diff --git a/content/academia/bpv-genetics.md b/content/academia/bpv-genetics.md new file mode 100644 index 0000000..edd678f --- /dev/null +++ b/content/academia/bpv-genetics.md @@ -0,0 +1,42 @@ +--- +title: "Genetic analysis of bovine papillomas" +date: 2024-09-19 +categories: + - poster +people: + - Thomas A. Christensen II + - Rachel Palinski + - Bob Gentry +journal: + "National Association of Animal Breeders Technical Conference Student Poster + session" +location: "Middleton, Wisconsin" +--- + +Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle. +In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is +always a cause to fail an animal on a breeding soundness exam. Historically, it +has been thought that BPV was transmitted via direct contact and could be +controlled by managing clinically presenting animals in the herd, but more +recent evidence suggests alternative modes of transmission. BPV has been found +repeatably in clinically healthy animals, and in non-cutaneous secretions +including milk, blood, urine and semen. Currently, no commercially available BPV +vaccine uses isolated viral particles and naturally occurring virus does not +produce cross-protective immunity. In order to develop a proper vaccine for +penile papillomas further studies are required to understand the epidemiology of +BPV in herds. While vulvar, cutaneous, and mammary papillomas have been +genotyped in recent years, this information is not available for penile +papillomas. In this study there were 31 submissions, collected from 7 states, +NE, KS, NY, TX, AL, MO and SD (14 different cattle operations) Samples were +collected between August of 2022 and April 2024. Twenty-two submissions were +penile papillomas and with pooling of samples represented over 50 penile +papillomas. Samples were metagenomically sequenced at the Kansas State +Veterinary Diagnostic Lab, and the genotype of each sample was determined using +the phylogenetic analysis. The clade of each sample was determined by aligning +consensus sequences of the L1 gene (used for both for phylogeny and as a vaccine +target) using MAFFT and a maximum-likelihood phylogeny generated in Mega X. +Analysis found that all penile papilloma submissions were composed of BPV type +2, with one sample showing co-infection with BPV type 1. Conversely, cutaneous +and teat papillomas had BPV genotypes that were more variable with genotypes of +1,2,7,12,14,29 and 40. These results indicate that BPV type 2 and type 1 provide +a unified target for bovine penile papilloma vaccine development. diff --git a/content/academia/got-warts-naab.md b/content/academia/got-warts-naab.md new file mode 100644 index 0000000..adea3d8 --- /dev/null +++ b/content/academia/got-warts-naab.md @@ -0,0 +1,14 @@ +--- +title: + "Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination" +date: 2024-09-19 +featured: false +categories: + - presentation +people: + - Bob Gentry + - Thomas A. Christensen II +journal: + "National Association of Animal Breeders Technical Conference Sponsor session" +location: "Middleton, Wisconsin" +--- diff --git a/content/academia/yavsap/index.md b/content/academia/yavsap/index.md new file mode 100644 index 0000000..3ffc79c --- /dev/null +++ b/content/academia/yavsap/index.md @@ -0,0 +1,54 @@ +--- +title: "YAVSAP: versatile viral quasispecies analysis for veterinary samples" +date: 2024-03-05 +featured: false +categories: + - presentation +people: + - Thomas A. Christensen II + - Steven Stancic + - Andrea Lu + - Dana Mitzel + - William Wilson + - Rachel Palinski +journal: "Phi Zeta Research Day" +location: "Manhattan, Kansas" +tags: + - virus + - quasispecies + - next-generation sequencing + - pipeline +awards: + - "2nd Place Large Animal Applied Research Presentation" +link: "/academia/yavsap/yavsap.pdf" +--- + +Viral populations within an infected host are composed of viral particles with a +spectrum of genetic mutations rather than a unified genome. This phenomenon is +referred to as viral "quasispecies," and has been useful for the understanding +of viral transmission and early detection of new viral variants. Next generation +sequencing (NGS) has enabled the study of these quasispecies for many viral +species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and +Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2 +(SARS CoV2), and established protocols and computer analysis tools have been +developed for these species. Some of the most important viruses, such as +emerging and exotic disease agents, however, do not have replicatable protocols +or software tools capable of producing valid output from their sequence data. +Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP +is a fully automated bioinformatic pipeline built from the ground up to identify +and analyze viral quasispecies of any arbitrary virus in human and veterinary +samples. YAVSAP provides reference-based genome mapping of both long- and +short-read sequencing reads to any reference genome that the user chooses, +identifies subconsensus variants and haplotypes, and assesses the phylogenies of +all viral sequences found within a sample. YAVSAP is written in Nextflow and +conforms to the nf-core initiative's standards, which allows it to run on +low-end computers, high performance computing (HPC) clusters, or anything in +between with zero configuration. YAVSAP has been tested on viruses of interest +to veterinary medicine and public health, including Japanese Encephalitis Virus +(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift +Valley Fever Virus (RVFV), and can correctly identify consensus genomes and +quasispecies within samples containing each of these viruses. This tool provides +a means for biologists with little bioinformatic experience to analyze deep +sequence data while correcting for many of the pitfalls associated with previous +and current analysis platforms. YAVSAP is open source software and is publicly +available at https://github.com/ksumngs/yavsap. diff --git a/content/academia/yavsap/yavsap.pdf b/content/academia/yavsap/yavsap.pdf new file mode 100644 index 0000000..14462c7 Binary files /dev/null and b/content/academia/yavsap/yavsap.pdf differ