<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
  <channel>
    <title>Andrea Lu on MillironX</title>
    <link>http://localhost:1313/people/andrea-lu/</link>
    <description>Recent content in Andrea Lu on MillironX</description>
    <generator>Hugo</generator>
    <language>en-us</language>
    <lastBuildDate>Tue, 05 Mar 2024 00:00:00 +0000</lastBuildDate>
    <atom:link href="http://localhost:1313/people/andrea-lu/index.xml" rel="self" type="application/rss+xml" />
    <item>
      <title>YAVSAP: versatile viral quasispecies analysis for veterinary samples</title>
      <link>http://localhost:1313/academia/yavsap/</link>
      <pubDate>Tue, 05 Mar 2024 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/yavsap/</guid>
      <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>
    </item>
    <item>
      <title>Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease</title>
      <link>http://localhost:1313/academia/rotavirus-virome/</link>
      <pubDate>Wed, 27 Apr 2022 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/rotavirus-virome/</guid>
      <description>&lt;p&gt;Enteric disease is the predominant cause of morbidity and mortality in young&#xA;mammals including pigs. Viral species involved in porcine enteric disease&#xA;complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses&#xA;and pestiviruses among others. The virome of three groups of swine samples&#xA;submitted to the Kansas State University Veterinary Diagnostic Laboratory for&#xA;routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a&#xA;Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All&#xA;groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C&#xA;and H such that samples positive for RVA only went in the RVA group, samples&#xA;positive for &amp;gt;1 rotavirus went in the RV group and samples negative for all were&#xA;grouped in the RVNeg group. All of the animals had clinical enteric disease&#xA;resulting in scours and swollen joints/lameness, enlarged heart and/or a cough.&#xA;All samples were metagenomic sequenced and analyzed for viral species&#xA;composition that identified 14 viral species and eight bacterial viruses/phages.&#xA;Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and&#xA;RV samples but were found at low or no prevalence in the RV Neg samples.&#xA;Picobirnavirus was identified at a high proportion and prevalence in RV Neg and&#xA;RV samples but at a low prevalence in the RVA group. A sequence analysis of the&#xA;possible host of Picobirnaviruses revealed fungi as the most likely host.&#xA;Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg&#xA;samples. Various sequences were extracted from the sample reads and a&#xA;phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA&#xA;genotypes. These data are important for pathogen surveillance and control&#xA;measures&lt;/p&gt;</description>
    </item>
  </channel>
</rss>
