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Article: Small Non-coding RNA Expression Following Respiratory Syncytial Virus or Measles Virus Infection of Neuronal Cells.

Bakre, Abhijeet A / Duffy, Catherine / Abdullah, Hani'ah / Cosby, S Louise / Tripp, Ralph A

2021 Volume 12, Page(s) 671852

Abstract: Respiratory syncytial virus (RSV) or measles virus (MeV) infection modifies host responses through small non-coding RNA (sncRNA) expression. We show that RSV or MeV infection of neuronal cells induces sncRNAs including various microRNAs and transfer RNA ... ...

Abstract	Respiratory syncytial virus (RSV) or measles virus (MeV) infection modifies host responses through small non-coding RNA (sncRNA) expression. We show that RSV or MeV infection of neuronal cells induces sncRNAs including various microRNAs and transfer RNA fragments (tRFs). We show that these tRFs originate from select tRNAs (GCC and CAC for glycine, CTT and AAC for Valine, and CCC and TTT for Lysine). Some of the tRNAs are rarely used by RSV or MeV as indicated by relative synonymous codon usage indices suggesting selective cleavage of the tRNAs occurs in infected neuronal cells. The data implies that differentially expressed sncRNAs may regulate host gene expression
Language	English
Publishing date	2021-09-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.671852
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Efficacy of single pass UVC air treatment for the inactivation of coronavirus, MS2 coliphage and

Snelling, William J / Afkhami, Arsalan / Turkington, Hannah L / Carlisle, Claire / Cosby, S Louise / Hamilton, Jeremy W J / Ternan, Nigel G / Dunlop, Patrick S M

Journal of aerosol science

2022 Volume 164, Page(s) 106003

Abstract: There is strong evidence that SARS-CoV-2 is spread predominantly by airborne transmission, with high viral loads released into the air as respiratory droplets and aerosols from the infected subject. The spread and persistence of SARS-CoV-2 in diverse ... ...

Abstract	There is strong evidence that SARS-CoV-2 is spread predominantly by airborne transmission, with high viral loads released into the air as respiratory droplets and aerosols from the infected subject. The spread and persistence of SARS-CoV-2 in diverse indoor environments reinforces the urgent need to supplement distancing and PPE based approaches with effective engineering measures for microbial decontamination - thereby addressing the significant risk posed by aerosols. We hypothesized that a portable, single-pass UVC air treatment device (air flow 1254 L/min) could effectively inactivate bioaerosols containing bacterial and viral indicator organisms, and coronavirus without reliance on filtration technology, at reasonable scale. Robust experiments demonstrated UVC dose dependent inactivation of
Language	English
Publishing date	2022-04-26
Publishing country	England
Document type	Journal Article
ZDB-ID	1499134-2
ISSN	1879-1964 ; 0021-8502
ISSN (online)	1879-1964
ISSN	0021-8502
DOI	10.1016/j.jaerosci.2022.106003
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Article: Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1

Esnault, Gaelle / Earley, Bernadette / Cormican, Paul / Waters, Sinead M. / Lemon, Ken / Cosby, S. Louise / Lagan, Paula / Barry, Thomas / Reddington, Kate / McCabe, Matthew S.

Viruses. 2022 Aug. 24, v. 14, no. 9

2022

Abstract: Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial ... ...

Abstract	Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.
Keywords	Bovine alphaherpesvirus 1 ; bovine respiratory disease ; cattle ; computer software ; databases ; diagnostic techniques ; metagenomics ; morbidity ; mortality ; nanopores ; nose ; pathogen identification ; sequence analysis ; vaccine development ; viral genome ; viruses
Language	English
Dates of publication	2022-0824
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091859
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Article: Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge.

O'Donoghue, Stephanie / Earley, Bernadette / Johnston, Dayle / McCabe, Matthew S / Kim, Jae Woo / Taylor, Jeremy F / Duffy, Catherine / Lemon, Ken / McMenamy, Michael / Cosby, S Louise / Morris, Derek W / Waters, Sinéad M

Frontiers in genetics

2023 Volume 14, Page(s) 1092877

Abstract: Bovine herpesvirus 1 (BoHV-1), is associated with several clinical syndromes in cattle, among which bovine respiratory disease (BRD) is of particular significance. Despite the importance of the disease, there is a lack of information on the molecular ... ...

Abstract	Bovine herpesvirus 1 (BoHV-1), is associated with several clinical syndromes in cattle, among which bovine respiratory disease (BRD) is of particular significance. Despite the importance of the disease, there is a lack of information on the molecular response to infection
Language	English
Publishing date	2023-02-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1092877
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Article ; Online: Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.

Esnault, Gaelle / Earley, Bernadette / Cormican, Paul / Waters, Sinead M / Lemon, Ken / Cosby, S Louise / Lagan, Paula / Barry, Thomas / Reddington, Kate / McCabe, Matthew S

Viruses

2022 Volume 14, Issue 9

Abstract	Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.
MeSH term(s)	Animals ; Anti-Bacterial Agents ; Cattle ; Cattle Diseases ; Genomics ; Herpesvirus 1, Bovine/genetics ; Metagenomics/methods ; Nanopores ; Viruses/genetics
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-08-24
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/v14091859
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Article: Diagnosis of sheep fasciolosis caused by Fasciola hepatica using cathepsin L enzyme-linked immunosorbent assays (ELISA)

López Corrales, Jesús / Cwiklinski, Krystyna / De Marco Verissimo, Carolina / Dorey, Amber / Lalor, Richard / Jewhurst, Heather / McEvoy, Amanda / Diskin, Michael / Duffy, Catherine / Cosby, S. Louise / Keane, Orla M. / Dalton, John Pius

Veterinary parasitology. 2021 Oct., v. 298

2021

Abstract: Fasciolosis, a global parasitic disease of agricultural livestock, is caused by the liver fluke Fasciola hepatica. Management and strategic control of fasciolosis on farms depends on early assessment of the extent of disease so that control measures can ... ...

Abstract	Fasciolosis, a global parasitic disease of agricultural livestock, is caused by the liver fluke Fasciola hepatica. Management and strategic control of fasciolosis on farms depends on early assessment of the extent of disease so that control measures can be implemented quickly. Traditionally, this has relied on the detection of eggs in the faeces of animals, a laborious method that lacks sensitivity, especially for sub-clinical infections, and identifies chronic infections only. Enzyme linked immunosorbent assays (ELISA) offer a quicker and more sensitive serological means of diagnosis that could detect early acute infection before significant liver damage occurs. The performance of three functionally-active recombinant forms of the major F. hepatica secreted cathepsins L, rFhCL1, rFhCL2, rFhCL3, and a cathepsin B, rFhCB3, were evaluated as antigens in an indirect ELISA to serologically diagnose liver fluke infection in experimentally and naturally infected sheep. rFhCL1 and rFhCL3 were the most effective of the four antigens detecting fasciolosis in sheep as early as three weeks after experimental infection, at least five weeks earlier than both coproantigen and faecal egg tests. In addition, the rFhCL1 and rFhCL3 ELISAs had a very low detection limit for liver fluke in lambs exposed to natural infection on pastures and thus could play a major role in the surveillance of farms and a ‘test and treat’ approach to disease management. Finally, antibodies to all three cathepsin L proteases remain high throughout chronic infection but decline rapidly after drug treatment with the flukicide, triclabendazole, implying that the test may be adapted to trace the effectiveness of drug treatment.
Keywords	Fasciola hepatica ; cathepsin B ; cathepsin L ; coproantigens ; detection limit ; disease control ; drug therapy ; eggs ; fascioliasis ; feces ; liver ; liver flukes ; monitoring ; triclabendazole ; veterinary parasitology
Language	English
Dates of publication	2021-10
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	196831-2
ISSN	1873-2550 ; 0304-4017
ISSN (online)	1873-2550
ISSN	0304-4017
DOI	10.1016/j.vetpar.2021.109517
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus.

Johnston, Dayle / Kim, JaeWoo / Taylor, Jeremy F / Earley, Bernadette / McCabe, Matthew S / Lemon, Ken / Duffy, Catherine / McMenamy, Michael / Cosby, S Louise / Waters, Sinéad M

BMC genomics

2021 Volume 22, Issue 1, Page(s) 14

Abstract: Background: Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be ... ...

Abstract	Background: Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues. Results: Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci. Conclusions: The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.
MeSH term(s)	Animals ; Cattle ; Cattle Diseases/genetics ; Chromatin ; Chromatin Immunoprecipitation Sequencing ; Lymph Nodes ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus Infections/veterinary ; Respiratory Syncytial Virus, Bovine/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-020-07268-5
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Article ; Online: Messenger RNA biomarkers of Bovine Respiratory Syncytial Virus infection in the whole blood of dairy calves.

Johnston, Dayle / Earley, Bernadette / McCabe, Matthew S / Kim, JaeWoo / Taylor, Jeremy F / Lemon, Ken / Duffy, Catherine / McMenamy, Michael / Cosby, S Louise / Waters, Sinead M

Scientific reports

2021 Volume 11, Issue 1, Page(s) 9392

Abstract: Bovine Respiratory Syncytial Virus (BRSV) is a primary viral cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in ... ...

Abstract	Bovine Respiratory Syncytial Virus (BRSV) is a primary viral cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are more accessible in live animals, such as whole blood, they may be used as biomarkers for diagnosis of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response of dairy calves to an experimental challenge with BRSV. Calves (Holstein-Friesian) were either administered BRSV inoculate (10
MeSH term(s)	Animals ; Biomarkers/blood ; Cattle ; Cattle Diseases/blood ; Cattle Diseases/diagnosis ; Cattle Diseases/genetics ; Cattle Diseases/virology ; Gene Expression Regulation ; RNA, Messenger/blood ; RNA, Messenger/genetics ; Respiratory Syncytial Virus Infections/diagnosis ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus Infections/veterinary ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Bovine/genetics ; Transcriptome
Chemical Substances	Biomarkers ; RNA, Messenger
Language	English
Publishing date	2021-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-88878-1
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Article ; Online: Canine and Phocine Distemper Viruses: Global Spread and Genetic Basis of Jumping Species Barriers.

Kennedy, Judith M / Earle, J A Philip / Omar, Shadia / Abdullah, Hani'ah / Nielsen, Ole / Roelke-Parker, Melody E / Cosby, S Louise

Viruses

2019 Volume 11, Issue 10

Abstract: Canine distemper virus (CDV) and phocine distemper (PDV) are closely-related members of ... ...

Abstract	Canine distemper virus (CDV) and phocine distemper (PDV) are closely-related members of the
MeSH term(s)	Animals ; Animals, Wild/virology ; Cats ; Cetacea/virology ; Climate Change ; Distemper Virus, Canine/genetics ; Distemper Virus, Canine/pathogenicity ; Distemper Virus, Phocine/genetics ; Distemper Virus, Phocine/pathogenicity ; Dogs ; Host Specificity ; Morbillivirus/genetics ; Morbillivirus/pathogenicity ; Morbillivirus/physiology ; Morbillivirus Infections/veterinary ; Pets/virology ; Primates/virology ; Viral Proteins/genetics
Chemical Substances	Viral Proteins
Language	English
Publishing date	2019-10-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v11100944
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Article: Elucidation of the Host Bronchial Lymph Node miRNA Transcriptome Response to Bovine Respiratory Syncytial Virus.

Johnston, Dayle / Earley, Bernadette / McCabe, Matthew S / Kim, Jaewoo / Taylor, Jeremy F / Lemon, Ken / McMenamy, Michael / Duffy, Catherine / Cosby, S Louise / Waters, Sinéad M

Frontiers in genetics

2021 Volume 12, Page(s) 633125

Abstract: Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting cattle of all ages. One of the main causes of BRD is an initial inflammatory response to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging ... ...

Abstract	Bovine respiratory disease (BRD) causes substantial morbidity and mortality, affecting cattle of all ages. One of the main causes of BRD is an initial inflammatory response to bovine respiratory syncytial virus (BRSV). MicroRNAs are novel and emerging non-coding small RNAs that regulate many biological processes and are implicated in various inflammatory diseases. The objective of the present study was to elucidate the changes in the bovine bronchial lymph node miRNA transcriptome in response to BRSV following an experimental viral challenge. Holstein-Friesian calves were either administered a challenge dose of BRSV (10
Language	English
Publishing date	2021-04-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.633125
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