scholarly journals Virological Sampling of Inaccessible Wildlife with Drones

2018 ◽  
Author(s):  
Jemma L. Geoghegan ◽  
Vanessa Pirotta ◽  
Erin Harvey ◽  
Alastair Smith ◽  
Jan P. Buchmann ◽  
...  
Keyword(s):  
Virus Disease ◽  
Mammalian Species ◽  
Virus Species ◽  
Northern Australia ◽  
Disease Emergence ◽  
Aerial Vehicle ◽  
Novel Virus ◽  
Winter Annual ◽  
Aquatic Mammals ◽  
Sydney Australia

There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the respiratory virome of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. Despite the relatively small number of animals surveyed, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.

scholarly journals Virological Sampling of Inaccessible Wildlife with Drones

2018 ◽  
Author(s):  
Jemma L. Geoghegan ◽  
Vanessa Pirotta ◽  
Erin Harvey ◽  
Alastair Smith ◽  
Jan P. Buchmann ◽  
...  
Keyword(s):  
Virus Disease ◽  
Mammalian Species ◽  
Initial Study ◽  
Exhaled Breath ◽  
Virus Species ◽  
Disease Emergence ◽  
Aerial Vehicle ◽  
Novel Virus ◽  
Winter Annual ◽  
First Time

There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.

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.

Coding-complete sequencing classifies parrot bornavirus 5 into a novel virus species

2015 ◽  
Vol 160 (11) ◽  
pp. 2763-2768 ◽  
Author(s):  
Szilvia Marton ◽  
Krisztián Bányai ◽  
János Gál ◽  
Katalin Ihász ◽  
Renáta Kugler ◽  
...  
Keyword(s):  
Virus Species ◽  
Complete Sequencing ◽  
Novel Virus

scholarly journals Novel hepatitis E like virus found in Swedish moose

2014 ◽  
Vol 95 (3) ◽  
pp. 557-570 ◽  
Author(s):  
Jay Lin ◽  
Heléne Norder ◽  
Henrik Uhlhorn ◽  
Sándor Belák ◽  
Frederik Widén
Keyword(s):  
Hepatitis E Virus ◽  
Sequence Similarity ◽  
Mammalian Species ◽  
Hepatitis E ◽  
Human Infection ◽  
Stem Loop ◽  
Novel Virus ◽  
Human Infections ◽  
Transmission Pathways

A novel virus was detected in a sample collected from a Swedish moose (Alces alces). The virus was suggested as a member of the Hepeviridae family, although it was found to be highly divergent from the known four genotypes (gt1–4) of hepatitis E virus (HEV). Moose are regularly hunted for consumption in the whole of Scandinavia. Thus, the finding of this virus may be important from several aspects: (a) as a new diverged HEV in a new animal species, and (b) potential unexplored HEV transmission pathways for human infections. Considering these aspects, we have started the molecular characterization of this virus. A 5.1 kb amplicon was sequenced, and corresponded to the partial ORF1, followed by complete ORF2, ORF3 and poly(A) sequence. In comparison with existing HEVs, the moose HEV genome showed a general nucleotide sequence similarity of 37–63 % and an extensively divergent putative ORF3 sequence. The junction region between the ORFs was also highly divergent; however, two putative secondary stem–loop structures were retained when compared to gt1–4, but with altered structural appearance. In the phylogenetic analysis, the moose HEV deviated and formed its own branch between the gt1–4 and other divergent animal HEVs. The characterization of this highly divergent genome provides important information regarding the diversity of HEV infecting various mammalian species. However, further studies are needed to investigate its prevalence in the moose populations and possibly in other host species, including the risk for human infection.

scholarly journals Characterization of Ti Ringspot-Associated Virus, a Novel Emaravirus Associated with an Emerging Ringspot Disease of Cordyline fruticosa

Plant Disease ◽  
2019 ◽  
Vol 103 (9) ◽  
pp. 2345-2352 ◽  
Author(s):  
Alejandro Olmedo-Velarde ◽  
Adam C. Park ◽  
Jari Sugano ◽  
Janice Y. Uchida ◽  
Michael Kawate ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
High Plains ◽  
Virus Species ◽  
Sequence Analyses ◽  
Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Eriophyid Mites ◽  
Cordyline Fruticosa ◽  
Novel Virus

Ti ringspot is an emerging foliar disease of the ti plant (Cordyline fruticosa) in Hawaii that is quickly spreading throughout the islands. Symptoms include small chlorotic ringspots on leaves that often coalesce to form larger lesions. Although several virus species have been discovered in symptomatic plants, none have been associated with these symptoms. Here, we report and characterize a novel virus closely associated with ti ringspot symptoms in Hawaii. The presence of double membrane bodies approximately 85 nm in diameter in symptomatic cells and sequence analyses of five genomic RNA segments obtained by high-throughput sequencing indicate that this virus is most closely related to members of the plant virus genus Emaravirus. Phylogenetic and sequence homology analyses place this virus on a distinct clade within the Emaravirus genus along with High Plains wheat mosaic emaravirus, blue palo verde broom virus, and Raspberry leaf blotch emaravirus. Sequence identity values with taxonomically relevant proteins indicate that this represents a new virus species, which we are tentatively naming ti ringspot-associated virus (TiRSaV). TiRSaV-specific reverse transcription PCR assays detected the virus in several experimental herbaceous host species following mechanical inoculation. TiRSaV was also detected in eriophyid mites collected from symptomatic ti plants, which may represent a putative arthropod vector of the virus.

scholarly journals Discovery and Characterization of Bukakata orbivirus (Reoviridae:Orbivirus), a Novel Virus from a Ugandan Bat

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 209 ◽  
Author(s):  
Anna Fagre ◽  
Justin Lee ◽  
Robert Kityo ◽  
Nicholas Bergren ◽  
Eric Mossel ◽  
...  
Keyword(s):  
Virus Species ◽  
Preliminary Screening ◽  
Fruit Bat ◽  
In Vitro Characterization ◽  
Archived Samples ◽  
Additional Testing ◽  
Novel Virus ◽  
Ongoing Surveillance

While serological and virological evidence documents the exposure of bats to medically-important arboviruses, their role as reservoirs or amplifying hosts is less well-characterized. We describe a novel orbivirus (Reoviridae:Orbivirus) isolated from an Egyptian fruit bat (Rousettus aegyptiacus leachii) trapped in 2013 in Uganda and named Bukakata orbivirus. This is the fifth orbivirus isolated from a bat, however genetic information had previously only been available for one bat-associated orbivirus. We performed whole-genome sequencing on Bukakata orbivirus and three other bat-associated orbiviruses (Fomede, Ife, and Japanaut) to assess their phylogenetic relationship within the genus Orbivirus and develop hypotheses regarding potential arthropod vectors. Replication kinetics were assessed for Bukakata orbivirus in three different vertebrate cell lines. Lastly, qRT-PCR and nested PCR were used to determine the prevalence of Bukakata orbivirus RNA in archived samples from three populations of Egyptian fruit bats and one population of cave-associated soft ticks in Uganda. Complete coding sequences were obtained for all ten segments of Fomede, Ife, and Japanaut orbiviruses and for nine of the ten segments for Bukakata orbivirus. Phylogenetic analysis placed Bukakata and Fomede in the tick-borne orbivirus clade and Ife and Japanaut within the Culicoides/phlebotomine sandfly orbivirus clade. Further, Bukakata and Fomede appear to be serotypes of the Chobar Gorge virus species. Bukakata orbivirus replicated to high titers (106–107 PFU/mL) in Vero, BHK-21 [C-13], and R06E (Egyptian fruit bat) cells. Preliminary screening of archived bat and tick samples do not support Bukakata orbivirus presence in these collections, however additional testing is warranted given the phylogenetic associations observed. This study provided complete coding sequence for several bat-associated orbiviruses and in vitro characterization of a bat-associated orbivirus. Our results indicate that bats may play an important role in the epidemiology of viruses in the genus Orbivirus and further investigation is warranted into vector-host associations and ongoing surveillance efforts.

scholarly journals Consensus proposals for classification of the family Hepeviridae

2014 ◽  
Vol 95 (10) ◽  
pp. 2223-2232 ◽  
Author(s):  
Donald B. Smith ◽  
Peter Simmonds ◽  
Shahid Jameel ◽  
Suzanne U. Emerson ◽  
Tim J. Harrison ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Cutthroat Trout ◽  
Hepatitis E ◽  
Amino Acid Sequences ◽  
Sequence Information ◽  
Virus Species ◽  
Wide Range ◽  
The Family ◽  
Novel Variants

The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.

scholarly journals Characterization of a Novel Influenza Virus in Cattle and Swine: Proposal for a New Genus in the Orthomyxoviridae Family

mBio ◽  
2014 ◽  
Vol 5 (2) ◽  
Author(s):  
Ben M. Hause ◽  
Emily A. Collin ◽  
Runxia Liu ◽  
Bing Huang ◽  
Zizhang Sheng ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Rna Sequencing ◽  
New Genus ◽  
Mammalian Species ◽  
Taxonomic Status ◽  
Viral Reservoir ◽  
Childhood And Adolescence ◽  
Human Pathogens ◽  
Novel Virus

ABSTRACTWe have recently reported the isolation of a novel virus, provisionally designated C/swine/Oklahoma/1334/2011 (C/OK), with 50% overall homology to human influenza C viruses (ICV), from a pig in Oklahoma. Deep RNA sequencing of C/OK virus found a matrix 1 (M1) protein expression strategy that differed from that of ICV. The novelty of C/OK virus prompted us to investigate whether C/OK virus could exist in a nonswine species. Significantly, we found that C/OK virus was widespread in U.S. bovine herds, as demonstrated by reverse transcription (RT)-PCR and serological assays. Genome sequencing of three bovine viruses isolated from two herds in different states further confirmed these findings. To determine whether swine/bovine C/OK viruses can undergo reassortment with human ICV, and to clarify the taxonomic status of C/OK,in vitroreassortment and serological typing by agar gel immunodiffusion (AGID) were conducted.In vitroreassortment using two human ICV and two swine and bovine C/OK viruses demonstrated that human ICV and C/OK viruses were unable to reassort and produce viable progeny. Antigenically, no cross-recognition of detergent split virions was observed in AGID between human and nonhuman viruses by using polyclonal antibodies that were reactive to cognate antigens. Taken together, these results demonstrate that C/OK virus is genetically and antigenically distinct from ICV. The classification of the new virus in a separate genus of theOrthomyxoviridaefamily is proposed. The finding of C/OK virus in swine and bovine indicates that this new virus may spread and establish infection in other mammals, including humans.IMPORTANCEInfluenza C viruses (ICV) are common human pathogens, infecting most people during childhood and adolescence, and typically cause mild respiratory symptoms. While ICV have been isolated from both pigs and dogs, humans are thought to be the natural viral reservoir. Previously, we characterized an ICV-like virus isolated from pigs exhibiting symptoms of influenza virus-like illness. Here, we show molecular and serological data demonstrating widespread circulation of similar viruses in bovines. Deep RNA sequencing, phylogenetic analysis, andin vitroreassortment experiments demonstrate that animal ICV-like viruses are genetically distinct from human ICV. Antigenically, we show that ICV-like viruses are not recognized by ICV antibodies. En masse, these results suggest that bovine influenza virus warrants classification as a new genus of influenza virus. The finding of this novel virus that can infect multiple mammalian species warrants further research into its role in human health.

scholarly journals Novel Mammalian Herpesviruses and Lineages within the Gammaherpesvirinae: Cospeciation and Interspecies Transfer

2008 ◽  
Vol 82 (7) ◽  
pp. 3509-3516 ◽  
Author(s):  
Bernhard Ehlers ◽  
Güzin Dural ◽  
Nezlisah Yasmum ◽  
Tiziana Lembo ◽  
Benoit de Thoisy ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Mammalian Host ◽  
Virus Species ◽  
Branching Pattern ◽  
Long Distance ◽  
Bayesian Monte Carlo ◽  
Long Distance Pcr

ABSTRACT Novel members of the subfamily Gammaherpesvirinae, hosted by eight mammalian species from six orders (Primates, Artiodactyla, Perissodactyla, Carnivora, Scandentia, and Eulipotyphla), were discovered using PCR with pan-herpesvirus DNA polymerase (DPOL) gene primers and genus-specific glycoprotein B (gB) gene primers. The gB and DPOL sequences of each virus species were connected by long-distance PCR, and contiguous sequences of approximately 3.4 kbp were compiled. Six additional gammaherpesviruses from four mammalian host orders (Artiodactyla, Perissodactyla, Primates, and Proboscidea), for which only short DPOL sequences were known, were analyzed in the same manner. Together with available corresponding sequences for 31 other gammaherpesviruses, alignments of encoded amino acid sequences were made and used for phylogenetic analyses by maximum-likelihood and Bayesian Monte Carlo Markov chain methods to derive a tree which contained two major loci of unresolved branching details. The tree was rooted by parallel analyses that included alpha- and betaherpesvirus sequences. This gammaherpesvirus tree contains 11 major lineages and presents the widest view to date of phylogenetic relationships in any subfamily of the Herpesviridae, as well as the most complex in the number of deep lineages. The tree's branching pattern can be interpreted only in part in terms of the cospeciation of virus and host lineages, and a substantial incidence of the interspecies transfer of viruses must also be invoked.

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