Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing

Two RNA virus families that pose a threat to human and animal health are Hantaviridae and Coronaviridae. These RNA viruses which originate in wildlife continue and will continue to cause disease, and hence, it is critical that scientific research define the mechanisms as to how these viruses spillover and adapt to new hosts to become endemic. One gap in our ability to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within reservoir and spillover hosts. In my research studies, I used the amplicon-based WGS approach to define the genetic plasticity of viral RNA within pathogenic and nonpathogenic hantavirus species. The standing genetic variation of Andes orthohantavirus and Prospect Hill orthohantavirus was mapped out and amino acid changes occurring outside of functional domains were identified within the nucleocapsid and glycoprotein. I observed several amino acid changes in functional domains of the RNA-dependent RNA polymerase, as well as single nucleotide polymorphisms (SNPs) within the 3’ non-coding region (NCR) of the S-segment. To identify whether virus adaptation would occur within the S- and L-segments we attempted to adapt hantaviruses in vitro in a spillover host model through passaging experiments. In early passages we identified few mutations in the M-segment with the majority being identified in the S-segment 3’ NCR and the L-segment. This work suggests that hantavirus adaptation occurs in the S- and L-segments although the effect of these mutants on pathology is yet to be determined. While sequencing laboratory isolates is easily accomplished, sequencing low concentrations of virus within the reservoir is a formidable task. I further translated our amplicon-based WGS approach into a pan-oligonucleotide amplicon-based WGS approach to sequence hantavirus vRNA and mRNA from reservoir and spillover hosts in Ukraine. This approach successfully identified a novel Puumala orthohantavirus (PUUV) strain in Ukraine and using Bayesian phylogenetics we found this strain to be associated with the PUUV Latvian lineage. Early during the SARS-CoV-2 pandemic, I applied the knowledge gained in the hantavirus WGS efforts to sequencing of SARS-CoV-2 from nasopharyngeal swabs collected in April 2020. The genetic diversity of 45 SARS-CoV-2 isolates was evaluated with the methods I developed. We identified D614G, a notable mutation known for increasing transmission, in over 90% of our isolates. Two major lineages distinguish SARS-CoV-2 variants worldwide, lineages A and B. While most of our isolates were found within B lineage, we also identified one isolate within lineage A. We performed in vitro work which confirmed A lineage isolates as having poor replication in the trachea as compared to the nasal cavity. Five of these isolates presented a unique array of mutations which were assessed in the keratin 18 human angiotensin-converting enzyme 2 (K18-hACE2) mouse model for its response immunologically and pathogenically. We identified a distinction of pathogenesis between the A and B lineages with emphysema being common amongst A lineage isolates. Additionally, we discovered a small cohort of likely SNPs that defined the late induction of eosinophils during infection. In summary, this work will further define the dynamics of genetic variation and plasticity within virus populations that cause disease outbreaks and will allow a deeper understanding of the virus-host relationship

The role of vaccination route with an adenovirus-vectored vaccine in protection, viral control, and transmission in the SARS-CoV-2/K18-hACE2 mouse infection model

IntroductionVaccination is the most effective mechanism to prevent severe COVID-19. However, breakthrough infections and subsequent transmission of SARS-CoV-2 remain a significant problem. Intranasal vaccination has the potential to be more effective in preventing disease and limiting transmission between individuals as it induces potent responses at mucosal sites.MethodsUtilizing a replication-deficient adenovirus serotype 5-vectored vaccine expressing the SARS-CoV-2 RBD (AdCOVID) in homozygous and heterozygous transgenic K18-hACE2, we investigated the impact of the route of administration on vaccine immunogenicity, SARS-CoV-2 transmission, and survival.ResultsMice vaccinated with AdCOVID via the intramuscular or intranasal route and subsequently challenged with SARS-CoV-2 showed that animals vaccinated intranasally had improved cellular and mucosal antibody responses. Additionally, intranasally vaccinated animals had significantly better viremic control, and protection from lethal infection compared to intramuscularly vaccinated animals. Notably, in a novel transmission model, intranasal vaccination reduced viral transmission to naïve co-housed mice compared to intramuscular vaccination.DiscussionOur data provide convincing evidence for the use of intranasal vaccination in protecting against SARS-CoV-2 infection and transmission

Volume 05

Introduction from Dean Dr. Charles Ross The Tallis House as an Extension of Emily Tallis in McEwan\u27s Atonement by Ian Karamarkovich Graphic Design by Jessica Cox Graphic Design by Kyle Fowlkes Graphic Design by Allison Pawlowski Incorporating Original Research in The Classroom: A Case Study Analyzing the Influence of the Chesapeake Bay on Local Temperatures by Kaitlin Major, Carrie Dunham and Dr. Kelsey Scheitlin Graphic Design by Kathryn Grayson Graphic Design by Ashley Johnson Facing the Music: Environmental Impact Assessment of Building A Concert Hall on North Campus by Jennifer Nehrt, Kelsey Stolzenbach And Dr. Kelsey Scheitlin Art by Kristin McQuarrie Art by Sara Nelson Art by Melisa Michelle Prosocial Behavior as a Result of Prosocial Music by Jessica Sudlow Graphic Design by Perry Bason Graphic Design by Danielle Dmuchawski Graphic Design by Mariah Asbell Graphic Design by Matthew Sakach Identifying Pathogenic Salmonella Serotypes Isolated from Prince Edward County, VA Waterways via Mutiplex PCR Analysis by Timothy Smith, Jr. Art by Annaliese Troxell Art by T. Dane Summerell Development of Salicylidene Anilines for Application in the High School Laboratory by Sarah Ganrude Graphic Design by Malina Rutherford Graphic Design by Hannah Hopper, and Matthew Sakach Because That\u27s What Daddies Do: Effects of Fathering Patterns on Son\u27s Self and Gender Identities by John Berry, Jr. Graphic Design by James Early Graphic Design by Colleen Festa The Influence of Tropical Cyclones on Chesapeake Bay Dead Zones by Chelsea D. Taylor and Dr. Kelsey Scheitlin Graphic Design by Michelle Maddox Graphic Design by Kaitlyn Smith Graphic Design by Sarah Schu Graphic Design by Perry Bason, Cabell Edmunds, Katherine Grayson, Matthew Sakach, and Kayla Torna