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      <title>Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination</title>
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      <pubDate>Thu, 19 Sep 2024 00:00:00 +0000</pubDate>
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      <title>YAVSAP: versatile viral quasispecies analysis for veterinary samples</title>
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      <pubDate>Tue, 05 Mar 2024 00:00:00 +0000</pubDate>
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      <description>&lt;p&gt;Viral populations within an infected host are composed of viral particles with a&#xA;spectrum of genetic mutations rather than a unified genome. This phenomenon is&#xA;referred to as viral &amp;ldquo;quasispecies,&amp;rdquo; and has been useful for the understanding&#xA;of viral transmission and early detection of new viral variants. Next generation&#xA;sequencing (NGS) has enabled the study of these quasispecies for many viral&#xA;species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and&#xA;Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2&#xA;(SARS CoV2), and established protocols and computer analysis tools have been&#xA;developed for these species. Some of the most important viruses, such as&#xA;emerging and exotic disease agents, however, do not have replicatable protocols&#xA;or software tools capable of producing valid output from their sequence data.&#xA;Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP&#xA;is a fully automated bioinformatic pipeline built from the ground up to identify&#xA;and analyze viral quasispecies of any arbitrary virus in human and veterinary&#xA;samples. YAVSAP provides reference-based genome mapping of both long- and&#xA;short-read sequencing reads to any reference genome that the user chooses,&#xA;identifies subconsensus variants and haplotypes, and assesses the phylogenies of&#xA;all viral sequences found within a sample. YAVSAP is written in Nextflow and&#xA;conforms to the nf-core initiative&amp;rsquo;s standards, which allows it to run on&#xA;low-end computers, high performance computing (HPC) clusters, or anything in&#xA;between with zero configuration. YAVSAP has been tested on viruses of interest&#xA;to veterinary medicine and public health, including Japanese Encephalitis Virus&#xA;(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift&#xA;Valley Fever Virus (RVFV), and can correctly identify consensus genomes and&#xA;quasispecies within samples containing each of these viruses. This tool provides&#xA;a means for biologists with little bioinformatic experience to analyze deep&#xA;sequence data while correcting for many of the pitfalls associated with previous&#xA;and current analysis platforms. YAVSAP is open source software and is publicly&#xA;available at &lt;a&#xA;  href=&#34;https://github.com/ksumngs/yavsap&#34;&gt;https://github.com/ksumngs/yavsap&lt;/a&gt;.&lt;/p&gt;</description>
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      <title>How to Build a Cow-Cud Fuel Cell</title>
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      <pubDate>Wed, 01 Aug 2018 00:00:00 +0000</pubDate>
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