Amanda Warr
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View article: Near-complete genome of two genotype II African swine fever viruses recovered from domestic pigs in Tanzania
Near-complete genome of two genotype II African swine fever viruses recovered from domestic pigs in Tanzania Open
Two near-complete genomes of genotype II African swine fever viruses (ASFV) recovered from domestic pigs in Mbozi district, Tanzania, in 2017 were generated using tiled amplicon Oxford nanopore sequencing. These two ASFV genomes described …
View article: Feline infectious peritonitis epizootic caused by a recombinant coronavirus
Feline infectious peritonitis epizootic caused by a recombinant coronavirus Open
Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health 1–3 . While the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed 4–7 …
View article: An Automated and Portable Platform for Rapid Cell-Free DNA Isolation and Its Application in Microbial DNA Sequencing from Human Blood Samples
An Automated and Portable Platform for Rapid Cell-Free DNA Isolation and Its Application in Microbial DNA Sequencing from Human Blood Samples Open
Background The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days a…
View article: FCoV‐23 causing FIP in a cat imported to the UK from Cyprus
FCoV‐23 causing FIP in a cat imported to the UK from Cyprus Open
cat imported to the UK from Cyprus
View article: Emergence and spread of feline infection peritonitis due to a highly pathogenic canine/feline recombinant coronavirus
Emergence and spread of feline infection peritonitis due to a highly pathogenic canine/feline recombinant coronavirus Open
Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health1-3. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and d…
View article: Emergence and spread of feline infectious peritonitis due to a highly pathogenic canine/feline recombinant coronavirus
Emergence and spread of feline infectious peritonitis due to a highly pathogenic canine/feline recombinant coronavirus Open
Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health 1–3 . Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and…
View article: Coding-Complete Genome Sequence of an African Swine Fever Virus from an Outbreak in 2021 among Domestic Pigs in Pangasinan, Philippines
Coding-Complete Genome Sequence of an African Swine Fever Virus from an Outbreak in 2021 among Domestic Pigs in Pangasinan, Philippines Open
We report a coding-complete genome sequence of an African swine fever virus from an outbreak in 2021 among domestic pigs in Pangasinan, Philippines using Oxford Nanopore Technologies minION. The linear genome assembly is a single contig wi…
View article: Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification
Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification Open
Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify the host factors involved and treatments to combat infection. Quantification of released virions often requires lengthy procedures, whereas quantification o…
View article: No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo
No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo Open
African Swine Fever virus (ASFV) is the causative agent of a deadly, panzootic disease, infecting wild and domesticated suid populations. Contained for a long time to the African continent, an outbreak of a particularly infectious variant …
View article: Direct lysis RT-qPCR of SARS-CoV-2 in cell culture supernatant allows for fast and accurate quantification of virus, opening a vast array of applications
Direct lysis RT-qPCR of SARS-CoV-2 in cell culture supernatant allows for fast and accurate quantification of virus, opening a vast array of applications Open
An enormous global effort is being made to study SARS-CoV-2 and develop safe and effective treatments. Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify host factors and treatments to combat the infection. …
View article: A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck <i>Aythya fuligula</i> (tufted duck)
A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck <i>Aythya fuligula</i> (tufted duck) Open
Background The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-p…
View article: Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family
Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family Open
Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances…
View article: A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck<i>Aythya fuligula</i>(Tufted Duck)
A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck<i>Aythya fuligula</i>(Tufted Duck) Open
Background The tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-path…
View article: An improved pig reference genome sequence to enable pig genetics and genomics research
An improved pig reference genome sequence to enable pig genetics and genomics research Open
Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa…
View article: Secrets of the hospital underbelly: patterns of abundance of antimicrobial resistance genes in hospital wastewater vary by specific antimicrobial and bacterial family
Secrets of the hospital underbelly: patterns of abundance of antimicrobial resistance genes in hospital wastewater vary by specific antimicrobial and bacterial family Open
Background Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances …
View article: Lost pigs and broken genes: the search for causes of embryonic loss in the pig and the assembly of a more contiguous reference genome
Lost pigs and broken genes: the search for causes of embryonic loss in the pig and the assembly of a more contiguous reference genome Open
The pig is an economically important species, with pork being the most
\nwidely consumed meat in the world. Genomic technologies have the potential
\nto improve reproduction, health and efficiency in the pig industry. Additionally,
\npigs …
View article: An improved pig reference genome sequence to enable pig genetics and genomics research
An improved pig reference genome sequence to enable pig genetics and genomics research Open
The domestic pig ( Sus scrofa ) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established u…
View article: An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome
An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome Open
In flat-faced dog breeds, air resistance caused by skull conformation is believed to be a major determinant of Brachycephalic Obstructive Airway Syndrome (BOAS). The clinical presentation of BOAS is heterogeneous, suggesting determinants i…
View article: The bacterial pedome associated with foot pathologies in sheep: : a case study
The bacterial pedome associated with foot pathologies in sheep: : a case study Open
Hoof lameness is considered to be a major health issue in sheep, and can impact on both animal welfare and production of livestock. However the causes, although generally assumed to have a microbiological basis, are poorly understood. The …
View article: The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics Open
Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialised stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enz…
View article: An ADAMTS3 Missense Variant is Associated with Norwich Terrier Upper Airway Syndrome - Supporting Data
An ADAMTS3 Missense Variant is Associated with Norwich Terrier Upper Airway Syndrome - Supporting Data Open
This dataset comprises of Variant Call Format (VCF) files associated with the BAM files in this publication. The full BAM files will be submitted to European Nucleotide Archive.
View article: Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen Open
The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. Here we present 913 draft bacterial and archaeal genomes assembled from over 800 G…
View article: Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism
Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism Open
The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interes…
View article: Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2)
Identification of Low-Confidence Regions in the Pig Reference Genome (Sscrofa10.2) Open
Many applications of high throughput sequencing rely on the availability of an accurate reference genome. Variant calling often produces large data sets that cannot be realistically validated and which may contain large numbers of false-po…
View article: Exome Sequencing: Current and Future Perspectives
Exome Sequencing: Current and Future Perspectives Open
The falling cost of DNA sequencing has made the technology af fordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and …