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  1. Article ; Online: FCoV-23 causing FIP in a cat imported to the UK from Cyprus.

    Warr, Amanda / Attipa, Charalampos / Gunn-Moore, Danielle / Tait-Burkard, Christine

    The Veterinary record

    2023  Volume 193, Issue 10, Page(s) 414–415

    MeSH term(s) Cats ; Animals ; Cyprus ; Feline Infectious Peritonitis ; Mutation ; United Kingdom ; Coronavirus, Feline ; Cat Diseases/diagnosis
    Language English
    Publishing date 2023-11-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 390015-0
    ISSN 2042-7670 ; 0042-4900
    ISSN (online) 2042-7670
    ISSN 0042-4900
    DOI 10.1002/vetr.3696
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Errors in long-read assemblies can critically affect protein prediction.

    Watson, Mick / Warr, Amanda

    Nature biotechnology

    2019  Volume 37, Issue 2, Page(s) 124–126

    MeSH term(s) Contig Mapping ; Genome, Human ; Humans ; Nanopores ; Sequence Analysis, Protein
    Language English
    Publishing date 2019-01-23
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-018-0004-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification.

    Craig, Nicky / Fletcher, Sarah L / Daniels, Alison / Newman, Caitlin / O'Shea, Marie / Tan, Wenfang Spring / Warr, Amanda / Tait-Burkard, Christine

    Viruses

    2022  Volume 14, Issue 3

    Abstract: 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 of viral RNA in ... ...

    Abstract 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 of viral RNA in supernatant is faster and applicable to clinical isolates. Viral RNA purification is expensive in terms of time and resources, and is often unsuitable for high-throughput screening. Direct lysis protocols were explored for patient swab samples, but the lack of virus inactivation, cost, sensitivity, and accuracy is hampering their application and usefulness for in vitro studies. Here, we show a highly sensitive, accurate, fast, and cheap direct lysis RT-qPCR method for quantification of SARS-CoV-2 in culture supernatant. This method inactivates the virus and permits detection limits of 0.043 TCID50 virus and <1.89 copy RNA template per reaction. Comparing direct lysis with RNA extraction, a mean difference of +0.69 ± 0.56 cycles was observed. Application of the method to established qPCR methods for RSV (-ve RNA), IAV (segmented -ve RNA), and BHV (dsDNA) showed wider applicability to other enveloped viruses, whereby IAV showed poorer sensitivity. This shows that accurate quantification of SARS-CoV-2 and other enveloped viruses can be achieved using direct lysis protocols, facilitating a wide range of high- and low-throughput applications.
    MeSH term(s) COVID-19/diagnosis ; Cell Culture Techniques ; Humans ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/genetics
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2022-02-28
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14030508
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Coding-Complete Genome Sequence of an African Swine Fever Virus from an Outbreak in 2021 among Domestic Pigs in Pangasinan, Philippines.

    Montecillo, Andrew D / Baybay, Zyne / Cabug, Ralph Carolyn / Cariaso, Wreahlen / Jose, John Paulo / Mantaring, Sheila / Briones, Annabelle / Warr, Amanda / Burkard, Christine / Villegas, Lucille / Pantua, Homer

    Microbiology resource announcements

    2022  Volume 11, Issue 12, Page(s) e0071922

    Abstract: 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 with 192,377 bp. ...

    Abstract 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 with 192,377 bp.
    Language English
    Publishing date 2022-11-09
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00719-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery.

    Stewart, Robert D / Auffret, Marc D / Warr, Amanda / Walker, Alan W / Roehe, Rainer / Watson, Mick

    Nature biotechnology

    2019  Volume 37, Issue 8, Page(s) 953–961

    Abstract: Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted ... ...

    Abstract Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted to digestion of the plant matter that dominates the ruminant diet. We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle. We present a genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete. Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, two of which represent previously unknown rumen species, assembled from long-read data. Using our rumen genome collection we predicted and annotated a large set of rumen proteins. Our set of rumen MAGs increases the rate of mapping of rumen metagenomic sequencing reads from 15% to 50-70%. These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota.
    MeSH term(s) Animals ; Archaea/genetics ; Archaeal Proteins ; Bacteria/genetics ; Bacterial Proteins ; Cattle/microbiology ; Databases, Protein ; Genome, Archaeal ; Genome, Bacterial ; Metagenome ; Metagenomics/methods ; Phylogeny ; Rumen/microbiology ; Sheep/microbiology
    Chemical Substances Archaeal Proteins ; Bacterial Proteins
    Language English
    Publishing date 2019-08-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-019-0202-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2167: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 137: Show issues
    Zs.MG 43: Show issues

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  6. Article: Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family.

    Perry, Meghan R / Lepper, Hannah C / McNally, Luke / Wee, Bryan A / Munk, Patrick / Warr, Amanda / Moore, Barbara / Kalima, Pota / Philip, Carol / de Roda Husman, Ana Maria / Aarestrup, Frank M / Woolhouse, Mark E J / van Bunnik, Bram A D

    Frontiers in microbiology

    2021  Volume 12, Page(s) 703560

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2021-09-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.703560
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Direct Lysis RT-qPCR of SARS-CoV-2 in Cell Culture Supernatant Allows for Fast and Accurate Quantification

    Craig, Nicky / Fletcher, Sarah L. / Daniels, Alison / Newman, Caitlin / O’Shea, Marie / Tan, Wenfang Spring / Warr, Amanda / Tait-Burkard, Christine

    Viruses. 2022 Feb. 28, v. 14, no. 3

    2022  

    Abstract: 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 of viral RNA in ... ...

    Abstract 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 of viral RNA in supernatant is faster and applicable to clinical isolates. Viral RNA purification is expensive in terms of time and resources, and is often unsuitable for high-throughput screening. Direct lysis protocols were explored for patient swab samples, but the lack of virus inactivation, cost, sensitivity, and accuracy is hampering their application and usefulness for in vitro studies. Here, we show a highly sensitive, accurate, fast, and cheap direct lysis RT-qPCR method for quantification of SARS-CoV-2 in culture supernatant. This method inactivates the virus and permits detection limits of 0.043 TCID₅₀ virus and <1.89 copy RNA template per reaction. Comparing direct lysis with RNA extraction, a mean difference of +0.69 ± 0.56 cycles was observed. Application of the method to established qPCR methods for RSV (-ve RNA), IAV (segmented -ve RNA), and BHV (dsDNA) showed wider applicability to other enveloped viruses, whereby IAV showed poorer sensitivity. This shows that accurate quantification of SARS-CoV-2 and other enveloped viruses can be achieved using direct lysis protocols, facilitating a wide range of high- and low-throughput applications.
    Keywords DNA ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; cell culture ; patients ; virus replication ; viruses
    Language English
    Dates of publication 2022-0228
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14030508
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: 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

    Craig, Nicky / Fletcher, Sarah Louise / Daniels, Alison / Newman, Caitlin / O'Shea, Marie / Warr, Amanda / Tait-Burkard, Christine

    bioRxiv

    Abstract: 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. However, ... ...

    Abstract 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. However, quantification of released virus often requires lengthy procedures, such as endpoint dilution assays or reinfection with engineered reporter viruses. Quantification of viral RNA in cell supernatant is faster and can be performed on clinical isolates. However, viral RNA purification is expensive in time and resources and often unsuitable for high-throughput screening. Here, we show a direct lysis RT-qPCR method allowing sensitive, accurate, fast, and cheap quantification of SARS-CoV-2 in culture supernatant. During lysis, the virus is completely inactivated, allowing further processing in low containment areas. This protocol facilitates a wide array of high- and low-throughput applications from basic quantification to studying the biology of SARS-CoV-2 and to identify novel antiviral treatments in vitro.
    Keywords covid19
    Language English
    Publishing date 2021-12-02
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.11.30.470550
    Database COVID19

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  9. Article ; Online: Emergence and spread of feline infection peritonitis due to a highly pathogenic canine/feline recombinant coronavirus

    Atippa, Charalampos / Warr, Amanda Susan / Epaminondas, Demetris / O'Shea, Marie / Fletcher, Sarah Louise / Malbon, Alexandra / Lyraki, Maria / Hammond, Rachael / Hardas, Alexandros / Zanti, Antria / Loukaidou, Stavroula / Gentil, Michaela / Gunn-Moore, Danielle / Mazeri, Stella / Tait-Burkard, Christine

    bioRxiv

    Abstract: Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated. ... ...

    Abstract Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated. Companion animals are often overlooked in the transmission cycle of viral diseases; however, the close relationship of feline (FCoV) and canine CoV (CCoV) to human hCoV-229E, as well as their susceptibility to SARS-CoV-2 highlight their importance in potential transmission cycles. Whilst recombination between CCoV and FCoV of a large fragment spanning orf1b to M has been previously described, here we report the emergence of a novel, highly pathogenic FCoV-CCoV recombinant responsible for a rapidly spreading outbreak of feline infectious peritonitis (FIP), originating in Cyprus. The recombination, spanning spike, shows 97% sequence identity to the pantropic canine coronavirus CB/05. Infection is spreading fast and infecting cats of all ages. Development of FIP appears rapid and likely non-reliant on biotype switch. High sequence identity of isolates from cats in different districts of the island is strongly supportive of direct transmission. A deletion and several amino acid changes in spike, particularly the receptor binding domain, compared to other FCoV-2s, indicate changes to receptor binding and likely cell tropism.
    Keywords covid19
    Language English
    Publishing date 2023-11-09
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.11.08.566182
    Database COVID19

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  10. Article ; Online: Emergence and spread of feline infectious peritonitis due to a highly pathogenic canine/feline recombinant coronavirus

    Atippa, Charalampos / Warr, Amanda Susan / Epaminondas, Demetris / O'Shea, Marie / Fletcher, Sarah Louise / Malbon, Alexandra / Lyraki, Maria / Hammond, Rachael / Hardas, Alexandros / Zanti, Antria / Loukaidou, Stavroula / Gentil, Michaela / Gunn-Moore, Danielle / Mazeri, Stella / Tait-Burkard, Christine

    bioRxiv

    Abstract: Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated. ... ...

    Abstract Cross-species transmission of coronaviruses (CoVs) poses a serious threat to both animal and human health. Whilst the large RNA genome of CoVs shows relatively low mutation rates, recombination within genera is frequently observed and demonstrated. Companion animals are often overlooked in the transmission cycle of viral diseases; however, the close relationship of feline (FCoV) and canine CoV (CCoV) to human hCoV-229E, as well as their susceptibility to SARS-CoV-2 highlight their importance in potential transmission cycles. Whilst recombination between CCoV and FCoV of a large fragment spanning orf1b to M has been previously described, here we report the emergence of a novel, highly pathogenic FCoV-CCoV recombinant responsible for a rapidly spreading outbreak of feline infectious peritonitis (FIP), originating in Cyprus. The recombination, spanning spike, shows 97% sequence identity to the pantropic canine coronavirus CB/05. Infection is spreading fast and infecting cats of all ages. Development of FIP appears rapid and likely non-reliant on biotype switch. High sequence identity of isolates from cats in different districts of the island is strongly supportive of direct transmission. A deletion and several amino acid changes in spike, particularly the receptor binding domain, compared to other FCoV-2s, indicate changes to receptor binding and likely cell tropism.
    Keywords covid19
    Language English
    Publishing date 2023-11-10
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.11.08.566182
    Database COVID19

    Full text online

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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