Virology Commons^™

Viruses In Astrobiology, Ignacio De La Higuera, Ester Lázaro

Biology Faculty Publications and Presentations

Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very …

Endothelial Cell Contributions To Covid-19, Alexandra E. Oxford, Fabio Halla, Evan B. Robertson, Brad E. Morrison

Biology Faculty Publications and Presentations

Understanding of the clinical, histological and molecular features of the novel coronavirus 2019 (Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)) has remained elusive. Coronavirus disease 2019 (COVID-19) caused by this virus has unusual clinical presentation with regard to other related coronaviruses. Recent reports suggest that SARS-CoV-2, unlike other related viruses, infects and replicates within endothelial cells, which may explain a significant portion of the observed clinical pathology. Likewise, mounting evidence associates vascular and endothelial cell dysfunction with increased mortality. This review focuses on understanding how endothelial cell pathology is caused by SARS-CoV-2 at the molecular and cellular levels and how …

Host-Dependent Differences In Replication Strategy Of The Sulfolobus Spindle-Shaped Virus Strain Ssv9 (A.K.A., Ssvk1): Infection Profiles In Hosts Of The Family Sulfolobaceae, Ruben M. Ceballos, Coyne Gareth Drummond, Carson Len Stacy, Elizabeth Padillo-Crespo, Kenneth M. Stedman

Biology Faculty Publications and Presentations

The Sulfolobus Spindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. Previously, we reported that SSVs exhibited differential infectivity on allopatric vs. sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as “non-lytic” double-stranded DNA viruses that infect species of the genus Sulfolobus and release virions via budding rather than host lysis. In this …

Unveiling Crucivirus Diversity By Mining Metagenomic Data, Ignacio De La Higuera, George Kasun, Ellis L. Torrance, Alyssa A. Pratt, Amberlee Maluenda, Jonathan Colombet, Maxime Bisseux, Viviane Ravet, Anisha Dayaram, Daisy Stainton, Simona Kraberger, Peyman Zawar-Reza, Sharyn Goldstien, James V. Briskie, Robyn White, Helen Taylor, Christopher Gomez, David G. Ainley, Jon S. Harding, Rafaela S. Fontenele, Joshua Schreck, Simone Ribeiro, Stephen A. Oswald, Jennifer M. Arnold, François Enault, Arvind Varsani, Kenneth M. Stedman

Biology Faculty Publications and Presentations

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESSDNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of …

Genome Sequences Of Three Cruciviruses Found In The Willamette Valley (Oregon), Ignacio De La Higuera, Ellis L. Torrance, Alyssa A. Pratt, George Kasun, Amberlee Maluenda, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Cruciviruses are single-stranded DNA (ssDNA) viruses whose genomes suggest the possibility of gene transfer between DNA and RNA viruses. Many crucivirus genome sequences have been found in metagenomic data sets, although no crucivirus has been isolated. Here, we present the complete genome sequences of three cruciviruses recovered from environmental samples from Oregon.

Peering Below The Diffraction Limit: Robust And Specific Sorting Of Viruses With Flow Cytometry, Shea T. Lance, David J. Sukovich, Kenneth M. Stedman, Adam R. Abate

Biology Faculty Publications and Presentations

Background: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the …

Structural Insights Into The Architecture Of The Hyperthermophilic Fusellovirus Ssv1, Kenneth M. Stedman, Melissa Deyoung, Mitul Saha, Michael B. Sherman, Marc C. Morais

Biology Faculty Publications and Presentations

The structure and assembly of many icosahedral and helical viruses are well-characterized. However, the molecular basis for the unique spindle-shaped morphology of many viruses that infect Archaea remains unknown. To understand the architecture and assembly of these viruses, the spindle-shaped virus SSV1 was examined using cryo-EM, providing the first 3D-structure of a spindle-shaped virus as well as insight into SSV1 biology, assembly and evolution. Furthermore, a geometric framework underlying the distinct spindle-shaped structure is proposed.

Reversible Inactivation And Desiccation Tolerance Of Silicified Viruses, James R. Laidler, Jessica A. Shugart, Sherry L. Cady, Keith S. Bahjat, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Long-distance host-independent virus dispersal is poorly understood, especially for viruses found in isolated ecosystems. To
demonstrate a possible dispersal mechanism, we show that bacteriophage T4, archaeal virus Sulfolobus spindle-shaped virus Kamchatka, and vaccinia virus are reversibly inactivated by mineralization in silica under conditions similar to volcanic hot
springs. In contrast, bacteriophage PRD1 is not silicified. Moreover, silicification provides viruses with remarkable desiccation
resistance, which could allow extensive aerial dispersal.

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …

Virus Silicification Under Simulated Hot Spring Conditions, James R. Laidler, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).