feat: Add BPV poster

content/academia/bpv-genetics.md

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+---
+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.

content/academia/got-warts-naab.md

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+---
+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"
+---

content/academia/yavsap/index.md

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+---
+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.