<?xml version="1.0" encoding="utf-8" standalone="yes"?><feed xmlns="http://www.w3.org/2005/Atom"><generator uri="https://gohugo.io" version="0.141.0">Hugo v0.141.0</generator><id>https://millironx.millironx.page/@indiewebpub/people/andrea-lu/</id><link rel="self" type="application/atom+xml" href="https://millironx.millironx.page/@indiewebpub/people/andrea-lu/feed.xml"/><link rel="alternate" type="text/html" href="https://millironx.millironx.page/@indiewebpub/people/andrea-lu/"/><updated>2025-03-31T00:14:19+00:00</updated><title>Andrea Lu's activity on Milliron X</title><entry><id>https://millironx.millironx.page/@indiewebpub/academia/yavsap/</id><link rel="alternate" href="/academia/yavsap/yavsap.pdf"/><title>YAVSAP: versatile viral quasispecies analysis for veterinary samples</title><published>2024-03-05T00:00:00+00:00</published><updated>2024-03-05T00:00:00+00:00</updated><author><name>Thomas A. Christensen II</name><uri>https://millironx.millironx.page/@indiewebpub/people/thomas-a.-christensen-ii/</uri></author><author><name>Steven Stancic</name><uri>https://millironx.millironx.page/@indiewebpub/people/steven-stancic/</uri></author><author><name>Andrea Lu</name><uri>https://millironx.millironx.page/@indiewebpub/people/andrea-lu/</uri></author><author><name>Dana Mitzel</name><uri>https://millironx.millironx.page/@indiewebpub/people/dana-mitzel/</uri></author><author><name>William Wilson</name><uri>https://millironx.millironx.page/@indiewebpub/people/william-wilson/</uri></author><author><name>Rachel Palinski</name><uri>https://millironx.millironx.page/@indiewebpub/people/rachel-palinski/</uri></author><category term="presentation"/><category term="virus"/><category term="quasispecies"/><category term="next-generation sequencing"/><category term="pipeline"/><summary type="text">
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.</summary><content type="html" xml:lang="en" xml:base="https://millironx.millironx.page/@indiewebpub/">
&lt;p>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 &amp;ldquo;quasispecies,&amp;rdquo; 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&amp;rsquo;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 &lt;a
 href="https://github.com/ksumngs/yavsap">https://github.com/ksumngs/yavsap&lt;/a>.&lt;/p>
</content></entry><entry><id>https://millironx.millironx.page/@indiewebpub/academia/rotavirus-virome/</id><link rel="alternate" href="https://doi.org/10.1016/j.vetmic.2022.109447"/><title>Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease</title><published>2022-04-27T00:00:00+00:00</published><updated>2022-04-27T00:00:00+00:00</updated><author><name>Tyler Doerksen</name><uri>https://millironx.millironx.page/@indiewebpub/people/tyler-doerksen/</uri></author><author><name>Thomas A. Christensen II</name><uri>https://millironx.millironx.page/@indiewebpub/people/thomas-a.-christensen-ii/</uri></author><author><name>Andrea Lu</name><uri>https://millironx.millironx.page/@indiewebpub/people/andrea-lu/</uri></author><author><name>Lance Noll</name><uri>https://millironx.millironx.page/@indiewebpub/people/lance-noll/</uri></author><author><name>Jianfa Bai</name><uri>https://millironx.millironx.page/@indiewebpub/people/jianfa-bai/</uri></author><author><name>Jamie Henningson</name><uri>https://millironx.millironx.page/@indiewebpub/people/jamie-henningson/</uri></author><author><name>Rachel Palinski</name><uri>https://millironx.millironx.page/@indiewebpub/people/rachel-palinski/</uri></author><category term="paper"/><category term="porcine rotavirus"/><category term="porcine enteric disease"/><category term="virome"/><category term="rotavirus"/><summary type="text">
Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C and H such that samples positive for RVA only went in the RVA group, samples positive for >1 rotavirus went in the RV group and samples negative for all were grouped in the RVNeg group. All of the animals had clinical enteric disease resulting in scours and swollen joints/lameness, enlarged heart and/or a cough. All samples were metagenomic sequenced and analyzed for viral species composition that identified 14 viral species and eight bacterial viruses/phages. Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and RV samples but were found at low or no prevalence in the RV Neg samples. Picobirnavirus was identified at a high proportion and prevalence in RV Neg and RV samples but at a low prevalence in the RVA group. A sequence analysis of the possible host of Picobirnaviruses revealed fungi as the most likely host. Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg samples. Various sequences were extracted from the sample reads and a phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA genotypes. These data are important for pathogen surveillance and control measures</summary><content type="html" xml:lang="en" xml:base="https://millironx.millironx.page/@indiewebpub/">
&lt;p>Enteric disease is the predominant cause of morbidity and mortality in young
mammals including pigs. Viral species involved in porcine enteric disease
complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses
and pestiviruses among others. The virome of three groups of swine samples
submitted to the Kansas State University Veterinary Diagnostic Laboratory for
routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a
Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All
groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C
and H such that samples positive for RVA only went in the RVA group, samples
positive for &amp;gt;1 rotavirus went in the RV group and samples negative for all were
grouped in the RVNeg group. All of the animals had clinical enteric disease
resulting in scours and swollen joints/lameness, enlarged heart and/or a cough.
All samples were metagenomic sequenced and analyzed for viral species
composition that identified 14 viral species and eight bacterial viruses/phages.
Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and
RV samples but were found at low or no prevalence in the RV Neg samples.
Picobirnavirus was identified at a high proportion and prevalence in RV Neg and
RV samples but at a low prevalence in the RVA group. A sequence analysis of the
possible host of Picobirnaviruses revealed fungi as the most likely host.
Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg
samples. Various sequences were extracted from the sample reads and a
phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA
genotypes. These data are important for pathogen surveillance and control
measures&lt;/p>
</content></entry></feed>