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 Twenty five new viruses associated with the Drosophilidae (Diptera)

2016 ◽  
Author(s):  
Claire L. Webster ◽  
Ben Longdon ◽  
Samuel H. Lewis ◽  
Darren J. Obbard
Keyword(s):  
Experimental Studies ◽  
Laboratory Model ◽  
Flock House Virus ◽  
Dna Viruses ◽  
Iridescent Virus ◽  
Comprehensive Listing ◽  
In The Wild ◽  
Drosophila X Virus ◽  
Close Relatives ◽  
Virus Host Range

AbstractDrosophila melanogasteris an important laboratory model for studies of antiviral immunity in invertebrates, andDrosophilaspecies provide a valuable system to study virus host range and host switching. Here we use metagenomic RNA sequencing ofca. 1600 adult flies to discover 25 new RNA viruses associated with six different drosophilid hosts in the wild. We also provide a comprehensive listing of viruses previously reported from the Drosophilidae. The new viruses include Iflaviruses, Rhabdoviruses, Nodaviruses, and Reoviruses, and members of unclassified lineages distantly related to Negeviruses, Sobemoviruses and Poleroviruses, Flaviviridae, and Tombusviridae. Among these are close relatives ofDrosophila X virusandFlock House virus, which we find in association with wildDrosophila immigrans. These two viruses are widely used in experimental studies but have not previously been reported to naturally infectDrosophila. Although we detect no new DNA viruses, inD. immigransandD. obscurawe identify sequences very closely related toArmadillidium vulgareIridescent virus (Invertebrate Iridescent virus 31), bringing the total number of DNA viruses found in the Drosophilidae to three.

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

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 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 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 Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 779
Author(s):  
Man Teng ◽  
Yongxiu Yao ◽  
Venugopal Nair ◽  
Jun Luo
Keyword(s):  
Biological Sciences ◽  
Gene Therapy ◽  
Genetic Engineering ◽  
Gene Function ◽  
Viral Genome ◽  
Gene Editing ◽  
Vaccine Development ◽  
Future Prospects ◽  
Dna Viruses ◽  
Viral Genomes

In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.

scholarly journals SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection

2021 ◽  
Author(s):  
Manish C Choudhary ◽  
Charles R Crain ◽  
Xueting Qiu ◽  
William Hanage ◽  
Jonathan Z Li
Keyword(s):  
Persistent Infection ◽  
Viral Evolution ◽  
Phylogenetic Reconstruction ◽  
Geographic Region ◽  
Antibody Treatment ◽  
Viral Genomes ◽  
Monoclonal Antibody Treatment ◽  
Viral Sequences ◽  
Sequence Characteristics ◽  
Baseline Health

Abstract Background Both SARS-CoV-2 reinfection and persistent infection have been reported, but sequence characteristics in these scenarios have not been described. We assessed published cases of SARS-CoV-2 reinfection and persistence, characterizing the hallmarks of reinfecting sequences and the rate of viral evolution in persistent infection. Methods A systematic review of PubMed was conducted to identify cases of SARS-CoV-2 reinfection and persistence with available sequences. Nucleotide and amino acid changes in the reinfecting sequence were compared to both the initial and contemporaneous community variants. Time-measured phylogenetic reconstruction was performed to compare intra-host viral evolution in persistent SARS-CoV-2 to community-driven evolution. Results Twenty reinfection and nine persistent infection cases were identified. Reports of reinfection cases spanned a broad distribution of ages, baseline health status, reinfection severity, and occurred as early as 1.5 months or >8 months after the initial infection. The reinfecting viral sequences had a median of 17.5 nucleotide changes with enrichment in the ORF8 and N genes. The number of changes did not differ by the severity of reinfection and reinfecting variants were similar to the contemporaneous sequences circulating in the community. Patients with persistent COVID-19 demonstrated more rapid accumulation of sequence changes than seen with community-driven evolution with continued evolution during convalescent plasma or monoclonal antibody treatment. Conclusions Reinfecting SARS-CoV-2 viral genomes largely mirror contemporaneous circulating sequences in that geographic region, while persistent COVID-19 has been largely described in immunosuppressed individuals and is associated with accelerated viral evolution.

scholarly journals Context-dependent ‘safekeeping’ of foraging tools in New Caledonian crows

2015 ◽  
Vol 282 (1808) ◽  
pp. 20150278 ◽  
Author(s):  
Barbara C. Klump ◽  
Jessica E. M. van der Wal ◽  
James J. H. St Clair ◽  
Christian Rutz
Keyword(s):  
Animal Species ◽  
Crack Open ◽  
Important Constraint ◽  
In The Wild ◽  
New Caledonian Crows ◽  
Context Dependent ◽  
Time And Energy

Several animal species use tools for foraging, such as sticks to extract embedded arthropods and honey, or stones to crack open nuts and eggs. While providing access to nutritious foods, these behaviours may incur significant costs, such as the time and energy spent searching for, manufacturing and transporting tools. These costs can be reduced by re-using tools, keeping them safe when not needed. We experimentally investigated what New Caledonian crows do with their tools between successive prey extractions, and whether they express tool ‘safekeeping’ behaviours more often when the costs (foraging at height), or likelihood (handling of demanding prey), of tool loss are high. Birds generally took care of their tools (84% of 176 prey extractions, nine subjects), either trapping them underfoot (74%) or storing them in holes (26%)—behaviours we also observed in the wild (19 cases, four subjects). Moreover, tool-handling behaviour was context-dependent, with subjects: keeping their tools safe significantly more often when foraging at height; and storing tools significantly more often in holes when extracting more demanding prey (under these conditions, foot-trapping proved challenging). In arboreal environments, safekeeping can prevent costly tool losses, removing a potentially important constraint on the evolution of habitual and complex tool behaviour.

Integration of viral DNA sequences in cells transformed by adenovirus 2 or SV40

1980 ◽  
Vol 210 (1180) ◽  
pp. 423-435 ◽  
Keyword(s):  
Cell Lines ◽  
Dna Sequences ◽  
Viral Genome ◽  
Viral Dna ◽  
Viral Genomes ◽  
Viral Dnas ◽  
Cellular Dna ◽  
Viral Insertion ◽  
Viral Sequences ◽  
Heteroduplex Formation

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonuclease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.

scholarly journals Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family

2006 ◽  
Vol 87 (10) ◽  
pp. 3045-3051 ◽  
Author(s):  
Mazen S. Habayeb ◽  
Sophia K. Ekengren ◽  
Dan Hultmark
Keyword(s):  
Persistent Infection ◽  
Open Reading Frames ◽  
Close Relative ◽  
Virus Family ◽  
Viral Genomes ◽  
Persistent Infections ◽  
New Family ◽  
Nora Virus ◽  
Persistent Virus ◽  
Viral Sequences

Several viruses, including picornaviruses, are known to establish persistent infections, but the mechanisms involved are poorly understood. Here, a novel picorna-like virus, Nora virus, which causes a persistent infection in Drosophila melanogaster, is described. It has a single-stranded, positive-sense genomic RNA of 11879 nt, followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RNA-dependent RNA polymerase and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viral sequences. The unusual sequence and genome organization in Nora virus suggest that it belongs to a new family of picorna-like viruses. Surprisingly, Nora virus could be detected in all tested D. melanogaster laboratory stocks, as well as in wild-caught material. The viral titres varied enormously, between 104 and 1010 viral genomes per fly in different stocks, without causing obvious pathological effects. The virus was also found in Drosophila simulans, a close relative of D. melanogaster, but not in more distantly related Drosophila species. It will now be possible to use Drosophila genetics to study the factors that control this persistent infection.

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