diff --git a/content/academia/bpv-genetics.md b/content/academia/bpv-genetics.md deleted file mode 100644 index edd678f..0000000 --- a/content/academia/bpv-genetics.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -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 deleted file mode 100644 index adea3d8..0000000 --- a/content/academia/got-warts-naab.md +++ /dev/null @@ -1,14 +0,0 @@ ---- -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 deleted file mode 100644 index 3ffc79c..0000000 --- a/content/academia/yavsap/index.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -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 deleted file mode 100644 index 14462c7..0000000 Binary files a/content/academia/yavsap/yavsap.pdf and /dev/null differ