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Dr. Yasmin Parr
MRC-University of Glasgow Centre for Virus Research

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Research Keywords & Expertise

0 FeLV
0 Veterinary virology
0 feline calicivirus
0 Immune response to viral infections
0 Viral diagnostics

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Journal article
Published: 12 March 2021 in Viruses
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Although the antibody response induced by primary vaccination with Fel-O-Vax® FIV (three doses, 2–4 weeks apart) is well described, the antibody response induced by annual vaccination with Fel-O-Vax® FIV (single dose every 12 months after primary vaccination) and how it compares to the primary antibody response has not been studied. Residual blood samples from a primary FIV vaccination study (n = 11), and blood samples from cats given an annual FIV vaccination (n = 10), were utilized. Samples from all 21 cats were tested with a commercially available PCR assay (FIV RealPCRTM), an anti-p24 microsphere immunoassay (MIA), an anti-FIV transmembrane (TM; gp40) peptide ELISA, and a range of commercially available point-of-care (PoC) FIV antibody kits. PCR testing confirmed all 21 cats to be FIV-uninfected for the duration of this study. Results from MIA and ELISA testing showed that both vaccination regimes induced significant antibody responses against p24 and gp40, and both anti-p24 and anti-gp40 antibodies were variably present 12 months after FIV vaccination. The magnitude of the antibody response against both p24 and gp40 was significantly higher in the primary FIV vaccination group than in the annual FIV vaccination group. The differences in prime versus recall post-vaccinal antibody levels correlated with FIV PoC kit performance. Two FIV PoC kits that detect antibodies against gp40, namely Witness® and Anigen Rapid®, showed 100% specificity in cats recently administered an annual FIV vaccination, demonstrating that they can be used to accurately distinguish vaccination and infection in annually vaccinated cats. A third FIV PoC kit, SNAP® Combo, had 0% specificity in annually FIV-vaccinated cats, and should not be used in any cat with a possible history of FIV vaccination. This study outlines the antibody response to inactivated Fel-O-Vax® FIV whole-virus vaccine, and demonstrates how best to diagnose FIV infection in jurisdictions where FIV vaccination is practiced.

ACS Style

Mark Westman; Dennis Yang; Jennifer Green; Jacqueline Norris; Richard Malik; Yasmin Parr; Mike McDonald; Margaret Hosie; Sue VandeWoude; Craig Miller. Antibody Responses in Cats Following Primary and Annual Vaccination against Feline Immunodeficiency Virus (FIV) with an Inactivated Whole-Virus Vaccine (Fel-O-Vax® FIV). Viruses 2021, 13, 470 .

AMA Style

Mark Westman, Dennis Yang, Jennifer Green, Jacqueline Norris, Richard Malik, Yasmin Parr, Mike McDonald, Margaret Hosie, Sue VandeWoude, Craig Miller. Antibody Responses in Cats Following Primary and Annual Vaccination against Feline Immunodeficiency Virus (FIV) with an Inactivated Whole-Virus Vaccine (Fel-O-Vax® FIV). Viruses. 2021; 13 (3):470.

Chicago/Turabian Style

Mark Westman; Dennis Yang; Jennifer Green; Jacqueline Norris; Richard Malik; Yasmin Parr; Mike McDonald; Margaret Hosie; Sue VandeWoude; Craig Miller. 2021. "Antibody Responses in Cats Following Primary and Annual Vaccination against Feline Immunodeficiency Virus (FIV) with an Inactivated Whole-Virus Vaccine (Fel-O-Vax® FIV)." Viruses 13, no. 3: 470.

Journal article
Published: 07 March 2021 in Viruses
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Retroviruses belong to an important and diverse family of RNA viruses capable of causing neoplastic disease in their hosts. Feline leukaemia virus (FeLV) is a gammaretrovirus that infects domestic and wild cats, causing immunodeficiency, cytopenia and neoplasia in progressively infected cats. The outcome of FeLV infection is influenced by the host immune response; progressively infected cats demonstrate weaker immune responses compared to regressively infected cats. In this study, humoral immune responses were examined in 180 samples collected from 123 domestic cats that had been naturally exposed to FeLV, using a novel ELISA to measure antibodies recognizing the FeLV surface unit (SU) glycoprotein in plasma samples. A correlation was demonstrated between the strength of the humoral immune response to the SU protein and the outcome of exposure. Cats with regressive infection demonstrated higher antibody responses to the SU protein compared to cats belonging to other outcome groups, and samples from cats with regressive infection contained virus neutralising antibodies. These results demonstrate that an ELISA that assesses the humoral response to FeLV SU complements the use of viral diagnostic tests to define the outcome of exposure to FeLV. Together these tests could allow the rapid identification of regressively infected cats that are unlikely to develop FeLV-related disease.

ACS Style

Yasmin Parr; Melissa Beall; Julie Levy; Michael McDonald; Natascha Hamman; Brian Willett; Margaret Hosie. Measuring the Humoral Immune Response in Cats Exposed to Feline Leukaemia Virus. Viruses 2021, 13, 428 .

AMA Style

Yasmin Parr, Melissa Beall, Julie Levy, Michael McDonald, Natascha Hamman, Brian Willett, Margaret Hosie. Measuring the Humoral Immune Response in Cats Exposed to Feline Leukaemia Virus. Viruses. 2021; 13 (3):428.

Chicago/Turabian Style

Yasmin Parr; Melissa Beall; Julie Levy; Michael McDonald; Natascha Hamman; Brian Willett; Margaret Hosie. 2021. "Measuring the Humoral Immune Response in Cats Exposed to Feline Leukaemia Virus." Viruses 13, no. 3: 428.

Methods and resources
Published: 25 February 2021 in PLOS Biology
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The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.

ACS Style

Suzannah J. Rihn; Andres Merits; Siddharth Bakshi; Matthew L. Turnbull; Arthur Wickenhagen; Akira J. T. Alexander; Carla Baillie; Benjamin Brennan; Fiona Brown; Kirstyn Brunker; Steven R. Bryden; Kerry A. Burness; Stephen Carmichael; Sarah J. Cole; Vanessa M. Cowton; Paul Davies; Chris Davis; Giuditta De Lorenzo; Claire L. Donald; Mark Dorward; James I. Dunlop; Matthew Elliott; Mazigh Fares; Ana Da Silva Filipe; Joseph R. Freitas; Wilhelm Furnon; Rommel J. Gestuveo; Anna Geyer; Daniel Giesel; Daniel M. Goldfarb; Nicola Goodman; Rory Gunson; C. James Hastie; Vanessa Herder; Joseph Hughes; Clare Johnson; Natasha Johnson; Alain Kohl; Karen Kerr; Hannah Leech; Laura Sandra Lello; Kathy Li; Gauthier Lieber; Xiang Liu; Rajendra Lingala; Colin Loney; Daniel Mair; Marion J. McElwee; Steven McFarlane; Jenna Nichols; Kyriaki Nomikou; Anne Orr; Richard J. Orton; Massimo Palmarini; Yasmin A. Parr; Rute Maria Pinto; Samantha Raggett; Elaine Reid; David L. Robertson; Jamie Royle; Natalia Cameron-Ruiz; James G. Shepherd; Katherine Smollett; Douglas G. Stewart; Meredith Stewart; Elena Sugrue; Agnieszka M. Szemiel; Aislynn Taggart; Emma C. Thomson; Lily Tong; Leah S. Torrie; Rachel Toth; Margus Varjak; Sainan Wang; Stuart G. Wilkinson; Paul G. Wyatt; Eva Zusinaite; Dario R. Alessi; Arvind H. Patel; Ali Zaid; Sam J. Wilson; Suresh Mahalingam. A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLOS Biology 2021, 19, e3001091 .

AMA Style

Suzannah J. Rihn, Andres Merits, Siddharth Bakshi, Matthew L. Turnbull, Arthur Wickenhagen, Akira J. T. Alexander, Carla Baillie, Benjamin Brennan, Fiona Brown, Kirstyn Brunker, Steven R. Bryden, Kerry A. Burness, Stephen Carmichael, Sarah J. Cole, Vanessa M. Cowton, Paul Davies, Chris Davis, Giuditta De Lorenzo, Claire L. Donald, Mark Dorward, James I. Dunlop, Matthew Elliott, Mazigh Fares, Ana Da Silva Filipe, Joseph R. Freitas, Wilhelm Furnon, Rommel J. Gestuveo, Anna Geyer, Daniel Giesel, Daniel M. Goldfarb, Nicola Goodman, Rory Gunson, C. James Hastie, Vanessa Herder, Joseph Hughes, Clare Johnson, Natasha Johnson, Alain Kohl, Karen Kerr, Hannah Leech, Laura Sandra Lello, Kathy Li, Gauthier Lieber, Xiang Liu, Rajendra Lingala, Colin Loney, Daniel Mair, Marion J. McElwee, Steven McFarlane, Jenna Nichols, Kyriaki Nomikou, Anne Orr, Richard J. Orton, Massimo Palmarini, Yasmin A. Parr, Rute Maria Pinto, Samantha Raggett, Elaine Reid, David L. Robertson, Jamie Royle, Natalia Cameron-Ruiz, James G. Shepherd, Katherine Smollett, Douglas G. Stewart, Meredith Stewart, Elena Sugrue, Agnieszka M. Szemiel, Aislynn Taggart, Emma C. Thomson, Lily Tong, Leah S. Torrie, Rachel Toth, Margus Varjak, Sainan Wang, Stuart G. Wilkinson, Paul G. Wyatt, Eva Zusinaite, Dario R. Alessi, Arvind H. Patel, Ali Zaid, Sam J. Wilson, Suresh Mahalingam. A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLOS Biology. 2021; 19 (2):e3001091.

Chicago/Turabian Style

Suzannah J. Rihn; Andres Merits; Siddharth Bakshi; Matthew L. Turnbull; Arthur Wickenhagen; Akira J. T. Alexander; Carla Baillie; Benjamin Brennan; Fiona Brown; Kirstyn Brunker; Steven R. Bryden; Kerry A. Burness; Stephen Carmichael; Sarah J. Cole; Vanessa M. Cowton; Paul Davies; Chris Davis; Giuditta De Lorenzo; Claire L. Donald; Mark Dorward; James I. Dunlop; Matthew Elliott; Mazigh Fares; Ana Da Silva Filipe; Joseph R. Freitas; Wilhelm Furnon; Rommel J. Gestuveo; Anna Geyer; Daniel Giesel; Daniel M. Goldfarb; Nicola Goodman; Rory Gunson; C. James Hastie; Vanessa Herder; Joseph Hughes; Clare Johnson; Natasha Johnson; Alain Kohl; Karen Kerr; Hannah Leech; Laura Sandra Lello; Kathy Li; Gauthier Lieber; Xiang Liu; Rajendra Lingala; Colin Loney; Daniel Mair; Marion J. McElwee; Steven McFarlane; Jenna Nichols; Kyriaki Nomikou; Anne Orr; Richard J. Orton; Massimo Palmarini; Yasmin A. Parr; Rute Maria Pinto; Samantha Raggett; Elaine Reid; David L. Robertson; Jamie Royle; Natalia Cameron-Ruiz; James G. Shepherd; Katherine Smollett; Douglas G. Stewart; Meredith Stewart; Elena Sugrue; Agnieszka M. Szemiel; Aislynn Taggart; Emma C. Thomson; Lily Tong; Leah S. Torrie; Rachel Toth; Margus Varjak; Sainan Wang; Stuart G. Wilkinson; Paul G. Wyatt; Eva Zusinaite; Dario R. Alessi; Arvind H. Patel; Ali Zaid; Sam J. Wilson; Suresh Mahalingam. 2021. "A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research." PLOS Biology 19, no. 2: e3001091.

Journal article
Published: 03 February 2021 in Viruses
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A field study undertaken in Australia compared the antibody responses induced in client-owned cats that had been vaccinated using two inactivated whole feline leukaemia virus (FeLV) vaccines, the monovalent vaccine Fel-O-Vax® Lv-K and the polyvalent vaccine Fel-O-Vax® 5. Serum samples from 428 FeLV-uninfected cats (118 FeLV-vaccinated and 310 FeLV-unvaccinated) were tested for anti-FeLV neutralising antibodies (NAb) using a live virus neutralisation assay to identify 378 FeLV-unexposed (NAb-negative) and 50 FeLV-exposed (NAb-positive; abortive infections) cats, following by anti-surface unit (SU) FeLV-A and FeLV-B antibody ELISA testing. An additional 42 FeLV-infected cats (28 presumptively regressively infected, 14 presumptively progressively infected) were also tested for anti-SU antibodies. NAb-positive cats displayed significantly higher anti-SU antibody ELISA responses compared to NAb-negative cats (p < 0.001). FeLV-unexposed cats (NAb-negative) that had been vaccinated less than 18 months after a previous FeLV vaccination using the monovalent vaccine (Fel-O-Vax® Lv-K) displayed higher anti-SU antibody ELISA responses than a comparable group vaccinated with the polyvalent vaccine (Fel-O-Vax® 5) (p < 0.001 for both anti-FeLV-A and FeLV-B SU antibody responses). This difference in anti-SU antibody responses between cats vaccinated with the monovalent or polyvalent vaccine, however, was not observed in cats that had been naturally exposed to FeLV (NAb-positive) (p = 0.33). It was postulated that vaccination with Fel-O-Vax® 5 primed the humoral response prior to FeLV exposure, such that antibody production increased when the animal was challenged, while vaccination with Fel-O-Vax® Lv-K induced an immediate preparatory antibody response that did not quantitatively increase after FeLV exposure. These results raise questions about the comparable vaccine efficacy of the different FeLV vaccine formulations and correlates of protection.

ACS Style

Mark Westman; Jacqueline Norris; Richard Malik; Regina Hofmann-Lehmann; Yasmin Parr; Emma Armstrong; Mike McDonald; Evelyn Hall; Paul Sheehy; Margaret Hosie. Anti-SU Antibody Responses in Client-Owned Cats Following Vaccination against Feline Leukaemia Virus with Two Inactivated Whole-Virus Vaccines (Fel-O-Vax® Lv-K and Fel-O-Vax® 5). Viruses 2021, 13, 240 .

AMA Style

Mark Westman, Jacqueline Norris, Richard Malik, Regina Hofmann-Lehmann, Yasmin Parr, Emma Armstrong, Mike McDonald, Evelyn Hall, Paul Sheehy, Margaret Hosie. Anti-SU Antibody Responses in Client-Owned Cats Following Vaccination against Feline Leukaemia Virus with Two Inactivated Whole-Virus Vaccines (Fel-O-Vax® Lv-K and Fel-O-Vax® 5). Viruses. 2021; 13 (2):240.

Chicago/Turabian Style

Mark Westman; Jacqueline Norris; Richard Malik; Regina Hofmann-Lehmann; Yasmin Parr; Emma Armstrong; Mike McDonald; Evelyn Hall; Paul Sheehy; Margaret Hosie. 2021. "Anti-SU Antibody Responses in Client-Owned Cats Following Vaccination against Feline Leukaemia Virus with Two Inactivated Whole-Virus Vaccines (Fel-O-Vax® Lv-K and Fel-O-Vax® 5)." Viruses 13, no. 2: 240.

Author correction
Published: 27 January 2021 in Nature Microbiology
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A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00869-0 .

ACS Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology 2021, 6, 414 -414.

AMA Style

Ana Da Silva Filipe, James G. Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha Jesudason, Natasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A. McAllister, John T. McCrone, Sarah E. McDonald, Martin P. McHugh, A. Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Benjamin J. Parcell, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B. Sreenu, Elizabeth Wastnedge, Matthew T. G. Holden, David L. Robertson, Kate Templeton, Emma C. Thomson. Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology. 2021; 6 (3):414-414.

Chicago/Turabian Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. 2021. "Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland." Nature Microbiology 6, no. 3: 414-414.

Publisher correction
Published: 18 January 2021 in Nature Microbiology
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A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00865-4.

ACS Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology 2021, 6, 271 -271.

AMA Style

Ana Da Silva Filipe, James G. Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha Jesudason, Natasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A. McAllister, John T. McCrone, Sarah E. McDonald, Martin P. McHugh, A. Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Benjamin J. Parcell, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B. Sreenu, Elizabeth Wastnedge, Matthew T. G. Holden, David L. Robertson, Kate Templeton, Emma C. Thomson. Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology. 2021; 6 (2):271-271.

Chicago/Turabian Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. 2021. "Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland." Nature Microbiology 6, no. 2: 271-271.

Journal article
Published: 21 December 2020 in Nature Microbiology
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Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and epidemiological approach. Sequencing of 1,314 SARS-CoV-2 viral genomes from available patient samples enabled us to estimate that SARS-CoV-2 was introduced to Scotland on at least 283 occasions during February and March 2020. Epidemiological analysis confirmed that early introductions of SARS-CoV-2 originated from mainland Europe (the majority from Italy and Spain). We identified subsequent early outbreaks in the community, within healthcare facilities and at an international conference. Community transmission occurred after 2 March, 3 weeks before control measures were introduced. Earlier travel restrictions or quarantine measures, both locally and internationally, would have reduced the number of COVID-19 cases in Scotland. The risk of multiple reintroduction events in future waves of infection remains high in the absence of population immunity. Genomic epidemiology reveals multiple travel-related introductions of SARS-CoV-2 from mainland Europe into Scotland during the first wave of COVID-19.

ACS Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology 2020, 6, 112 -122.

AMA Style

Ana Da Silva Filipe, James G. Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha Jesudason, Natasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A. McAllister, John T. McCrone, Sarah E. McDonald, Martin P. McHugh, A. Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Benjamin J. Parcell, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B. Sreenu, Elizabeth Wastnedge, Matthew T. G. Holden, David L. Robertson, Kate Templeton, Emma C. Thomson. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology. 2020; 6 (1):112-122.

Chicago/Turabian Style

Ana Da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; David A. McAllister; John T. McCrone; Sarah E. McDonald; Martin P. McHugh; A. Keith Morris; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Benjamin J. Parcell; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Vattipally B. Sreenu; Elizabeth Wastnedge; Matthew T. G. Holden; David L. Robertson; Kate Templeton; Emma C. Thomson. 2020. "Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland." Nature Microbiology 6, no. 1: 112-122.

Other
Published: 09 June 2020
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SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks.We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland.From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions.The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.FundingMRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/ZResearch in contextEvidence before this studyCoronavirus disease-2019 (COVID-19) was first diagnosed in Scotland on the 1st of March 2020 following the emergence of the causative severe acute respiratory system coronavirus 2 (SARS-CoV-2) virus in China in December 2019. During the first month of the outbreak in Scotland, 2310 positive cases of COVID-19 were detected, associated with 1832 hospital admissions, 207 intensive care admissions and 126 deaths. The number of introductions into Scotland and the source of those introductions was not known prior to this study.Added value of this studyUsing a combined phylogenetic and epidemiological approach following real-time next generation sequencing of 452 SARS-CoV-2 samples, it was estimated that the virus was introduced to Scotland on at least 113 occasions, mostly from other European countries, including Italy, Austria and Spain. Localised outbreaks occurred in the community across multiple Scottish health boards, within healthcare facilities and an international conference and community transmission was established rapidly, before local and international lockdown measures were introduced.

ACS Style

Ana Da Silva Filipe; James Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Carlos Balcazar; Kirstyn Brunker; Stephen Carmichael; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Antonia Ho; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; Sarah E. McDonald; Martin McHugh; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Sreenu Vattipally; Elizabeth Wastnedge; David L. Robertson; Matthew T.G. Holden; Kate Templeton; Emma C. Thomson. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence. 2020, 1 .

AMA Style

Ana Da Silva Filipe, James Shepherd, Thomas Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Carlos Balcazar, Kirstyn Brunker, Stephen Carmichael, Rebecca Dewar, Michael D. Gallagher, Rory Gunson, Antonia Ho, Natasha Jesudason, Natasha Johnson, E. Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, Sarah E. McDonald, Martin McHugh, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J. Orton, Áine O’Toole, Massimo Palmarini, Yasmin A. Parr, Andrew Rambaut, Stefan Rooke, Sharif Shaaban, Rajiv Shah, Joshua B. Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Sreenu Vattipally, Elizabeth Wastnedge, David L. Robertson, Matthew T.G. Holden, Kate Templeton, Emma C. Thomson. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence. . 2020; ():1.

Chicago/Turabian Style

Ana Da Silva Filipe; James Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Carlos Balcazar; Kirstyn Brunker; Stephen Carmichael; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Antonia Ho; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean; Daniel Mair; Sarah E. McDonald; Martin McHugh; Jenna Nichols; Marc Niebel; Kyriaki Nomikou; Richard J. Orton; Áine O’Toole; Massimo Palmarini; Yasmin A. Parr; Andrew Rambaut; Stefan Rooke; Sharif Shaaban; Rajiv Shah; Joshua B. Singer; Katherine Smollett; Igor Starinskij; Lily Tong; Sreenu Vattipally; Elizabeth Wastnedge; David L. Robertson; Matthew T.G. Holden; Kate Templeton; Emma C. Thomson. 2020. "Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence." , no. : 1.

Research article
Published: 07 February 2019 in PLOS Pathogens
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Virus ecology and evolution play a central role in disease emergence. However, their relative roles will vary depending on the viruses and ecosystems involved. We combined field studies, phylogenetics and experimental infections to document with unprecedented detail the stages that precede initial outbreaks during viral emergence in nature. Using serological surveys we showed that in the absence of large-scale outbreaks, horses in Mongolia are routinely exposed to and infected by avian influenza viruses (AIVs) circulating among wild birds. Some of those AIVs are genetically related to an avian-origin virus that caused an epizootic in horses in 1989. Experimental infections showed that most AIVs replicate in the equine respiratory tract without causing lesions, explaining the absence of outbreaks of disease. Our results show that AIVs infect horses but do not spread, or they infect and spread but do not cause disease. Thus, the failure of AIVs to evolve greater transmissibility and to cause disease in horses is in this case the main barrier preventing disease emergence. Viral diseases pose a constant threat to humans and animals. Occasionally, viruses establish in new hosts, sometimes with devastating consequences. While we still do not know what allows a virus to infect and become transmissible in a new population, it is clear that ecology and evolution play an important part in this process. Influenza A viruses (IAVs) constitute the archetypical example of emerging viruses: their main natural reservoir is in wild birds but they have also established in humans, pigs and horses. To better understand how IAVs circulate in nature we sequenced over twenty avian influenza viruses collected from wild birds in Mongolia. We show that these viruses are partially related to a virus that caused an equine influenza epizootic in 1989, that they can infect and replicate in the respiratory tract of the horse without causing any tissue damage, and that -based on serological evidence- horses in Mongolia have been regularly exposed to them over a broad geographical area without causing clinically evident outbreaks. We conclude that equine infections by avian viruses able to replicate in horses are more common than originally thought and that the failure to acquire key genetic changes is in this case the main barrier to disease emergence.

ACS Style

Henan Zhu; Batchuluun Damdinjav; Gaelle Gonzalez; Livia Victoria Patrono; Humberto Ramirez-Mendoza; Julien A. R. Amat; Joanna Crispell; Yasmin Amy Parr; Toni-Ann Hammond; Enkhtuvshin Shiilegdamba; Y. H. Connie Leung; Joseph Sriyal Malik Peiris; John F. Marshall; Joseph Hughes; Martin Gilbert; Pablo R. Murcia. Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLOS Pathogens 2019, 15, e1007531 .

AMA Style

Henan Zhu, Batchuluun Damdinjav, Gaelle Gonzalez, Livia Victoria Patrono, Humberto Ramirez-Mendoza, Julien A. R. Amat, Joanna Crispell, Yasmin Amy Parr, Toni-Ann Hammond, Enkhtuvshin Shiilegdamba, Y. H. Connie Leung, Joseph Sriyal Malik Peiris, John F. Marshall, Joseph Hughes, Martin Gilbert, Pablo R. Murcia. Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLOS Pathogens. 2019; 15 (2):e1007531.

Chicago/Turabian Style

Henan Zhu; Batchuluun Damdinjav; Gaelle Gonzalez; Livia Victoria Patrono; Humberto Ramirez-Mendoza; Julien A. R. Amat; Joanna Crispell; Yasmin Amy Parr; Toni-Ann Hammond; Enkhtuvshin Shiilegdamba; Y. H. Connie Leung; Joseph Sriyal Malik Peiris; John F. Marshall; Joseph Hughes; Martin Gilbert; Pablo R. Murcia. 2019. "Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds." PLOS Pathogens 15, no. 2: e1007531.