scholarly journals Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Ashleigh F Porter ◽  
John H -O Pettersson ◽  
Wei-Shan Chang ◽  
Erin Harvey ◽  
Karrie Rose ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Animal Species ◽  
Rna Viruses ◽  
Mammalian Species ◽  
Virus Transmission ◽  
Whole Genome ◽  
Ixodes Holocyclus ◽  
Positive Sense ◽  
Novel Variant ◽  
History Of

Abstract The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera—Hepacivirus, Pegivirus, Pestivirus, and Flavivirus—each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.

scholarly journals A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 585
Author(s):  
Rebecca M. Grimwood ◽  
Edward C. Holmes ◽  
Jemma L. Geoghegan
Keyword(s):  
Evolutionary History ◽  
Mammalian Species ◽  
Virus Transmission ◽  
Health Concern ◽  
Virus Species ◽  
Vast Number ◽  
The Pacific ◽  
Positive Sense ◽  
History Of ◽  
Fish Viruses

Rubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Recently, two new rubella-like matonaviruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses, we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica—order Torpediniformes (Pacific electric ray)—that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses that remain undiscovered.

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

2020 ◽  
Author(s):  
Ashleigh F. Porter ◽  
John H.-O. Pettersson ◽  
Wei-Shan Chang ◽  
Erin Harvey ◽  
Karrie Rose ◽  
...  
Keyword(s):  
Large Scale ◽  
Animal Species ◽  
Rna Virus ◽  
Mammalian Species ◽  
Evolutionary Time ◽  
Virus Family ◽  
Ixodes Holocyclus ◽  
Short Read Archive ◽  
Novel Variant ◽  
Additional Support

AbstractThe RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

scholarly journals A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae

2021 ◽  
Author(s):  
Rebecca M. Grimwood ◽  
Edward C. Holmes ◽  
Jemma L. Geoghegan
Keyword(s):  
Evolutionary History ◽  
Mammalian Species ◽  
Virus Transmission ◽  
Health Concern ◽  
Virus Species ◽  
Vast Number ◽  
The Pacific ◽  
Positive Sense ◽  
History Of ◽  
Fish Viruses

AbstractRubella virus (RuV) is the causative agent of rubella (“German measles”) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Other matonaviruses, including two new rubella-like viruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica (Pacific electric ray) that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses still to be discovered.

scholarly journals Clinical characteristics of COVID-19 and personal protective equipment for trauma surgeons

2020 ◽  
pp. 81-83
Keyword(s):  
Infectious Disease ◽  
Phylogenetic Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Clinical Characteristics ◽  
Rna Viruses ◽  
Protective Equipment ◽  
Whole Genome ◽  
Positive Sense ◽  
Novel Coronavirus ◽  
Trauma Surgeons

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by a new virus from the coronavirus family (1) regarded as enveloped, positive-sense, single-stranded ribonucleic acid (RNA) viruses with helical symmetric nucleocapsid (2). According to the whole genome sequencing and phylogenetic analysis of coronavirus strains, a distinct clade of betacoronavirus is shown to be associated with severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (3). This novel clade is called the 2019 novel coronavirus (2019-nCoV) and due to more similarity to the SARS virus is also called severe acute respiratory syndrome coronavirus 2. The disease is known as COVID-19.

Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1249-1257
Author(s):  
Ilya Ruvinsky ◽  
Lee M Silver ◽  
Jeremy J Gibson-Brown
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Families ◽  
Vertebrate Evolution ◽  
Whole Genome ◽  
Vertebrate Genome ◽  
T Box ◽  
Genetic Complexity ◽  
History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

2020 ◽  
Vol 142 ◽  
pp. 203-211
Author(s):  
AJ Tighe ◽  
MD Gallagher ◽  
J Carlsson ◽  
I Matejusova ◽  
F Swords ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Whole Genome ◽  
Pancreas Disease ◽  
Codon Positions ◽  
History Of ◽  
Unique Strain ◽  
Salmon Pancreas Disease Virus

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

scholarly journals Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae

2013 ◽  
Vol 94 (4) ◽  
pp. 738-748 ◽  
Author(s):  
Ying Tao ◽  
Mang Shi ◽  
Christina Conrardy ◽  
Ivan V. Kuzmin ◽  
Sergio Recuenco ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary History ◽  
Evolutionary Rate ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Viral Pathogens ◽  
Genomic Features ◽  
Wide Range ◽  
History Of ◽  
Multiple Species

Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus–host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.

scholarly journals Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol

2018 ◽  
Author(s):  
Astrid Cruaud ◽  
Sabine Nidelet ◽  
Pierre Arnal ◽  
Audrey Weber ◽  
Lucian Fusu ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Evolutionary History ◽  
Animal Species ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Target Enrichment ◽  
Library Preparation ◽  
Single Person ◽  
History Of ◽  
Set Up

AbstractEnriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.

scholarly journals Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Julie Callanan ◽  
Stephen R. Stockdale ◽  
Evelien M. Adriaenssens ◽  
Jens H. Kuhn ◽  
Janis Rumnieks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Open Access ◽  
Markov Models ◽  
Rna Viruses ◽  
Hidden Markov ◽  
International Committee ◽  
Double Stranded Rna ◽  
Positive Sense ◽  
Taxonomic Framework

The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive-sense RNA viruses have been classified in two genera (Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework.

An audit and insights from clinical exome sequencing in psychiatry: genotype-phenotype correlation

2020 ◽  
Author(s):  
Jayant Mahadevan ◽  
Reeteka Sud ◽  
Ravi Kumar Nadella ◽  
Vani P ◽  
Anand G Subramaniam ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Psychiatric Symptoms ◽  
Pathogenic Variant ◽  
Clinical Exome Sequencing ◽  
Mapt Gene ◽  
Nf1 Gene ◽  
Novel Variant ◽  
History Of ◽  
Atypical Presentations ◽  
Minor Physical Anomalies

BACKGROUND:Psychiatric syndromes have polymorphic symptomatology, and are known to be heritable. Psychiatric symptoms (and even syndromes) often occur as part of the clinical presentation in rare Mendelian syndromes. Clinical exome sequencing reports may help with refining diagnosis and influence treatment decisions, in addition to providing a window into the biology of brain and behaviour. We describe a clinical audit of 12 individuals who sought treatment at our hospital, and for whom targeted sequencing was ordered. Three cases are discussed in detail to demonstrate correlations between genotype and phenotype in the clinic.METHODS:Targeted Next-Generation Sequencing (NGS) was done using Clinical Exome Panel (TruSight One, Illumina) covering coding exons and flanking intronic sequences of 4811 genes associated with known inherited diseases. Variants detected were classified according to the American College for Medical Genetics (ACMG) recommendation for standards of interpretation and reporting of sequence variations.RESULTS:Ten out of twelve cases had at least one pathogenic variant. In one of these cases, we detected a known pathogenic variant in MAPT gene in a suspected FTD case, which helped us to confirm the diagnosis. In another case, we detected a novel variant predicted to be deleterious in NF1 gene. Identification of this mutation suggested a change in treatment for the patient, that was of benefit. The same patient also harboured a novel variant in the TRIO gene. This gene may be involved in biological processes that underlie the patient’s psychiatric illness.CONCLUSIONS:The cases discussed here exemplify different scenarios under which targeted exome sequencing can find meaningful application in the clinic: confirming diagnosis (MAPT variant), or modifying treatment (NF1). We suggest that clinical exome sequencing can be a helpful addition to a clinician’s toolkit when there are expediting factors to consider— such as early-onset, strong family history of mental illness, complex/atypical presentations and minor physical anomalies or neurocutaneous markers.

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