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- Genre: Masters Thesis
Description
Despite the prevalence of coyotes (Canis latrans) little is known about the viruses associated with this species. To assess the extent of viral research that has been conducted on coyotes, a literature review was performed. Over the last six decades, there have been many viruses that have been identified infecting coyotes. The pathology of some cases implies that infection is rare and lethal while others have been demonstrated to be endemic to coyotes. In addition, the majority of the prior analyses were done through serological assays that were limited to investigating target viruses. To help expand what is known about coyote-virus dynamics, viral assays were conducted on coyote scat. The samples were collected as part of transects established along the Salt River near Phoenix, Arizona, United States (USA). The recovered viral genomes were clustered with other deoxynucleic acid (DNA) viruses and analyzed to determine phylogeny and genetic identity. From the recovered viral genomes, there are two novel circoviruses, one novel naryavirus, five unclassified cressdnaviruses, and two previously identified species of anelloviruses from the Wawtorquevirus genus. For these viruses, new phylogenies for their groups and pairwise identity plots have been generated. These figures give insight into the potential hosts and the evolutionary history. In the case of the anelloviruses, they likely derived from a wood rat (Neotoma) host, given the anellovirus family’s host specificity and its similarity to another viral genome derived from a wood rat in Arizona, USA. Of the recovered circovirus genomes, one is associated with a viral isolate collected from a dust sample in Arizona, USA. The second circovirus species identified is within a clade that consists of rodent associated circoviruses and canine circovirus. Other recovered genomes expand clusters of unclassified cressdnaviruses. The recovered genomes support further genomic analysis. These findings help support the notion that there is a wealth of viral information to be identified from animals like coyotes. By understanding the viruses that coyotes are associated with, it is possible to better understand the viral impact on the urban environment, domesticated animals, and wildlife in general.
ContributorsHess, Savage Cree (Author) / Varsani, Arvind (Thesis advisor) / Kraberger, Simona (Committee member) / Upham, Nathan S (Committee member) / Arizona State University (Publisher)
Created2023
DescriptionA
ContributorsLund, Michael (Author) / Varsani, Arvind (Thesis advisor) / Upham, Nathan (Committee member) / Harris, Robin (Committee member) / Arizona State University (Publisher)
Created2023
Description
Arachnids belong to the phylum Arthropoda, the largest phylum in the animal kingdom. Ticks are blood-feeding arachnids that vector numerous pathogens of significant medical and veterinary importance, while scorpions have become a common concern in urban desert cities due to the high level of toxicity in their venom. To date, viruses associated with arachnids have been under sampled and understudied. Here viral metagenomics was used to explore the diversity of viruses present in ticks and scorpions. American dog ticks (Dermacentor variabilis) and blacklegged ticks (Ixodes scapularis) were collected in Pennsylvania while one hairy scorpion (Hadrurus arizonensis) and four bark scorpions (Centruroides sculpturatus) were collected in Phoenix. Novel viral genomes described here belong to the families Polyomaviridae, Anelloviridae, Genomoviridae, and a newly proposed family, Arthropolviridae.
Polyomaviruses are non-enveloped viruses with a small, circular double-stranded DNA (dsDNA) genomes that have been identified in a variety of mammals, birds and fish and are known to cause various diseases. Arthropolviridae is a proposed family of circular, large tumor antigen encoding dsDNA viruses that have a unidirectional genome organization. Genomoviruses and anelloviruses are ssDNA viruses that have circular genomes ranging in size from 2–2.4 kb and 2.1–3.8 kb, respectively. Genomoviruses are ubiquitous in the environment, having been identified in a wide range of animal, plant and environmental samples, while anelloviruses have been associated with a plethora of animals.
Here, 16 novel viruses are reported that span four viral families. Eight novel polyomaviruses were recovered from bark scorpions, three arthropolviruses were recovered from dog ticks and one arthropolvirus from a hairy scorpion. Viruses belonging to the families Polyomaviridae and Arthropolviridae are highly divergent. This is the first more extensive study of these viruses in arachnids. Three genomoviruses were recovered from both dog and deer ticks and one anellovirus was recovered from deer ticks, which are the first records of these viruses being recovered from ticks. This work highlights the diversity of dsDNA and ssDNA viruses in the arachnid population and emphasizes the importance of performing viral surveys on these populations.
Polyomaviruses are non-enveloped viruses with a small, circular double-stranded DNA (dsDNA) genomes that have been identified in a variety of mammals, birds and fish and are known to cause various diseases. Arthropolviridae is a proposed family of circular, large tumor antigen encoding dsDNA viruses that have a unidirectional genome organization. Genomoviruses and anelloviruses are ssDNA viruses that have circular genomes ranging in size from 2–2.4 kb and 2.1–3.8 kb, respectively. Genomoviruses are ubiquitous in the environment, having been identified in a wide range of animal, plant and environmental samples, while anelloviruses have been associated with a plethora of animals.
Here, 16 novel viruses are reported that span four viral families. Eight novel polyomaviruses were recovered from bark scorpions, three arthropolviruses were recovered from dog ticks and one arthropolvirus from a hairy scorpion. Viruses belonging to the families Polyomaviridae and Arthropolviridae are highly divergent. This is the first more extensive study of these viruses in arachnids. Three genomoviruses were recovered from both dog and deer ticks and one anellovirus was recovered from deer ticks, which are the first records of these viruses being recovered from ticks. This work highlights the diversity of dsDNA and ssDNA viruses in the arachnid population and emphasizes the importance of performing viral surveys on these populations.
ContributorsSchmidlin, Kara (Author) / Varsani, Arvind (Thesis advisor) / Van Doorslaer, Koenraad (Committee member) / Stenglein, Mark (Committee member) / Arizona State University (Publisher)
Created2019
Description
Viruses infect organisms in all domains of life and are abundant entities in ecosystems. In particular, single-stranded DNA viruses have been found in a wide variety of hosts and ecosystems. Using a metagenomic approach, novel circular viruses have been identified in multiple environmental samples. This thesis focuses on viruses and virus dynamics from avian sources. As part of this thesis, a novel phapecoctavirus was identified in a pigeon cloacal swab. The phapecoctavirus is most closely related to Klebsiella phage ZCKP1, identified from a freshwater sample. Beyond this, this thesis addresses circoviruses, which are of interest due to disease they cause to avian species. Evolution of circovirus recombination was studied in a closed system of uninfected and infected pigeons. 178 genomes of pigeon circovirus were sequenced, and patterns of recombination determined. Seven genotypes were present in the population and genotype 4 was shown to be present in a majority of samples after the experiment was finished. Circoviruses were also identified in waterfowl feces and the ten genomes recovered represent two new circovirus species. Overall, the research described in this thesis helped to gain a deeper understanding of the diversity and evolution of circular DNA viruses associated with avian species.
ContributorsKhalifeh, Anthony (Author) / Varsani, Arvind (Thesis advisor) / Kraberger, Simona J (Committee member) / Dolby, Greer (Committee member) / Arizona State University (Publisher)
Created2021
Description
Globally, about two-thirds of the population is latently infected with herpes simplex virus type 1 (HSV-1). HSV-1 is a large double stranded DNA virus with a genome size of ~150kbp. Small defective genomes, which minimally contain an HSV-1 origin of replication and packaging signal, arise naturally via recombination during viral DNA replication. These small defective genomes can be mimicked by constructing a bacterial plasmid containing the HSV-1 origin of replication and packaging signal, transfecting these recombinant plasmids into mammalian cells, and infecting with a replicating helper virus. The absence of most viral genes in the amplicon vector allows large pieces of foreign DNA (up to 150kbp) to be incorporated. The HSV-1 amplicon is replicated and packaged by the helper virus to form HSV-1 particles containing the amplicon DNA. We constructed a novel HSV-1 amplicon vector system containing lambda phage-derived attR sites to facilitate insertion of transgenes by Invitrogen Gateway recombination. To demonstrate that the amplicon vectors work as expected, we packaged the vector constructs expressing Emerald GFP using the replication-competent helper viruses OK-14 or HSV-mScartlet-I-UL25 in Vero cells and demonstrate that the vector stock can subsequently transduce and express Emerald GFP. In further work, we will insert transgenes into the amplicon vector using Invitrogen Gateway recombination to study their functionality.
ContributorsVelarde, Kimberly (Author) / Hogue, Ian B (Thesis advisor) / Manfredsson, Fredric (Committee member) / Sandoval, Ivette (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2021