About OpenKnowledge@NAU | For NAU Authors

Investigation of novel mycoviruses in Coccidioides genomes

Elmore, Alexis Marie (2021) Investigation of novel mycoviruses in Coccidioides genomes. Masters thesis, Northern Arizona University.

[thumbnail of Elmore_2021_investigation_novel_mycoviruses_coccidioides_genomes.pdf] Text
Elmore_2021_investigation_novel_mycoviruses_coccidioides_genomes.pdf - Published Version
Restricted to Repository staff only

Download (981kB) | Request a copy


Coccidioides immitis and C. posadasii are the causative agents of Coccidioidomycosis, commonly known as Valley fever. Valley fever incidence is increasing every year, but only 40% of infections are symptomatic. The reason for this variation in disease is unknown, but one possibility lies in the presence or absence of mycoviral infection in Coccidioides. In this investigation, DNA and RNA genomic datasets were analyzed with two different bioinformatic pipelines to look for mycoviral sequences. Many viral sequences were found in DNA genomes, such as human gammaherpesvirus type 4, viruses belonging to the genus Terrestrivirus, viruses belonging to the order Caudovirales, and various phage of human pathogenic bacteria. The main viral sequences identified in RNA datasets included members of the genera Flavivirus, Gammaretrovirus, Alpharetrovirus, and Lentivirus. Some of the human-pathogenic viral sequences may have come from viruses associated with human hosts, as most Coccidioides samples have been isolated from biopsies of infected human tissue. Additionally, the fungus may be infected by viruses of soil-dwelling hosts in its natural arid soil environment. Finally, sequence identifications may be the result of in-lab contamination. Within the limits of our study, no mycoviral sequences were identified. Thus, direct molecular methods are needed to determine the exact source and significance of viral sequences we detected, and necessitates the development of specific methods to extract and enrich for double stranded RNA from Coccidioides total RNA. Based on lack of mycoviral sequence detection in the existing genome datasets, we hypothesize that direct targeted sequencing of dsRNA will be the most likely ii method to discover mycoviruses if they exist in Coccidioides. The current study represents a proof-of-concept approach for bioinformatic identification of novel viral sequences present in Coccidioides WGS datasets.

Item Type: Thesis (Masters)
Publisher’s Statement: © Copyright is held by the author. Digital access to this material is made possible by the Cline Library, Northern Arizona University. Further transmission, reproduction or presentation of protected items is prohibited except with permission of the author.
Keywords: Bioinformatics; Biology; Coccidioides; Mycology; Mycovirus; Virology; Valley fever
Subjects: R Medicine > RB Pathology
MeSH Subjects: C Diseases > C02 Virus Diseases
NAU Depositing Author Academic Status: Student
Department/Unit: Graduate College > Theses and Dissertations
College of the Environment, Forestry, and Natural Sciences > Biological Sciences
Date Deposited: 09 Feb 2022 17:00
Last Modified: 09 Feb 2022 17:00
URI: https://openknowledge.nau.edu/id/eprint/5672

Actions (login required)

IR Staff Record View IR Staff Record View


Downloads per month over past year