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- All Subjects: Virology
- Genre: Masters Thesis
- Creators: Chung, Yunro YC
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
This project analyzed the sequencing results of 230 bat samples to investigatenovel Coronaviruses (CoVs) appearance. A bioinformatics workflow solution was developed to process the Next-Generation Sequencing (NGS) data to identify novel CoV genomes. A parallel computing scheme was implemented to enhance performance. Among the 230 bat samples, 14 samples previously tested positive for CoV appearance by a pan-CoV quantitative polymerase chain reaction (qPCR). The Illumina NGS techniques are used to generate the shotgun readings. With the newly developed bioinformatics pipeline, the sequencing reads from each bat sample, and a positive control sample were quality controlled and assembled to generate longer viral contigs. They then went through a Basic Local Alignment Search Tool X (BLASTx) query against a customized CoV database from the National Center for Biotechnology Information (NCBI) databases. After further filtering with BLASTx and megaBLAST against the NCBI nucleotide collection (nr/nt) database, the confirmed CoV contigs were used to build bootstrapped phylogenetic trees with several representative Alpha, Beta, and Gamma-CoV genomes. Two bat samples contained potentially novel CoV fragments corresponding to the Open Reading Frame 1ab (ORF1ab), ORF7, and Nucleocapsid (N) gene regions. The phylogenetic trees showed that the fragments are Alpha-CoVs, which are closely related to Eptesicus Bat Coronavirus, Pipistrellus Bat Coronavirus, and Tadarida Brasiliensis Bat Alphacoronavirus 1.
ContributorsMu, Tianchen Nil (Author) / Lim, Efrem EL (Thesis advisor) / Lee, Kookjin KL (Thesis advisor) / Chung, Yunro YC (Committee member) / Arizona State University (Publisher)
Created2023