Virology Commons^™

Exploring The Application Of Wastewater Monitoring To Determine The Prevalence And Diversity Of Influenza On The Campus Of West Virginia University, Lakyn Renee Sanders

Graduate Theses, Dissertations, and Problem Reports (ETD)

Influenza viruses (IV) affect populations globally, with the World Health Organization (WHO) estimating that IV are responsible for an estimated 3-5 million infections and 290,000 – 650,000 deaths annually^1–3. More specifically, the 2019-2020 IV season is associated with an estimated 38 million illnesses and 22,000 deaths in the United States alone⁴. IV are rapidly spread between individuals through direct contact with infected individuals, contaminated surfaces, or aerosolized virus particles². Traditional IV infection monitoring relies on clinical screening of patients presenting influenza-like symptoms, commonly through the use of multi-target panel tests such as the BioFire …

Discovery And Identification Of Muwow Bacteriophage From Columbus, Ms, Olivia Reese Carlisle, Jess Holden Collins, Kaliyah J. Moore, Nykeria J. Pratt

Undergraduate Research Conference

Bacteriophages are an abundant type of virus with the ability to infect and kill bacteria while using them to replicate through lytic or lysogenic processes. Bacteriophages play a key role in the regulation of bacterial populations in various environments and are being explored as potential tools in phage therapy. The aim of this study was to isolate, characterize, and manually annotate the genome of the bacteriophage MUWow collected from the campus of the Mississippi University for Women in Columbus, MS at GPS coordinates 33.493021 N, 88.419611 W. MUWow was isolated from a soil sample on Arthrobacter globiformis B-2979. Plaque assays, …

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

Ribomoe: An Application Of Mixture Of Experts On Artificial Riboswitch Classification, Hainian Audrey Long

Master's Projects

Urban water sewage is a potential health concern due to its possibility to spread contagious RNA viruses such as Coxsackievirus B3. However, detection of viral particles remains challenging because of low viral concentrations in wastewater and high mutation rates of the RNA virus. To address this, this study proposes a novel viral detection method using synthetic riboswitches that bind to the target virus and trigger a reporter gene, amplifying the detection signals. To support the design of effective riboswitches, we present a machine learning model for classifying riboswitch performance, integrating RNA sequence data with secondary structural features. This model used …

Interactions Of The Sars-Cov-2 Viral Genome 3’-Untranslated Region With Viral And Host Rnas, Caleb Frye, Mihaela Rita Mihailescu

Electronic Theses and Dissertations

This dissertation focuses on the characterization of RNA-RNA interactions within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and with host microRNAs. As the causative agent of coronavirus disease 2019 (COVID-19), SARS-CoV-2 has evolved rapidly since its appearance. This has warranted prompt characterization of the virus particularly of its single stranded RNA (ssRNA) genome. By using a combination of bioinformatics, biophysics, and/or biological assays, we analyzed the SARS-CoV-2 viral genomic RNA and uncovered interactions of genomic RNA with host RNAs, highlighting an underutilized method of targeting RNA viruses. We showed here that the conserved elements in the viral genomic …

Metagenomic Analysis Of Antarctic Microbial Communities, David Michael Robinson

Biology ETDs

The research presented in this dissertation focuses on microbial roles in biogeochemical cycling in Antarctic aquatic environments. The major objective of my research was to examine the impact of biotic and abiotic pressures on nutrient cycling in microbially dominated systems. I used three perennially ice covered lakes in the McMurdo Dry Valleys (MDVs) along with subglacial lakes Whillans and Mercer as natural case studies. The MDVs are located in Victoria Land, East Antarctica and have been studied since 1993 as part of the McMurdo Long Term Ecological Research Project. Viruses in the MDVs were shown to be seasonally abundant and …

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

Increased Coding Potential Of Bovine Herpesvirus 1, Victoria Jefferson

Theses and Dissertations

Bovine respiratory disease (BRD) costs the cattle industry millions of dollars in costs in treatment and loss every year in the United States. A significant pathogen often contributes to BRD is Bovine Herpesvirus 1 (BoHV-1), a double stranded DNA virus with the ability to establish latency in the trigeminal ganglia and neurons. Primary infection with BoHV-1 results in immunosuppression that increases the risk of secondary bacterial infection and pneumonia. Because herpesviruses infect their hosts for life and can be reactivated in times of stress, BoHV-1 can present a recurring risk of BRD. The following research aims to expand the knowledge …

Predicted Structure And Analysis Of The Glycoprotein From Sars-Cov-2 Variants Of Interest, Boris Shabaltiy

Honors Program: Senior Projects (Public)

SARS-CoV-2 has had a devastating effect on the world, and while the public concern and severity of the diseased caused by it have decreased, it is still crucial to monitor the virus for mutations so we can rapidly identify new variants of concern, and then rapidly prepare new vaccines and treatments. The SARS-CoV-2 spike (S) protein from the first isolates of the virus (root variant) was structurally characterized in early 2021. The spike protein structure, designated 7CZW, was uploaded to RCSB Protein Data Bank (RCSB PDB). All subsequent mutations the S protein has accumulated are based on the amino acid …

Mutation-Induced Changes In The Stability, B-Cell Epitope, And Antigenicity Of The Sars-Cov-2 Variant Spike Protein: A Comparative Computational Stud, Nira Meirita Wijayanti, Muhammad Hermawan Widyananda, Lailil Muflikhah, Nashi Widodo

Karbala International Journal of Modern Science

The spike (S) protein is a major antigenicity site that targets neutralizing antibodies and drugs. The growing number of S protein mutations has become a severe problem for developing effective vaccines. Here, we investigated four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that were the most infectious and widespread during the COVID-19 pandemic to determine the trends and patterns of mutation-induced changes in the stability, B-cell epitope, and antigenicity of the SARS-CoV-2 S protein. The data showed that the Beta and Gamma variants had three mutations on the receptor-binding domain (RBD), which is the specific site on the S …

Exploring The Interactions Between Sars-Cov-2 And Host Proteins, Sojan Shrestha

School of Biological Sciences: Dissertations, Theses, and Student Research

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated …

Functional Domains Of The Hsv-1 Ul37 Protein In Virus Infectivity And Retrograde Transport In Neurons, Carolyn Clark

LSU Doctoral Dissertations

Herpes simplex virus type 1 is large alphaherpesvirus with 20 envelope proteins and 23 tegument proteins. Virus entry is via fusion of the viral envelope with cellular membranes mediated by a complex of viral glycoproteins. Glycoprotein B (gB) is the only fusogenic glycoprotein, while other viral glycoproteins and membrane proteins including gD, gH, gL, gK and UL20 membrane protein modulate gB’s fusogenicity. Previously, Our laboratory developed the HSV-1 (VC2) vaccines strain with partial deletions in the amino termini of gK (ΔgK(31–68)) and the UL20 membrane protein (ΔUL20(4–22)). VC2 enters epithelial cells only via endocytosis followed by release of the capsid …

Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase

Graduate Industrial Research Symposium

Genetic frameshifts are a mutation in which
a nucleotide skip leads to a shift in the
reading frame. In viruses, these frameshifts
can be programmed using a slippery
sequence to bypass the stop codon
associated with the initial protein. This
allows for variable control of protein
expression. In bacteriophages, translational
frameshifts have been identified but only a
few have been proven experimentally. Using
experimental data and comparative
genomics, non-traditional slippery
sequences can be identified as assisting in
controlling the protein coding throughout
viruses. Novel slippery sequences can aid in
the understanding of protein expression in
biological environments and further the …

Meta-Analysis Of Transcriptomic Datasets For The Investigation Of Differential Expression In Hantavirus-Infected Human Tissue, John Krapohl

Annual Research Symposium

No abstract provided.

The Isolation And Characterization Of Bacteriophage Hasitha, Gillian Brown

Mahurin Honors College Capstone Experience/Thesis Projects

Microbacteriophage Hasitha is a virus that infects Microbacterium foliorum, a bacterium associated with grasses that was first discovered in Germany. Hasitha was isolated from an enriched compost sample and is of particular interest due to its unusual growth pattern. Most bacteriophages require actively growing host cells to produce new phage progeny. However, Hasitha can infect and kill stationary (non-replicating) bacterial cells. We discovered this unusual characteristic through a fortuitous observation of infected lawns that were allowed to incubate in the lab workspace for approximately one month. During this time, a noticeable “halo” grew around the initial site of infection …

Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences, Ahmed Al Qaffas

Theses and Dissertations

Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although most of the virus genomic content has been studied extensively, the terminal repeating region sequences remain understudied. Two main challenges hindered the study of the region: a) limitations of sequencing technologies; and b) misassembly of the repeats due to its complex nature. Here I show a novel bioinformatics pipeline that takes advantage of PacBio's long reads to resolve the challenges mentioned …

Rotavirus A Genome Segments Show Distinct Segregation And Codon Usage Patterns, Irene Hoxie, John J. Dennehy

Publications and Research

Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other …

Assembly And Identification Of Novel Viruses In The Aquatic Invertebrate Daphnia Magna, Freddy L. Gonzalez, Reilly O. Cooper, Clayton E. Cressler

UCARE: Research Products

Microbiome studies have been critical to understanding host health and life history. Many studies primarily focus on understanding the impacts of bacteria on the host, while fewer examine the impacts of viruses on host fitness or the interaction between viruses and bacteria within a host. Here, we utilized shotgun sequencing to identify whether viruses were present in the model organism Daphnia magna. VIBRANT, a bioinformatic tool that utilizes hybrid machine learning and protein similarity to identify lytic genomes and other novel viruses, was used on sequencing data from four samples of adult and juvenile Daphnia. We found a …

Two (Or More) Viruses In One Bat: A Systematic Quantitative Literature Review Of Viral Coinfection In Bats, Eli J. Kaufman

Independent Study Project (ISP) Collection

Viral coinfection is an important topic in pathogen dynamics, and can increase viral shedding and change disease outcomes. As bats are carriers of important zoonoses, such as the SARS coronaviruses, rabies, and other deadly viruses, knowing more about their coinfection dynamics is important. This quantitative systematic literature review sought to show how many papers reported bat viral coinfections, and created three databases. The first database, the SQLR database was based on searches for coinfections. The second database, the Astrovirus database was to determine how much of the literature was being missed by examining a single viral family more in depth …

On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson

United States Public Health Resources

The ongoing pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing significant damage to public health and economic livelihoods, and is putting significant strains on healthcare services globally. This unfolding emergency has prompted the preparation and dissemination of the article “Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate” by Araújo and Naimi (2020). The authors present the results of an ensemble forecast made from a suite of species distribution models (SDMs), where they attempt to predict the suitability of the climate for the spread of SARS-CoV-2 over the coming months. They argue that climate is …

Biological And Computational Studies Of The Structure And Function Of Pul103, A Human Cytomegalovirus Tegument Protein, Ashley N. Anderson

Wayne State University Dissertations

Human cytomegalovirus (HCMV) is an enveloped, single segment, double-stranded DNA virus. HCMV infection causes disease in immunocompromised (HIV patients, transplant recipients) and immunodeficient (fetuses, neonates) populations. Current treatments are effective but are either limited in use or can lead to organ damage and/or antiviral resistance, and no vaccines are available. Additional antiviral targets are needed. HCMV pUL103 is a potential antiviral target. pUL103 is a conserved herpesvirus protein present in the tegument, layer of proteins and RNA between the envelope and capsid of HCMV virions. pUL103 helps reorganize cellular secretory machinery (Golgi, endosomes) to form the cytoplasmic virion assembly compartment …

Role Of Gp120 Glycosylation In Sexual Transmission Of Hiv, Yingxue Sun, Adam Meadows, Najwa Zebian, Eric Arts, Carole Creuzenet

Western Research Forum

Background:

In chronic HIV patients, the viral populations are genetically diverse due to mutations introduced by the viral reverse transcriptase during HIV replication. However, more than 80% new infections result from single transmission founder (TF) viruses; therefore, targeting the TFs is key to control AIDS worldwide.

Gp120 is a glycosylated envelope protein required for HIV infection, propagation, and transmission. Glycans on gp120 influence HIV infectivity through their interactions with lectins, the carbohydrate-binding immune proteins in the host mucosa. To transmit sexually, viruses must overcome the lectin traps to access more target T cells.

Hypothesis:

TF viruses are less likely to …

The Evolution Of Molecular Compatibility Between Bacteriophage Φx174 And Its Host, Alexander Kula, Joseph Saelens, Alyxandria M. Schubert, Michael Travisano, Catherine Putonti

Bioinformatics Faculty Publications

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

The Use Of Informativity In The Development Of Robust Viromics-Based Examinations, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer …

Genomes Of Gardnerella Strains Reveal An Abundance Of Prophages Within The Bladder Microbiome, Kema Malki, Jason W. Shapiro, Travis Kyle Price, Evann Elizabeth Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates …

Freshwater Metaviromics And Bacteriophages: A Current Assessment Of The State Of The Art In Relation To Bioinformatic Challenges, Katherine Bruder, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with …

Phylogenetic Analysis Of Human Cytomegalovirus Pus27 And Pus28: Ascertaining An Independent Or Linked Evolutionary History, Jessica A. Scarborough

Undergraduate Honors Theses

Human cytomegalovirus (HCMV) is a widespread pathogen that is particularly skilled at evading immune detection and defense mechanisms, largely due to extensive co-evolution with its host’s immune system. One aspect of this co-evolution involves the acquisition of four virally encoded GPCR chemokine receptor homologs, products of the US27, US28, UL33 and UL78 genes. G protein-coupled receptors (GPCR) are the largest family of cell surface proteins, found in organisms from yeast to humans. In this research, phylogenetic analysis was used to investigate the origins of the US27 and US28 genes, which are adjacent in the viral genome. The results indicate that …

Phagephisher: A Pipeline For The Discovery Of Covert Viral Sequences In Complex Genomic Datasets, Thomas Hatzopoulos, Siobhan C. Watkins, Catherine Putonti

Bioinformatics Faculty Publications

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with …