journals Genomic Diversity of CRESS DNA Viruses in the Eukaryotic Virome of Swine Feces

2021 ◽  
Vol 9 (7) ◽  
pp. 1426
Author(s):  
Enikő Fehér ◽  
Eszter Mihalov-Kovács ◽  
Eszter Kaszab ◽  
Yashpal S. Malik ◽  
Szilvia Marton ◽  
...  
Keyword(s):  
Genomic Diversity ◽  
The Novel ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Fur Seal ◽  
Show Evidence ◽  
Simultaneous Infection ◽  
Swine Feces ◽  
Swine Herds ◽  
Viral Sequences

Replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viruses are a diverse group of viruses, and their persistence in the environment has been studied for over a decade. However, the persistence of CRESS DNA viruses in herds of domestic animals has, in some cases, serious economic consequence. In this study, we describe the diversity of CRESS DNA viruses identified during the metagenomics analysis of fecal samples collected from a single swine herd with apparently healthy animals. A total of nine genome sequences were assembled and classified into two different groups (CRESSV1 and CRESSV2) of the Cirlivirales order (Cressdnaviricota phylum). The novel CRESS DNA viral sequences shared 85.8–96.8% and 38.1–94.3% amino acid sequence identities for the Rep and putative capsid protein sequences compared to their respective counterparts with extant GenBank record. Data presented here show evidence for simultaneous infection of swine herds with multiple novel CRESS DNA viruses, including po-circo-like viruses and fur seal feces-associated circular DNA viruses. Given that viral genomes with similar sequence and structure have been detected in swine fecal viromes from independent studies, investigation of the association between presence of CRESS DNA viruses and swine health conditions seems to be justified.

scholarly journals Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 604
Author(s):  
Mohd Faiz Mat Saad ◽  
Aziz Ramlee Sau ◽  
Muhamad Afiq Akbar ◽  
Syarul Nataqain Baharum ◽  
Ahmad Bazli Ramzi ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Potential Threat ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Agriculture Sector ◽  
Infectious Clones ◽  
And Function ◽  
Virus Genomes ◽  
Considerable Loss

Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

scholarly journals Discovery and initial analysis of novel viral genomes in the soybean cyst nematode

2011 ◽  
Vol 92 (8) ◽  
pp. 1870-1879 ◽  
Author(s):  
Sadia Bekal ◽  
Leslie L. Domier ◽  
Terry L. Niblack ◽  
Kris N. Lambert
Keyword(s):  
Soybean Cyst Nematode ◽  
High Throughput Sequencing ◽  
Nematode Species ◽  
Cyst Nematode ◽  
Parasitic Nematodes ◽  
The Novel ◽  
Viral Pathogens ◽  
Viral Genomes ◽  
Virus Genomes ◽  
Viral Sequences

Nematodes are the most abundant multicellular animals on earth, yet little is known about their natural viral pathogens. To date, only two nematode virus genomes have been reported. Consequently, nematode viruses have been overlooked as important biotic factors in the study of nematode ecology. Here, we show that one plant parasitic nematode species, Heterodera glycines, the soybean cyst nematode (SCN), harbours four different RNA viruses. The nematode virus genomes were discovered in the SCN transcriptome after high-throughput sequencing and assembly. All four viruses have negative-sense RNA genomes, and are distantly related to nyaviruses and bornaviruses, rhabdoviruses, bunyaviruses and tenuiviruses. Some members of these families replicate in and are vectored by insects, and can cause significant diseases in animals and plants. The novel viral sequences were detected in both eggs and the second juvenile stage of SCN, suggesting that these viruses are transmitted vertically. While there was no evidence of integration of viral sequences into the nematode genome, we indeed detected transcripts from these viruses by using quantitative PCR. These data are the first finding of virus genomes in parasitic nematodes. This discovery highlights the need for further exploration for nematode viruses in all tropic groups of these diverse and abundant animals, to determine how the presence of these viruses affects the fitness of the nematode, strategies of viral transmission and mechanisms of viral pathogenesis.

scholarly journals Unravelling the Single-Stranded DNA Virome of the New Zealand Blackfly

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 532 ◽  
Author(s):  
Simona Kraberger ◽  
Kara Schmidlin ◽  
Rafaela S. Fontenele ◽  
Matthew Walters ◽  
Arvind Varsani
Keyword(s):  
New Zealand ◽  
Viral Metagenomics ◽  
Dna Viruses ◽  
Rep Protein ◽  
Viral Genomes ◽  
Rich Diversity ◽  
Protein Encoding ◽  
Ssdna Viruses ◽  
Virus Genomes ◽  
Flying Fox

Over the last decade, arthropods have been shown to harbour a rich diversity of viruses. Through viral metagenomics a large diversity of single-stranded (ss) DNA viruses have been identified. Here we examine the ssDNA virome of the hematophagous New Zealand blackfly using viral metagenomics. Our investigation reveals a plethora of novel ssDNA viral genomes, some of which cluster in the viral families Genomoviridae (n = 9), Circoviridae (n = 1), and Microviridae (n = 108), others in putative families that, at present, remain unclassified (n = 20) and one DNA molecule that only encodes a replication associated protein. Among these novel viruses, two putative multi-component virus genomes were recovered, and these are most closely related to a Tongan flying fox faeces-associated multi-component virus. Given that the only other known multi-component circular replication-associated (Rep) protein encoding single-stranded (CRESS) DNA viruses infecting plants are in the families Geminiviridae (members of the genus Begomovirus) and Nanoviridae, it appears these are likely a new multi-component virus group which may be associated with animals. This study reiterates the diversity of ssDNA viruses in nature and in particular with the New Zealand blackflies.

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