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Wasik BR, Rothschild E, Voorhees IEH, Reedy SE, Murcia PR, Pusterla N, Chambers TM, Goodman LB, Holmes EC, Kile JC, Parrish CR. Understanding the divergent evolution and epidemiology of H3N8 influenza viruses in dogs and horses. Virus Evol 2023; 9:vead052. [PMID: 37692894 PMCID: PMC10484056 DOI: 10.1093/ve/vead052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Evin Rothschild
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Stephanie E Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, Scotland
| | - Nicola Pusterla
- Department of Medicine & Epidemiology, School Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | - Laura B Goodman
- Baker Institute for Animal Health, Department of Public and Ecosystems Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Kile
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Tyson GB, Jones S, Montreuil-Spencer C, Logan N, Scott S, Sasvari H, McDonald M, Marshall L, Murcia PR, Willett BJ, Weir W, Hosie MJ. Increase in SARS-CoV-2 Seroprevalence in UK Domestic Felids Despite Weak Immunogenicity of Post-Omicron Variants. Viruses 2023; 15:1661. [PMID: 37632004 PMCID: PMC10458763 DOI: 10.3390/v15081661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Throughout the COVID-19 pandemic, SARS-CoV-2 infections in domestic cats have caused concern for both animal health and the potential for inter-species transmission. Cats are known to be susceptible to the Omicron variant and its descendants, however, the feline immune response to these variants is not well defined. We aimed to estimate the current seroprevalence of SARS-CoV-2 in UK pet cats, as well as characterise the neutralising antibody response to the Omicron (BA.1) variant. A neutralising seroprevalence of 4.4% and an overall seroprevalence of 13.9% was observed. Both purebred and male cats were found to have the highest levels of seroprevalence, as well as cats aged between two and five years. The Omicron variant was found to have a lower immunogenicity in cats than the B.1, Alpha and Delta variants, which reflects previous reports of immune and vaccine evasion in humans. These results further underline the importance of surveillance of SARS-CoV-2 infections in UK cats as the virus continues to evolve.
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Affiliation(s)
- Grace B. Tyson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Sarah Jones
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Chloe Montreuil-Spencer
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Hagar Sasvari
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Michael McDonald
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Leigh Marshall
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - William Weir
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
| | - Margaret J. Hosie
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G61 1QH, UK
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3
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Tyson GB, Jones S, Logan N, McDonald M, Marshall L, Murcia PR, Willett BJ, Weir W, Hosie MJ. SARS-CoV-2 Seroprevalence and Cross-Variant Antibody Neutralization in Cats, United Kingdom. Emerg Infect Dis 2023; 29:1223-1227. [PMID: 37141617 PMCID: PMC10202862 DOI: 10.3201/eid2906.221755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Anthropogenic transmission of SARS-CoV-2 to pet cats highlights the importance of monitoring felids for exposure to circulating variants. We tested cats in the United Kingdom for SARS-CoV-2 antibodies; seroprevalence peaked during September 2021-February 2022. The variant-specific response in cats trailed circulating variants in humans, indicating multiple human-to-cat transmissions over a prolonged period.
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Manali M, Bissett LA, Amat JAR, Logan N, Scott S, Hughes EC, Harvey WT, Orton R, Thomson EC, Gunson RN, Viana M, Willett B, Murcia PR. SARS-CoV-2 Evolution and Patient Immunological History Shape the Breadth and Potency of Antibody-Mediated Immunity. J Infect Dis 2022; 227:40-49. [PMID: 35920058 PMCID: PMC9384671 DOI: 10.1093/infdis/jiac332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/19/2023] Open
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), humans have been exposed to distinct SARS-CoV-2 antigens, either by infection with different variants, and/or vaccination. Population immunity is thus highly heterogeneous, but the impact of such heterogeneity on the effectiveness and breadth of the antibody-mediated response is unclear. We measured antibody-mediated neutralization responses against SARS-CoV-2Wuhan, SARS-CoV-2α, SARS-CoV-2δ, and SARS-CoV-2ο pseudoviruses using sera from patients with distinct immunological histories, including naive, vaccinated, infected with SARS-CoV-2Wuhan, SARS-CoV-2α, or SARS-CoV-2δ, and vaccinated/infected individuals. We show that the breadth and potency of the antibody-mediated response is influenced by the number, the variant, and the nature (infection or vaccination) of exposures, and that individuals with mixed immunity acquired by vaccination and natural exposure exhibit the broadest and most potent responses. Our results suggest that the interplay between host immunity and SARS-CoV-2 evolution will shape the antigenicity and subsequent transmission dynamics of SARS-CoV-2, with important implications for future vaccine design.
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Affiliation(s)
- Maria Manali
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Laura A Bissett
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Julien A R Amat
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicola Logan
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sam Scott
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ellen C Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - William T Harvey
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Richard Orton
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Emma C Thomson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Mafalda Viana
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Brian Willett
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Pablo R Murcia
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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5
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Dee K, Schultz V, Haney J, Bissett LA, Magill C, Murcia PR. Influenza A and respiratory syncytial virus trigger a cellular response that blocks severe acute respiratory syndrome virus 2 infection in the respiratory tract. J Infect Dis 2022:6957417. [PMID: 36550077 DOI: 10.1093/infdis/jiac494] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Multiple viruses cocirculate and contribute to the burden of respiratory disease. Virus-virus interactions can decrease susceptibility to infection and this interference can have an epidemiological impact. As humans are normally exposed to a community of cocirculating respiratory viruses, experimental coinfection studies are necessary to understand the disease mechanisms of multi-pathogen systems. We aimed to characterize interactions within the respiratory tract between severe acute respiratory syndrome virus 2 (SARS-CoV-2) and two major respiratory viruses: influenza A virus (IAV), and respiratory syncytial virus (RSV). METHODS We performed single infections and coinfections with SARS-CoV-2 combined with IAV or RSV in cultures of human bronchial epithelial cells. We combined microscopy with quantification of viral replication in the presence or absence of an innate immune inhibitor to determine changes in virus-induced pathology, virus spread, and virus replication. RESULTS SARS-CoV-2 replication is inhibited by both IAV and RSV. This inhibition is dependent on a functional antiviral response and the level of inhibition is proportional to the timing of secondary viral infection. CONCLUSIONS Infections by other respiratory viruses might provide transient resistance to SARS-CoV-2. It would therefore be expected that the incidence of COVID-19 may decrease during periods of high circulation of IAV and RSV.Virus-virus interactions impact the infection dynamics of respiratory viruses at multiple levels, from cells to populations. Using three-dimensional cultures of airway epithelium, we showed that SARS-CoV-2 replication is impaired in coinfections with either influenza A or respiratory syncytial virus.
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Affiliation(s)
- Kieran Dee
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
| | - Verena Schultz
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
| | - Joanne Haney
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
| | - Laura A Bissett
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
| | - Callum Magill
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research. Glasgow, G61 1QH, United Kingdom
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6
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Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol 2022; 7:1709. [PMID: 36114232 PMCID: PMC9483304 DOI: 10.1038/s41564-022-01241-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Manali
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Matthew T G Holden
- Public Health Scotland, Glasgow, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | | | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
- NHS Greater Glasgow & Clyde, Glasgow, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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7
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Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol 2022; 7:1161-1179. [PMID: 35798890 PMCID: PMC9352574 DOI: 10.1038/s41564-022-01143-7] [Citation(s) in RCA: 274] [Impact Index Per Article: 137.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.
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Affiliation(s)
- Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Manali
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Matthew T G Holden
- Public Health Scotland, Glasgow, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | | | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
- NHS Greater Glasgow & Clyde, Glasgow, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
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8
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Whitlock F, Murcia PR, Newton JR. A Review on Equine Influenza from a Human Influenza Perspective. Viruses 2022; 14:v14061312. [PMID: 35746783 PMCID: PMC9229935 DOI: 10.3390/v14061312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/12/2022] Open
Abstract
Influenza A viruses (IAVs) have a main natural reservoir in wild birds. IAVs are highly contagious, continually evolve, and have a wide host range that includes various mammalian species including horses, pigs, and humans. Furthering our understanding of host-pathogen interactions and cross-species transmissions is therefore essential. This review focuses on what is known regarding equine influenza virus (EIV) virology, pathogenesis, immune responses, clinical aspects, epidemiology (including factors contributing to local, national, and international transmission), surveillance, and preventive measures such as vaccines. We compare EIV and human influenza viruses and discuss parallels that can be drawn between them. We highlight differences in evolutionary rates between EIV and human IAVs, their impact on antigenic drift, and vaccine strain updates. We also describe the approaches used for the control of equine influenza (EI), which originated from those used in the human field, including surveillance networks and virological analysis methods. Finally, as vaccination in both species remains the cornerstone of disease mitigation, vaccine technologies and vaccination strategies against influenza in horses and humans are compared and discussed.
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Affiliation(s)
- Fleur Whitlock
- Medical Research Council, University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, UK; (F.W.); (P.R.M.)
- Equine Infectious Disease Surveillance (EIDS), Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Pablo R. Murcia
- Medical Research Council, University of Glasgow Centre for Virus Research, Garscube Estate, Glasgow G61 1QH, UK; (F.W.); (P.R.M.)
| | - J. Richard Newton
- Equine Infectious Disease Surveillance (EIDS), Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
- Correspondence:
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9
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Conley MJ, Short JM, Burns AM, Streetley J, Hutchings J, Bakker SE, Power BJ, Jaffery H, Haney J, Zanetti G, Murcia PR, Stewart M, Fearns R, Vijayakrishnan S, Bhella D. Helical ordering of envelope-associated proteins and glycoproteins in respiratory syncytial virus. EMBO J 2022; 41:e109728. [PMID: 34935163 PMCID: PMC8804925 DOI: 10.15252/embj.2021109728] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
Human respiratory syncytial virus (RSV) causes severe respiratory illness in children and the elderly. Here, using cryogenic electron microscopy and tomography combined with computational image analysis and three-dimensional reconstruction, we show that there is extensive helical ordering of the envelope-associated proteins and glycoproteins of RSV filamentous virions. We calculated a 16 Å resolution sub-tomogram average of the matrix protein (M) layer that forms an endoskeleton below the viral envelope. These data define a helical lattice of M-dimers, showing how M is oriented relative to the viral envelope. Glycoproteins that stud the viral envelope were also found to be helically ordered, a property that was coordinated by the M-layer. Furthermore, envelope glycoproteins clustered in pairs, a feature that may have implications for the conformation of fusion (F) glycoprotein epitopes that are the principal target for vaccine and monoclonal antibody development. We also report the presence, in authentic virus infections, of N-RNA rings packaged within RSV virions. These data provide molecular insight into the organisation of the virion and the mechanism of its assembly.
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Affiliation(s)
- Michaela J Conley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Judith M Short
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Andrew M Burns
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - James Streetley
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joshua Hutchings
- Department of Biological SciencesBirkbeck CollegeLondonUK
- Present address:
Division of Biological SciencesUniversity of California San DiegoLa JollaCAUSA
| | - Saskia E Bakker
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
School of Life SciencesUniversity of WarwickCoventryUK
| | - B Joanne Power
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
- Present address:
Department of Biochemistry and Molecular BiologyThe Huck Center for Malaria ResearchPennsylvania State UniversityUniversity ParkPAUSA
| | - Hussain Jaffery
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Joanne Haney
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Giulia Zanetti
- Department of Biological SciencesBirkbeck CollegeLondonUK
| | - Pablo R Murcia
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
| | - Rachel Fearns
- Department of MicrobiologyBoston University School of MedicineBostonMAUSA
- National Emerging Infectious Diseases LaboratoriesBoston UniversityBostonMAUSA
| | | | - David Bhella
- Medical Research Council – University of Glasgow Centre for Virus ResearchGlasgowUK
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10
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Herder V, Dee K, Wojtus JK, Epifano I, Goldfarb D, Rozario C, Gu Q, Da Silva Filipe A, Nomikou K, Nichols J, Jarrett RF, Stevenson A, McFarlane S, Stewart ME, Szemiel AM, Pinto RM, Masdefiol Garriga A, Davis C, Allan J, Graham SV, Murcia PR, Boutell C. Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of IFN-mediated innate immune defenses. PLoS Biol 2021; 19:e3001065. [PMID: 34932557 PMCID: PMC8765667 DOI: 10.1371/journal.pbio.3001065] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/18/2022] [Accepted: 12/03/2021] [Indexed: 01/08/2023] Open
Abstract
The pandemic spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiological agent of Coronavirus Disease 2019 (COVID-19), represents an ongoing international health crisis. A key symptom of SARS-CoV-2 infection is the onset of fever, with a hyperthermic temperature range of 38 to 41°C. Fever is an evolutionarily conserved host response to microbial infection that can influence the outcome of viral pathogenicity and regulation of host innate and adaptive immune responses. However, it remains to be determined what effect elevated temperature has on SARS-CoV-2 replication. Utilizing a three-dimensional (3D) air-liquid interface (ALI) model that closely mimics the natural tissue physiology of SARS-CoV-2 infection in the respiratory airway, we identify tissue temperature to play an important role in the regulation of SARS-CoV-2 infection. Respiratory tissue incubated at 40°C remained permissive to SARS-CoV-2 entry but refractory to viral transcription, leading to significantly reduced levels of viral RNA replication and apical shedding of infectious virus. We identify tissue temperature to play an important role in the differential regulation of epithelial host responses to SARS-CoV-2 infection that impact upon multiple pathways, including intracellular immune regulation, without disruption to general transcription or epithelium integrity. We present the first evidence that febrile temperatures associated with COVID-19 inhibit SARS-CoV-2 replication in respiratory epithelia. Our data identify an important role for tissue temperature in the epithelial restriction of SARS-CoV-2 independently of canonical interferon (IFN)-mediated antiviral immune defenses.
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Affiliation(s)
- Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Kieran Dee
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Joanna K. Wojtus
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Ilaria Epifano
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Daniel Goldfarb
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Christoforos Rozario
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Ruth F. Jarrett
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Andrew Stevenson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Meredith E. Stewart
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Agnieszka M. Szemiel
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Rute M. Pinto
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Andreu Masdefiol Garriga
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
- University of Glasgow School of Veterinary Medicine, Glasgow, Scotland United Kingdom
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
| | - Sheila V. Graham
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
- * E-mail: (SVG); (PRM); (CB)
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
- * E-mail: (SVG); (PRM); (CB)
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland United Kingdom
- * E-mail: (SVG); (PRM); (CB)
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11
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Amat JAR, Patton V, Chauché C, Goldfarb D, Crispell J, Gu Q, Coburn AM, Gonzalez G, Mair D, Tong L, Martinez-Sobrido L, Marshall JF, Marchesi F, Murcia PR. Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage. PLoS Pathog 2021; 17:e1010174. [PMID: 34919598 PMCID: PMC8735595 DOI: 10.1371/journal.ppat.1010174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/06/2022] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanisms and consequences of genome evolution on viral fitness following host shifts are poorly understood. In addition, viral fitness -the ability of an organism to reproduce and survive- is multifactorial and thus difficult to quantify. Influenza A viruses (IAVs) circulate broadly among wild birds and have jumped into and become endemic in multiple mammalian hosts, including humans, pigs, dogs, seals, and horses. H3N8 equine influenza virus (EIV) is an endemic virus of horses that originated in birds and has been circulating uninterruptedly in equine populations since the early 1960s. Here, we used EIV to quantify changes in infection phenotype associated to viral fitness due to genome-wide changes acquired during long-term adaptation. We performed experimental infections of two mammalian cell lines and equine tracheal explants using the earliest H3N8 EIV isolated (A/equine/Uruguay/63 [EIV/63]), and A/equine/Ohio/2003 (EIV/2003), a monophyletic descendant of EIV/63 isolated 40 years after the emergence of H3N8 EIV. We show that EIV/2003 exhibits increased resistance to interferon, enhanced viral replication, and a more efficient cell-to-cell spread in cells and tissues. Transcriptomics analyses revealed virus-specific responses to each virus, mainly affecting host immunity and inflammation. Image analyses of infected equine respiratory explants showed that despite replicating at higher levels and spreading over larger areas of the respiratory epithelium, EIV/2003 induced milder lesions compared to EIV/63, suggesting that adaptation led to reduced tissue pathogenicity. Our results reveal previously unknown links between virus genotype and the host response to infection, providing new insights on the relationship between virus evolution and fitness. As viruses are obligate intracellular pathogens, their ability to replicate and spread within their hosts is key for survival, even if it leads to severe disease or death of the host. Understanding the consequences of long-term virus adaptation after viral emergence is key for pandemic preparedness. H3N8 equine influenza virus (EIV) originated in birds and has circulated in horses since 1963, thus providing unique opportunities to study virus adaptation. We compared the replication kinetics of two EIVs of the same lineage but with different evolutionary histories: the earliest virus (EIV/63, isolated in 1963), and EIV/2003, which was isolated after 40 years of continuous circulation in horses. Experimental infections of cell lines (MDCK and E.Derm cells) and equine respiratory explants show that EIV evolved towards enhanced replication and cell-to-cell spread; but reduced tissue damage, confirming that viral fitness is adaptive and does not necessarily result in higher virulence.
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Affiliation(s)
- Julien A. R. Amat
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Veronica Patton
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Caroline Chauché
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, Scotland, United Kingdom
| | - Daniel Goldfarb
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Joanna Crispell
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Alice M. Coburn
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Gaelle Gonzalez
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | | | - John F. Marshall
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Francesco Marchesi
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail:
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12
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Davis C, Logan N, Tyson G, Orton R, Harvey WT, Perkins JS, Mollett G, Blacow RM, Peacock TP, Barclay WS, Cherepanov P, Palmarini M, Murcia PR, Patel AH, Robertson DL, Haughney J, Thomson EC, Willett BJ. Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathog 2021; 17:e1010022. [PMID: 34855916 PMCID: PMC8639073 DOI: 10.1371/journal.ppat.1010022] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
Vaccines are proving to be highly effective in controlling hospitalisation and deaths associated with SARS-CoV-2 infection but the emergence of viral variants with novel antigenic profiles threatens to diminish their efficacy. Assessment of the ability of sera from vaccine recipients to neutralise SARS-CoV-2 variants will inform the success of strategies for minimising COVID19 cases and the design of effective antigenic formulations. Here, we examine the sensitivity of variants of concern (VOCs) representative of the B.1.617.1 and B.1.617.2 (first associated with infections in India) and B.1.351 (first associated with infection in South Africa) lineages of SARS-CoV-2 to neutralisation by sera from individuals vaccinated with the BNT162b2 (Pfizer/BioNTech) and ChAdOx1 (Oxford/AstraZeneca) vaccines. Across all vaccinated individuals, the spike glycoproteins from B.1.617.1 and B.1.617.2 conferred reductions in neutralisation of 4.31 and 5.11-fold respectively. The reduction seen with the B.1.617.2 lineage approached that conferred by the glycoprotein from B.1.351 (South African) variant (6.29-fold reduction) that is known to be associated with reduced vaccine efficacy. Neutralising antibody titres elicited by vaccination with two doses of BNT162b2 were significantly higher than those elicited by vaccination with two doses of ChAdOx1. Fold decreases in the magnitude of neutralisation titre following two doses of BNT162b2, conferred reductions in titre of 7.77, 11.30 and 9.56-fold respectively to B.1.617.1, B.1.617.2 and B.1.351 pseudoviruses, the reduction in neutralisation of the delta variant B.1.617.2 surpassing that of B.1.351. Fold changes in those vaccinated with two doses of ChAdOx1 were 0.69, 4.01 and 1.48 respectively. The accumulation of mutations in these VOCs, and others, demonstrate the quantifiable risk of antigenic drift and subsequent reduction in vaccine efficacy. Accordingly, booster vaccines based on updated variants are likely to be required over time to prevent productive infection. This study also suggests that two dose regimes of vaccine are required for maximal BNT162b2 and ChAdOx1-induced immunity.
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Affiliation(s)
- Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Grace Tyson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - William T. Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Jonathan S. Perkins
- Clinical Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Guy Mollett
- Clinical Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Rachel M. Blacow
- Clinical Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | | | - Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - John Haughney
- Clinical Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
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13
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de Souza WM, Fumagalli MJ, Carrera JP, de Araujo J, Cardoso JF, de Carvalho C, Durigon EL, Queiroz LH, Faria NR, Murcia PR, Figueiredo LTM. Paramyxoviruses from neotropical bats suggest a novel genus and nephrotropism. Infect Genet Evol 2021; 95:105041. [PMID: 34411742 DOI: 10.1016/j.meegid.2021.105041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/21/2022]
Abstract
Paramyxoviruses have a broad host range and geographic distribution, including human pathogens transmitted by bats, such as Nipah and Hendra viruses. In this study, we combined high-throughput sequencing and molecular approaches to investigate the presence of paramyxoviruses in neotropical bats (Microchiroptera suborder) in Brazil. We discovered and characterized three novel paramyxoviruses in the kidney tissues of apparently healthy common vampire bats (D. rotundus) and Seba's short-tailed bats (C. perspicillata), which we tentatively named Kanhgág virus (KANV), Boe virus (BOEV), and Guató virus (GUATV). In this study, we classified these viruses as putative species into the Macrojêvirus genus, a newly proposed genus of the Orthoparamyxovirinae subfamily. Using RT-PCR, we detected these viruses in 20.9% (9 out of 43) of bats tested, and viral RNA was detected exclusively in kidney tissues. Attempts to isolate infectious virus were successful for KANV and GUATV. Our results expand the viral diversity, host range, and geographical distribution of the paramyxoviruses.
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Affiliation(s)
- William Marciel de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Marcilio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jean Paul Carrera
- Department of Zoology, University of Oxford, Oxford, UK; Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Cristiano de Carvalho
- Faculty of Veterinary Medicine, São Paulo State University, Araçatuba, São Paulo, Brazil
| | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Luzia Helena Queiroz
- Faculty of Veterinary Medicine, São Paulo State University, Araçatuba, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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14
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Dee K, Goldfarb DM, Haney J, Amat JAR, Herder V, Stewart M, Szemiel AM, Baguelin M, Murcia PR. Human Rhinovirus Infection Blocks Severe Acute Respiratory Syndrome Coronavirus 2 Replication Within the Respiratory Epithelium: Implications for COVID-19 Epidemiology. J Infect Dis 2021; 224:31-38. [PMID: 33754149 PMCID: PMC8083659 DOI: 10.1093/infdis/jiab147] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/15/2021] [Indexed: 01/24/2023] Open
Abstract
Virus-virus interactions influence the epidemiology of respiratory infections. However, the impact of viruses causing upper respiratory infections on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and transmission is currently unknown. Human rhinoviruses cause the common cold and are the most prevalent respiratory viruses of humans. Interactions between rhinoviruses and cocirculating respiratory viruses have been shown to shape virus epidemiology at the individual host and population level. Here, we examined the replication kinetics of SARS-CoV-2 in the human respiratory epithelium in the presence or absence of rhinovirus. We show that human rhinovirus triggers an interferon response that blocks SARS-CoV-2 replication. Mathematical simulations show that this virus-virus interaction is likely to have a population-wide effect as an increasing prevalence of rhinovirus will reduce the number of new coronavirus disease 2019 cases.
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Affiliation(s)
- Kieran Dee
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel M Goldfarb
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joanne Haney
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Julien A R Amat
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Vanessa Herder
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Meredith Stewart
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Agnieszka M Szemiel
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Pablo R Murcia
- MRC–University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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15
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Hughes EC, Amat JAR, Haney J, Parr YA, Logan N, Palmateer N, Nickbakhsh S, Ho A, Cherepanov P, Rosa A, McAuley A, Broos A, Herbert I, Arthur U, Szemiel AM, Roustan C, Dickson E, Gunson RN, Viana M, Willett BJ, Murcia PR. Severe Acute Respiratory Syndrome Coronavirus 2 Serosurveillance in a Patient Population Reveals Differences in Virus Exposure and Antibody-Mediated Immunity According to Host Demography and Healthcare Setting. J Infect Dis 2021; 223:971-980. [PMID: 33367847 PMCID: PMC7798933 DOI: 10.1093/infdis/jiaa788] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Identifying drivers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure and quantifying population immunity is crucial to prepare for future epidemics. We performed a serial cross-sectional serosurvey throughout the first pandemic wave among patients from the largest health board in Scotland. Screening of 7480 patient serum samples showed a weekly seroprevalence ranging from 0.10% to 8.23% in primary and 0.21% to 17.44% in secondary care, respectively. Neutralization assays showed that highly neutralizing antibodies developed in about half of individuals who tested positive with enzyme-linked immunosorbent assay, mainly among secondary care patients. We estimated the individual probability of SARS-CoV-2 exposure and quantified associated risk factors. We show that secondary care patients, male patients, and 45–64-year-olds exhibit a higher probability of being seropositive. The identification of risk factors and the differences in virus neutralization activity between patient populations provided insights into the patterns of virus exposure during the first pandemic wave and shed light on what to expect in future waves.
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Affiliation(s)
- Ellen C Hughes
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Julien A R Amat
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joanne Haney
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Yasmin A Parr
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Norah Palmateer
- Public Health Scotland (Health Protection Scotland), Glasgow, United Kingdom.,School of Health $ Life Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew McAuley
- Public Health Scotland (Health Protection Scotland), Glasgow, United Kingdom.,School of Health $ Life Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Alice Broos
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Imogen Herbert
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ursula Arthur
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Agnieszka M Szemiel
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chloe Roustan
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Elizabeth Dickson
- Public Health Scotland (Health Protection Scotland), Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Mafalda Viana
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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16
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Hosie MJ, Epifano I, Herder V, Orton RJ, Stevenson A, Johnson N, MacDonald E, Dunbar D, McDonald M, Howie F, Tennant B, Herrity D, Da Silva Filipe A, Streicker DG, Willett BJ, Murcia PR, Jarrett RF, Robertson DL, Weir W. Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Vet Rec 2021; 188:e247. [PMID: 33890314 PMCID: PMC8251078 DOI: 10.1002/vetr.247] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 01/29/2023]
Abstract
OBJECTIVES The aim of the study was to find evidence of SARS-CoV-2 infection in UK cats. DESIGN Tissue samples were tested for SARS-CoV-2 antigen using immunofluorescence and for viral RNA by in situ hybridisation. A set of 387 oropharyngeal swabs that had been submitted for routine respiratory pathogen testing was tested for SARS-CoV-2 RNA using reverse transcriptase quantitative PCR. RESULTS Lung tissue collected post-mortem from cat 1 tested positive for both SARS-CoV-2 nucleocapsid antigen and RNA. SARS-CoV-2 RNA was detected in an oropharyngeal swab collected from cat 2 that presented with rhinitis and conjunctivitis. High throughput sequencing of the viral genome revealed five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence, and this human virus contained eight SNPs compared to the original Wuhan-Hu-1 reference sequence. An analysis of the viral genome of cat 2 together with nine other feline-derived SARS-CoV-2 sequences from around the world revealed no shared cat-specific mutations. CONCLUSIONS These findings indicate that human-to-cat transmission of SARS-CoV-2 occurred during the COVID-19 pandemic in the UK, with the infected cats developing mild or severe respiratory disease. Given the ability of the new coronavirus to infect different species, it will be important to monitor for human-to-cat, cat-to-cat and cat-to-human transmission.
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Affiliation(s)
| | - Ilaria Epifano
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Vanessa Herder
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | | | | | - Natasha Johnson
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Emma MacDonald
- Veterinary Diagnostics Service, School of Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Dawn Dunbar
- Veterinary Diagnostics Service, School of Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Michael McDonald
- Veterinary Diagnostics Service, School of Veterinary MedicineUniversity of GlasgowGlasgowUK
| | - Fiona Howie
- SRUC Veterinary ServicesPentlands Science ParkPenicuikMidlothianUK
| | - Bryn Tennant
- SRUC Veterinary ServicesPentlands Science ParkPenicuikMidlothianUK
| | | | | | - Daniel G. Streicker
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
- Animal Health and Comparative MedicineInstitute of Biodiversity University of GlasgowGlasgowUK
| | | | | | - Pablo R. Murcia
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Ruth F. Jarrett
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | | | - William Weir
- Veterinary Diagnostics Service, School of Veterinary MedicineUniversity of GlasgowGlasgowUK
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17
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Nickbakhsh S, Ho A, Marques DFP, McMenamin J, Gunson RN, Murcia PR. Reply to Li et al. J Infect Dis 2020; 222:696-698. [PMID: 32497172 DOI: 10.1093/infdis/jiaa322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Diogo F P Marques
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Jim McMenamin
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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18
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Nickbakhsh S, Ho A, Marques DFP, McMenamin J, Gunson RN, Murcia PR. Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019. J Infect Dis 2020; 222:17-25. [PMID: 32296837 PMCID: PMC7184404 DOI: 10.1093/infdis/jiaa185] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/14/2020] [Indexed: 12/23/2022] Open
Abstract
Public health preparedness for coronavirus (CoV) disease 2019 (COVID-19) is challenging in the absence of setting-specific epidemiological data. Here we describe the epidemiology of seasonal CoVs (sCoVs) and other cocirculating viruses in the West of Scotland, United Kingdom. We analyzed routine diagnostic data for >70 000 episodes of respiratory illness tested molecularly for multiple respiratory viruses between 2005 and 2017. Statistical associations with patient age and sex differed between CoV-229E, CoV-OC43, and CoV-NL63. Furthermore, the timing and magnitude of sCoV outbreaks did not occur concurrently, and coinfections were not reported. With respect to other cocirculating respiratory viruses, we found evidence of positive, rather than negative, interactions with sCoVs. These findings highlight the importance of considering cocirculating viruses in the differential diagnosis of COVID-19. Further work is needed to establish the occurrence/degree of cross-protective immunity conferred across sCoVs and with COVID-19, as well as the role of viral coinfection in COVID-19 disease severity.
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Affiliation(s)
- Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Diogo F P Marques
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Jim McMenamin
- Public Health Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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19
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Mair C, Nickbakhsh S, Reeve R, McMenamin J, Reynolds A, Gunson RN, Murcia PR, Matthews L. Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Comput Biol 2019; 15:e1007492. [PMID: 31834896 PMCID: PMC6934324 DOI: 10.1371/journal.pcbi.1007492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/27/2019] [Accepted: 10/16/2019] [Indexed: 11/22/2022] Open
Abstract
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness. Disease-causing microorganisms, including viruses, bacteria, protozoa and fungi, form complex communities within animals and plants. These microorganisms can coexist harmoniously or even beneficially, or they may competitively interact for host resources. Well-studied examples include interactions between viruses and bacteria in the respiratory tract. Whilst ecological studies have revealed that some pathogens do interact within their hosts, identifying interactions from available population scale data from health authorities is challenging. This is exacerbated by a lack of large-scale data describing the infection patterns of multiple pathogens within single populations over long time frames. Furthermore, methods for evaluating whether infection frequencies of different pathogens fluctuate together or not over time cannot readily account for alternative explanations. For example, human pathogens may have related seasonal patterns depending on the age groups they infect and the weather conditions they survive in, and not because they are interacting. We developed a robust statistical framework to identify pathogen-pathogen interactions from population scale diagnostic data. This framework serves as a crucial step in identifying such important interactions and will guide new studies to elucidate their underpinning mechanisms. This will have important consequences for public health preparedness and the design of effective disease control interventions.
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Affiliation(s)
- Colette Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jim McMenamin
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Arlene Reynolds
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N. Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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20
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Blanco-Lobo P, Rodriguez L, Reedy S, Oladunni FS, Nogales A, Murcia PR, Chambers TM, Martinez-Sobrido L. A Bivalent Live-Attenuated Vaccine for the Prevention of Equine Influenza Virus. Viruses 2019; 11:v11100933. [PMID: 31614538 PMCID: PMC6832603 DOI: 10.3390/v11100933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
Vaccination remains the most effective approach for preventing and controlling equine influenza virus (EIV) in horses. However, the ongoing evolution of EIV has increased the genetic and antigenic differences between currently available vaccines and circulating strains, resulting in suboptimal vaccine efficacy. As recommended by the World Organization for Animal Health (OIE), the inclusion of representative strains from clade 1 and clade 2 Florida sublineages of EIV in vaccines may maximize the protection against presently circulating viral strains. In this study, we used reverse genetics technologies to generate a bivalent EIV live-attenuated influenza vaccine (LAIV). We combined our previously described clade 1 EIV LAIV A/equine/Ohio/2003 H3N8 (Ohio/03 LAIV) with a newly generated clade 2 EIV LAIV that contains the six internal genes of Ohio/03 LAIV and the HA and NA of A/equine/Richmond/1/2007 H3N8 (Rich/07 LAIV). The safety profile, immunogenicity, and protection efficacy of this bivalent EIV LAIV was tested in the natural host, horses. Vaccination of horses with the bivalent EIV LAIV, following a prime-boost regimen, was safe and able to confer protection against challenge with clade 1 (A/equine/Kentucky/2014 H3N8) and clade 2 (A/equine/Richmond/2007) wild-type (WT) EIVs, as evidenced by a reduction of clinical signs, fever, and virus excretion. This is the first description of a bivalent LAIV for the prevention of EIV in horses that follows OIE recommendations. In addition, since our bivalent EIV LAIV is based on the use of reverse genetics approaches, our results demonstrate the feasibility of using the backbone of clade 1 Ohio/03 LAIV as a master donor virus (MDV) for the production and rapid update of LAIVs for the control and protection against other EIV strains of epidemiological relevance to horses.
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Affiliation(s)
- Pilar Blanco-Lobo
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
| | - Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
- Agencia Española de Medicamentos y Productos Sanitarios, E28022 Madrid, Spain.
| | - Stephanie Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Fatai S Oladunni
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
- Center for Animal Health Research- National Institute for Agricultural and Food Research and Technology, Valdeolmos, 28130 Madrid, Spain.
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1AF, UK.
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA.
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21
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Maabar M, Davison AJ, Vučak M, Thorburn F, Murcia PR, Gunson R, Palmarini M, Hughes J. DisCVR: Rapid viral diagnosis from high-throughput sequencing data. Virus Evol 2019; 5:vez033. [PMID: 31528358 PMCID: PMC6735924 DOI: 10.1093/ve/vez033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-throughput sequencing (HTS) enables most pathogens in a clinical sample to be detected from a single analysis, thereby providing novel opportunities for diagnosis, surveillance, and epidemiology. However, this powerful technology is difficult to apply in diagnostic laboratories because of its computational and bioinformatic demands. We have developed DisCVR, which detects known human viruses in clinical samples by matching sample k-mers (twenty-two nucleotide sequences) to k-mers from taxonomically labeled viral genomes. DisCVR was validated using published HTS data for eighty-nine clinical samples from adults with upper respiratory tract infections. These samples had been tested for viruses metagenomically and also by real-time polymerase chain reaction assay, which is the standard diagnostic method. DisCVR detected human viruses with high sensitivity (79%) and specificity (100%), and was able to detect mixed infections. Moreover, it produced results comparable to those in a published metagenomic analysis of 177 blood samples from patients in Nigeria. DisCVR has been designed as a user-friendly tool for detecting human viruses from HTS data using computers with limited RAM and processing power, and includes a graphical user interface to help users interpret and validate the output. It is written in Java and is publicly available from http://bioinformatics.cvr.ac.uk/discvr.php.
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Affiliation(s)
- Maha Maabar
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Matej Vučak
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Fiona Thorburn
- Microbiology Department, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
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22
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Zhu H, Damdinjav B, Gonzalez G, Patrono LV, Ramirez-Mendoza H, Amat JAR, Crispell J, Parr YA, Hammond TA, Shiilegdamba E, Leung YHC, Peiris M, Marshall JF, Hughes J, Gilbert M, Murcia PR. Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS Pathog 2019; 15:e1007531. [PMID: 30731004 PMCID: PMC6366691 DOI: 10.1371/journal.ppat.1007531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Batchuluun Damdinjav
- State Central Veterinary Laboratory, Transboundary Animal Disease Laboratory, Avian Influenza Section, Ulaanbaatar, Mongolia
| | - Gaelle Gonzalez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Livia Victoria Patrono
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Humberto Ramirez-Mendoza
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de Mexico, México
| | - Julien A R Amat
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Joanna Crispell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Yasmin Amy Parr
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Toni-Ann Hammond
- Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, United Kingdom
| | | | - Y H Connie Leung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Laboratory Animal Unit, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John F Marshall
- Weipers Centre Equine Hospital, School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Martin Gilbert
- Wildlife Conservation Society, Bronx, NY, United States of America
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Population Medicine and Diagnostic Science, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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23
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Affiliation(s)
- J M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - P R Murcia
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary Life Science, University of Glasgow, Centre for Virus Research, Glasgow, UK
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24
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Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, Toohey-Kurth K, Su S, Kriti D, Van Bakel H, Goodman LB, Leutenegger C, Holmes EC, Parrish CR. Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States. J Virol 2018; 92:e00323-18. [PMID: 29875234 PMCID: PMC6069211 DOI: 10.1128/jvi.00323-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/03/2018] [Indexed: 01/13/2023] Open
Abstract
Avian-origin H3N2 canine influenza virus (CIV) transferred to dogs in Asia around 2005, becoming enzootic throughout China and South Korea before reaching the United States in early 2015. To understand the posttransfer evolution and epidemiology of this virus, particularly the cause of recent and ongoing increases in incidence in the United States, we performed an integrated analysis of whole-genome sequence data from 64 newly sequenced viruses and comprehensive surveillance data. This revealed that the circulation of H3N2 CIV within the United States is typified by recurrent epidemic burst-fade-out dynamics driven by multiple introductions of virus from Asia. Although all major viral lineages displayed similar rates of genomic sequence evolution, H3N2 CIV consistently exhibited proportionally more nonsynonymous substitutions per site than those in avian reservoir viruses, which is indicative of a large-scale change in selection pressures. Despite these genotypic differences, we found no evidence of adaptive evolution or increased viral transmission, with epidemiological models indicating a basic reproductive number, R0, of between 1 and 1.5 across nearly all U.S. outbreaks, consistent with maintained but heterogeneous circulation. We propose that CIV's mode of viral circulation may have resulted in evolutionary cul-de-sacs, in which there is little opportunity for the selection of the more transmissible H3N2 CIV phenotypes necessary to enable circulation through a general dog population characterized by widespread contact heterogeneity. CIV must therefore rely on metapopulations of high host density (such as animal shelters and kennels) within the greater dog population and reintroduction from other populations or face complete epidemic extinction.IMPORTANCE The relatively recent appearance of influenza A virus (IAV) epidemics in dogs expands our understanding of IAV host range and ecology, providing useful and relevant models for understanding critical factors involved in viral emergence. Here we integrate viral whole-genome sequence analysis and comprehensive surveillance data to examine the evolution of the emerging avian-origin H3N2 canine influenza virus (CIV), particularly the factors driving ongoing circulation and recent increases in incidence of the virus within the United States. Our results provide a detailed understanding of how H3N2 CIV achieves sustained circulation within the United States despite widespread host contact heterogeneity and recurrent epidemic fade-out. Moreover, our findings suggest that the types and intensities of selection pressures an emerging virus experiences are highly dependent on host population structure and ecology and may inhibit an emerging virus from acquiring sustained epidemic or pandemic circulation.
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Affiliation(s)
- Ian E H Voorhees
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Benjamin D Dalziel
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
- Department of Mathematics, Oregon State University, Corvallis, Oregon, USA
| | - Amy Glaser
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Edward J Dubovi
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Pablo R Murcia
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sandra Newbury
- Department of Medical Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, Wisconsin, USA
| | - Kathy Toohey-Kurth
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, Wisconsin, USA
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm Van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Laura B Goodman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- School of Life & Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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25
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Rodriguez L, Reedy S, Nogales A, Murcia PR, Chambers TM, Martinez-Sobrido L. Development of a novel equine influenza virus live-attenuated vaccine. Virology 2018; 516:76-85. [PMID: 29331866 PMCID: PMC5840510 DOI: 10.1016/j.virol.2018.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 11/16/2022]
Abstract
H3N8 equine influenza virus (EIV) is an important and significant respiratory pathogen of horses. EIV is enzootic in Europe and North America, mainly due to the suboptimal efficacy of current vaccines. We describe, for the first time, the generation of a temperature sensitive (ts) H3N8 EIV live-attenuated influenza vaccine (LAIV) using reverse-genetics approaches. Our EIV LAIV was attenuated (att) in vivo and able to induce, upon a single intranasal administration, protection against H3N8 EIV wild-type (WT) challenge in both a mouse model and the natural host, the horse. Notably, since our EIV LAIV was generated using reverse genetics, the vaccine can be easily updated against drifting or emerging strains of EIV using the safety backbone of our EIV LAIV as master donor virus (MDV). These results demonstrate the feasibility of implementing a novel EIV LAIV approach for the prevention and control of currently circulating H3N8 EIVs in horse populations.
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Affiliation(s)
- Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States
| | - Stephanie Reedy
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas M Chambers
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, United States.
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26
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Goldstein EJ, Harvey WT, Wilkie GS, Shepherd SJ, MacLean AR, Murcia PR, Gunson RN. Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses. Microb Genom 2017; 4. [PMID: 29310750 PMCID: PMC5857367 DOI: 10.1099/mgen.0.000137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.
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Affiliation(s)
- Emily J Goldstein
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - William T Harvey
- 2Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Gavin S Wilkie
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Samantha J Shepherd
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Alasdair R MacLean
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Pablo R Murcia
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Rory N Gunson
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
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27
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Rodriguez L, Nogales A, Reilly EC, Topham DJ, Murcia PR, Parrish CR, Martinez Sobrido L. A live-attenuated influenza vaccine for H3N2 canine influenza virus. Virology 2017; 504:96-106. [PMID: 28167384 DOI: 10.1016/j.virol.2017.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 11/24/2022]
Abstract
Canine influenza is a contagious respiratory disease in dogs caused by two subtypes (H3N2 and H3N8) of canine influenza virus (CIV). Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIVs. Historically, live-attenuated influenza vaccines (LAIVs) have been shown to produce better immunogenicity and protection efficacy than IIVs. Here, we have engineered a CIV H3N2 LAIV by using the internal genes of a previously described CIV H3N8 LAIV as a master donor virus (MDV) and the surface HA and NA genes of a circulating CIV H3N2 strain. Our findings show that CIV H3N2 LAIV replicates efficiently at low temperature but its replication is impaired at higher temperatures. The CIV H3N2 LAIV was attenuated in vivo but induced better protection efficacy in mice against challenge with wild-type CIV H3N2 than a commercial CIV H3N2 IIV. This is the first description of a LAIV for the prevention of CIV H3N2 in dogs.
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Affiliation(s)
- Laura Rodriguez
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, US
| | - Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, US
| | - Emma C Reilly
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, US; David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY, US
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, US; David H. Smith Center for Vaccine Biology and Immunology, University of Rochester, Rochester, NY, US
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, US
| | - Luis Martinez Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, US.
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28
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Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment. eLife 2016; 5. [PMID: 27834632 PMCID: PMC5156527 DOI: 10.7554/elife.18491] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022] Open
Abstract
The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of which spark sustained transmission in humans. To date, no pandemic emergence of a new influenza strain has been preceded by detection of a closely related precursor in an animal or human. Nonetheless, influenza surveillance efforts are expanding, prompting a need for tools to assess the pandemic risk posed by a detected virus. The goal would be to use genetic sequence and/or biological assays of viral traits to identify those non-human influenza viruses with the greatest risk of evolving into pandemic threats, and/or to understand drivers of such evolution, to prioritize pandemic prevention or response measures. We describe such efforts, identify progress and ongoing challenges, and discuss three specific traits of influenza viruses (hemagglutinin receptor binding specificity, hemagglutinin pH of activation, and polymerase complex efficiency) that contribute to pandemic risk.
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Affiliation(s)
- Marc Lipsitch
- Center for Communicable Disease Dynamics, Harvard T. H Chan School of Public Health, Boston, United States.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, United States
| | - Wendy Barclay
- Division of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, United States
| | - Jessica A Belser
- Centers for Disease Control and Prevention, Atlanta, United States
| | - Sarah Cobey
- Department of Ecology and Evolutionary Biology, University of Chicago, Chicago, United States
| | - Peter M Kasson
- Department of Biomedical Engineering, University of Virginia, Charlottesville, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, United States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore.,National Public Health Laboratory, Communicable Diseases Division, Ministry of Health, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, United States
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, United States
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pablo R Murcia
- MRC-University of Glasgow Centre For Virus Research, Glasgow, United Kingdom
| | | | - Claus O Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, United States.,Department of Integrative Biology, The University of Texas at Austin, Austin, United States
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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29
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Nogales A, Huang K, Chauché C, DeDiego ML, Murcia PR, Parrish CR, Martínez-Sobrido L. Canine influenza viruses with modified NS1 proteins for the development of live-attenuated vaccines. Virology 2016; 500:1-10. [PMID: 27750071 DOI: 10.1016/j.virol.2016.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/06/2016] [Accepted: 10/08/2016] [Indexed: 12/24/2022]
Abstract
Canine Influenza Virus (CIV) H3N8 is the causative agent of canine influenza, a common and contagious respiratory disease of dogs. Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIV H3N8. However, live-attenuated influenza vaccines (LAIVs) are known to provide better immunogenicity and protection efficacy than IIVs. Influenza NS1 is a virulence factor that offers an attractive target for the preparation of attenuated viruses as LAIVs. Here we generated recombinant H3N8 CIVs containing truncated or a deleted NS1 protein to test their potential as LAIVs. All recombinant viruses were attenuated in mice and showed reduced replication in cultured canine tracheal explants, but were able to confer complete protection against challenge with wild-type CIV H3N8 after a single intranasal immunization. Immunogenicity and protection efficacy was better than that observed with an IIV. This is the first description of a LAIV for the prevention of H3N8 CIV in dogs.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | - Kai Huang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Caroline Chauché
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Marta L DeDiego
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA; Center for Vaccine Biology and Immunology (CVBI), University of Rochester, Rochester, NY, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA.
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30
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Murcia PR, Palmarini M, Belák S. Introduction : Potential applications of pathogen genomics. REV SCI TECH OIE 2016; 35:13-23. [PMID: 27217165 DOI: 10.20506/rst.35.1.2414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brennan B, Weber F, Kormelink R, Schnettler E, Bouloy M, Failloux AB, Weaver SC, Fazakerley JK, Fragkoudis R, Harris M, Barr JN, Palese P, García-Sastre A, Dalziel RG, Dutia BM, Lowen AC, Steel J, Randall RE, Paul Duprex W, Rice CM, Tesh RB, Murphy FA, Ebihara H, Vasconcelos PFC, Nunes MR, Fooks AR, Smith GL, Goodfellow I, Pappu HR, Lamb RA, Paterson RG, Higgs S, Vanlandingham DL, Dietzgen RG, Stephen Lodmell J, Nichol ST, Daly J, Ullman DE, Plyusnin A, Plyusnina A, Efstathiou S, Hewson R, Tordo N, Cherry S, Boutell C, Hosie MJ, Murcia PR, Neil JC, Palmarini M, Patel AH, Willett BJ, Kohl A, McLauchlan J. In memoriam--Richard M. Elliott (1954-2015). J Gen Virol 2015; 96:1975-1978. [PMID: 26315040 DOI: 10.1099/jgv.0.000241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Friedemann Weber
- Institute for Virology, FB10 - Veterinary Medicine, Justus-Liebig University, 35392 Gießen, Germany
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Michèle Bouloy
- Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris cedex 15, France
| | | | - Scott C Weaver
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX 77555-0610, USA
| | | | | | - Mark Harris
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - John N Barr
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter Palese
- Icahn School of Medicine at Mount Sinai, , New York, NY 10029, USA
| | | | - Robert G Dalziel
- The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | | | - Anice C Lowen
- Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia, GA 30322, USA
| | - John Steel
- Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia, GA 30322, USA
| | - Richard E Randall
- Biomolecular Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
| | - W Paul Duprex
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Charles M Rice
- Laboratory of Virology & Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Frederick A Murphy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Hideki Ebihara
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Pedro F C Vasconcelos
- Seção de Arbovirologia e Febres Haemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, CEP 67030000, Ananindeua, Pará, Brasil
| | - Marcio R Nunes
- Seção de Arbovirologia e Febres Haemorrágicas, Instituto Evandro Chagas, Ministério da Saúde, CEP 67030000, Ananindeua, Pará, Brasil
| | - Anthony R Fooks
- APHA Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Geoffrey L Smith
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Reay G Paterson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stephen Higgs
- Biosecurity Research Institute, Kansas State University, Manhattan, KS 66506-7600, USA
| | - Dana L Vanlandingham
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, KS 66506, USA
| | | | - J Stephen Lodmell
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, , Atlanta, GA 30329-4027, USA
| | - Janet Daly
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire LE12 5RD, UK
| | - Diane E Ullman
- Department of Entomology, University of California, Davis, CA 95616, USA
| | | | | | - Stacey Efstathiou
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK
| | - Roger Hewson
- Public Health England - Microbiology Services, , Porton Down, Salisbury SP4 0JG, UK
| | - Noël Tordo
- WHO Collaborative Centre for Arboviruses and Viral Haemorrhagic Fevers, OIE Reference Laboratory for RVFV and CCHFV, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Sara Cherry
- University of Pennsylvania, 304K Lynch Laboratories, Philadelphia, PA 19104, USA
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Margaret J Hosie
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - James C Neil
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
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32
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Chedom DF, Murcia PR, Greenman CD. Inferring the Clonal Structure of Viral Populations from Time Series Sequencing. PLoS Comput Biol 2015; 11:e1004344. [PMID: 26571026 PMCID: PMC4646700 DOI: 10.1371/journal.pcbi.1004344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/17/2015] [Indexed: 11/18/2022] Open
Abstract
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be identified, although the solutions may not be unique, even for complete sets of information. This is applied to a chain of influenza infection, where we infer evolutionary structures, including reassortment, and demonstrate some of the difficulties of interpretation that arise from deep sequencing due to artifacts such as template switching during PCR amplification.
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Affiliation(s)
- Donatien F. Chedom
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Chris D. Greenman
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
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33
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Fusaro A, Tassoni L, Hughes J, Milani A, Salviato A, Schivo A, Murcia PR, Bonfanti L, Cattoli G, Monne I. Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences. Infect Genet Evol 2015; 34:457-66. [PMID: 26003682 DOI: 10.1016/j.meegid.2015.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/05/2015] [Accepted: 05/19/2015] [Indexed: 11/27/2022]
Abstract
Influenza A virus can quickly acquire genetic mutations that may be associated with increased virulence, host switching or antigenic changes. To provide new insights into the evolutionary dynamics and the adaptive strategies of distinct avian influenza lineages in response to environmental and host factors, we compared two distinct avian influenza epidemics caused by the H7N1 and H7N3 subtypes that circulated under similar epidemiological conditions, including the same domestic species reared in the same densely populated poultry area for similar periods of time. The two strains appear to have experienced largely divergent evolution: the H7N1 viruses evolved into a highly pathogenic form, while the H7N3 did not. However, a more detailed molecular and evolutionary analysis revealed several common features: (i) the independent acquisition of 32 identical mutations throughout the entire genome; (ii) the evolution and persistence of two sole genetic groups with similar genetic characteristics; (iii) a comparable pattern of amino acid variability of the HA proteins during the low pathogenic epidemics; and (iv) similar rates of nucleotide substitutions. These findings suggest that the evolutionary trajectories of viruses with the same virulence level circulating in analogous epidemiological conditions may be similar. In addition, our deep sequencing analysis of 15 samples revealed that 17 of the 32 parallel mutations were already present at the beginning of the two epidemics, suggesting that fixation of these mutations may occur with different mechanisms, which may depend on the fitness gain provided by each mutation. This highlighted the difficulties in predicting the acquisition of mutations that can be correlated to viral adaptation to specific epidemiological conditions or to changes in virus virulence.
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Affiliation(s)
- Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy.
| | - Luca Tassoni
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Joseph Hughes
- MRC-University of Glasgow Center for Virus Research, 464 Bearsden Road, Glasgow, United Kingdom
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Annalisa Salviato
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Alessia Schivo
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Pablo R Murcia
- MRC-University of Glasgow Center for Virus Research, 464 Bearsden Road, Glasgow, United Kingdom
| | - Lebana Bonfanti
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Giovanni Cattoli
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università, 10, Legnaro (PD), Italy
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34
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Patrono LV, Bonfante F, Zanardello C, Terregino C, Capua I, Murcia PR. Phylogenetically distinct equine influenza viruses show different tropism for the swine respiratory tract. J Gen Virol 2015; 96:969-974. [PMID: 25593159 PMCID: PMC4631061 DOI: 10.1099/vir.0.000049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/10/2015] [Indexed: 12/16/2022] Open
Abstract
Influenza A viruses circulate in a wide range of animals. H3N8 equine influenza virus (EIV) is an avian-origin virus that has established in dogs as canine influenza virus (CIV) and has also been isolated from camels and pigs. Previous work suggests that mutations acquired during EIV evolution might have played a role in CIV emergence. Given the potential role of pigs as a source of human infections, we determined the ability of H3N8 EIVs to replicate in pig cell lines and in respiratory explants. We show that phylogenetically distinct EIVs display different infection phenotypes along the pig respiratory tract, but not in cell lines. Our results suggest that EIV displays a dynamic host range along its evolutionary history, supporting the view that evolutionary processes play important roles in host range and tropism and also underscoring the utility of using explant cultures to study influenza pathogenesis.
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Affiliation(s)
- Livia V. Patrono
- Department of Animal Medicine, Production and Health, Doctoral School of Veterinary Sciences, University of Padova, Padova, Italy
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Francesco Bonfante
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Claudia Zanardello
- Division of Specialised Diagnostics and Histopathology, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Ilaria Capua
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padova, Italy
| | - Pablo R. Murcia
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
- Correspondence Pablo R. Murcia
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35
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Gonzalez G, Marshall JF, Morrell J, Robb D, McCauley JW, Perez DR, Parrish CR, Murcia PR. Infection and pathogenesis of canine, equine, and human influenza viruses in canine tracheas. J Virol 2014; 88:9208-19. [PMID: 24899186 PMCID: PMC4136294 DOI: 10.1128/jvi.00887-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Influenza A viruses (IAVs) can jump species barriers and occasionally cause epidemics, epizootics, pandemics, and panzootics. Characterizing the infection dynamics at the target tissues of natural hosts is central to understanding the mechanisms that control host range, tropism, and virulence. Canine influenza virus (CIV; H3N8) originated after the transfer of an equine influenza virus (EIV) into dogs. Thus, comparing CIV and EIV isolates provides an opportunity to study the determinants of influenza virus emergence. Here we characterize the replication of canine, equine, and human IAVs in the trachea of the dog, a species to which humans are heavily exposed. We define a phenotype of infection for CIV, which is characterized by high levels of virus replication and extensive tissue damage. CIV was compared to evolutionarily distinct EIVs, and the early EIV isolates showed an impaired ability to infect dog tracheas, while EIVs that circulated near the time of CIV emergence exhibited a CIV-like infection phenotype. Inoculating dog tracheas with various human IAVs (hIAVs) showed that they infected the tracheal epithelium with various efficiencies depending on the virus tested. Finally, we show that reassortant viruses carrying gene segments of CIV and hIAV are viable and that addition of the hemagglutinin (HA) and neuraminidase (NA) of CIV to the 2009 human pandemic virus results in a virus that replicates at high levels and causes significant lesions. This provides important insights into the role of evolution on viral emergence and on the role of HA and NA as determinants of pathogenicity. IMPORTANCE Influenza A viruses (IAVs) have entered new host species in recent history, sometimes with devastating consequences. Canine influenza virus (CIV) H3N8 originated from a direct transfer of an equine influenza virus (EIV) in the early 2000s. We studied the infection patterns of IAVs that circulate in dogs or to which dogs are commonly exposed and showed that CIV emergence was likely caused by an adaptive driver, as evolutionarily distinct EIVs display distinct infection phenotypes. We also showed that many human viruses can infect dog tracheas and that reassortment with CIV results in viable viruses. Finally, we showed that the hemagglutinin and neuraminidase of CIV act as virulence factors. Our findings have significant implications because they show that dogs might act as "mixing vessels" in which novel viruses with pandemic potential could emerge and also provide experimental evidence supporting the role of viral evolution in influenza virus emergence.
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Affiliation(s)
- Gaelle Gonzalez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - John F Marshall
- Weipers Centre Equine Hospital, School of Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Joanna Morrell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - David Robb
- Charles River Laboratories Preclinical Services, Tranent, United Kingdom
| | - John W McCauley
- Division of Virology, Medical Research Council, National Institute for Medical Research, London, United Kingdom
| | - Daniel R Perez
- Virginia-Maryland Regional College of Veterinary Medicine, Department of Veterinary Medicine, University of Maryland, Maryland, USA
| | - Colin R Parrish
- Baker Institute of Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Abstract
Poxviruses are important pathogens of man and numerous domestic and wild animal species. Cross species (including zoonotic) poxvirus infections can have drastic consequences for the recipient host. Bats are a diverse order of mammals known to carry lethal viral zoonoses such as Rabies, Hendra, Nipah, and SARS. Consequent targeted research is revealing bats to be infected with a rich diversity of novel viruses. Poxviruses were recently identified in bats and the settings in which they were found were dramatically different. Here, we review the natural history of poxviruses in bats and highlight the relationship of the viruses to each other and their context in the Poxviridae family. In addition to considering the zoonotic potential of these viruses, we reflect on the broader implications of these findings. Specifically, the potential to explore and exploit this newfound relationship to study coevolution and cross species transmission together with fundamental aspects of poxvirus host tropism as well as bat virology and immunology.
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Affiliation(s)
- Kate S Baker
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Pablo R Murcia
- University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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Kao RR, Haydon DT, Lycett SJ, Murcia PR. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol 2014; 22:282-91. [PMID: 24661923 PMCID: PMC7125769 DOI: 10.1016/j.tim.2014.02.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 01/08/2023]
Abstract
Whole-genome sequencing is used for forensic epidemiology. Big data can transform forensic epidemiology. Clustering, biases, wildlife reservoirs, and emerging infections can all be addressed. Phylodynamics approaches to integrate epidemiological and evolutionary data have been highly successful but still face scientific challenges.
In epidemiology, the identification of ‘who infected whom’ allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control.
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Affiliation(s)
- Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - Samantha J Lycett
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - Pablo R Murcia
- Medical Research Council (MRC) Centre for Virus Research, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
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Baker KS, Suu-Ire R, Barr J, Hayman DTS, Broder CC, Horton DL, Durrant C, Murcia PR, Cunningham AA, Wood JLN. Viral antibody dynamics in a chiropteran host. J Anim Ecol 2014; 83:415-28. [PMID: 24111634 PMCID: PMC4413793 DOI: 10.1111/1365-2656.12153] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 09/14/2013] [Indexed: 12/20/2022]
Abstract
Bats host many viruses that are significant for human and domestic animal health, but the dynamics of these infections in their natural reservoir hosts remain poorly elucidated. In these, and other, systems, there is evidence that seasonal life-cycle events drive infection dynamics, directly impacting the risk of exposure to spillover hosts. Understanding these dynamics improves our ability to predict zoonotic spillover from the reservoir hosts. To this end, we followed henipavirus antibody levels of >100 individual E. helvum in a closed, captive, breeding population over a 30-month period, using a powerful novel antibody quantitation method. We demonstrate the presence of maternal antibodies in this system and accurately determine their longevity. We also present evidence of population-level persistence of viral infection and demonstrate periods of increased horizontal virus transmission associated with the pregnancy/lactation period. The novel findings of infection persistence and the effect of pregnancy on viral transmission, as well as an accurate quantitation of chiropteran maternal antiviral antibody half-life, provide fundamental baseline data for the continued study of viral infections in these important reservoir hosts.
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Affiliation(s)
- Kate S Baker
- Disease Dynamics Unit, University of Cambridge, Cambridge, UK, CB3 0ES
- Institute of Zoology, Zoological Society of London, London, UK, NW1 4RY
| | - Richard Suu-Ire
- Wildlife Division, Forestries Commission, Accra, Ghana, PO Box 239
| | - Jennifer Barr
- Australian Animal Health Laboratories, Commonwealth Scientific and Industrial Research Organisation, Geelong, Vic, Australia, 3219
| | - David T S Hayman
- Department of Biology, Colorado State University, Fort Collins, CO, USA, 80523
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA, 20814-4799
| | - Daniel L Horton
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal Health and Veterinary Laboratories Agency, Surrey, UK, KT15 3NB
| | | | - Pablo R Murcia
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK, G12 8QQ
| | | | - James L N Wood
- Disease Dynamics Unit, University of Cambridge, Cambridge, UK, CB3 0ES
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Baker KS, Leggett RM, Bexfield NH, Alston M, Daly G, Todd S, Tachedjian M, Holmes CEG, Crameri S, Wang LF, Heeney JL, Suu-Ire R, Kellam P, Cunningham AA, Wood JLN, Caccamo M, Murcia PR. Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. Virology 2013; 441:95-106. [PMID: 23562481 PMCID: PMC3667569 DOI: 10.1016/j.virol.2013.03.014] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 02/21/2013] [Accepted: 03/11/2013] [Indexed: 12/12/2022]
Abstract
Viral emergence as a result of zoonotic transmission constitutes a continuous public health threat. Emerging viruses such as SARS coronavirus, hantaviruses and henipaviruses have wildlife reservoirs. Characterising the viruses of candidate reservoir species in geographical hot spots for viral emergence is a sensible approach to develop tools to predict, prevent, or contain emergence events. Here, we explore the viruses of Eidolon helvum, an Old World fruit bat species widely distributed in Africa that lives in close proximity to humans. We identified a great abundance and diversity of novel herpes and papillomaviruses, described the isolation of a novel adenovirus, and detected, for the first time, sequences of a chiropteran poxvirus closely related with Molluscum contagiosum. In sum, E. helvum display a wide variety of mammalian viruses, some of them genetically similar to known human pathogens, highlighting the possibility of zoonotic transmission.
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Affiliation(s)
- Kate S Baker
- University of Cambridge, Department of Veterinary Medicine, Madingley Rd, Cambridge, Cambridgeshire, CB3 0ES, United Kingdom.
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Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JLN, Holmes EC, Murcia PR. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathog 2012; 8:e1003081. [PMID: 23308065 PMCID: PMC3534375 DOI: 10.1371/journal.ppat.1003081] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/25/2012] [Indexed: 12/30/2022] Open
Abstract
The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales – from the individual to the population – are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV) to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics. Influenza A viruses (IAVs) are major pathogens of humans and animals. Understanding how IAVs spread and evolve at different scales (individual, regional, global) in natural conditions is critical for preventing or managing influenza epidemics. A vast body of knowledge has been generated on the evolution of IAVs at the global scale. Additionally, recent experimental transmission studies have examined the diversity and transmission of influenza viruses within and between hosts. However, most studies on the spread of IAVs during epidemics have been based on consensus viral sequences, an approach that does not have enough discriminatory power to reveal exact transmission pathways. Here, we analyzed multiple within-host viral populations from different horses infected with equine influenza virus (EIV) during the course of an outbreak in a population within a confined area. This provided an opportunity to examine the genetic diversity of the viruses within single animals, the transmission of the viruses between each closely confined population within a yard, and the transmission between horses in different yards. We show that individual horses can be infected by viruses from more than one other horse, which has important implications for facilitating segment reassortment and the evolution of EIV. Additionally, by combining viral sequencing data and epidemiological data we show that the high levels of mixed infections can reveal the underlying epidemiological dynamics of the outbreak, and that epidemic size could be underestimated if only epidemiological data is considered. As sequencing technologies become cheaper and faster, these analyses could be undertaken almost in real-time and help control future outbreaks.
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Affiliation(s)
- Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard C. Allen
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marc Baguelin
- Immunisation, Hepatitis and Blood Safety Department, Health Protection Agency, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Katie Hampson
- Boyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Gregory J. Baillie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Debra Elton
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - J. Richard Newton
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - James L. N. Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, United States of America
| | - Pablo R. Murcia
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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41
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Stack JC, Murcia PR, Grenfell BT, Wood JLN, Holmes EC. Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation. Proc Biol Sci 2012; 280:20122173. [PMID: 23135678 DOI: 10.1098/rspb.2012.2173] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Influenza A viruses (IAVs) cause acute, highly transmissible infections in a wide range of animal species. Understanding how these viruses are transmitted within and between susceptible host populations is critical to the development of effective control strategies. While viral gene sequences have been used to make inferences about IAV transmission dynamics at the epidemiological scale, their utility in accurately determining patterns of inter-host transmission in the short-term--i.e. who infected whom--has not been strongly established. Herein, we use intra-host sequence data from the viral HA1 (hemagglutinin) gene domain from two transmission studies employing different IAV subtypes in their natural hosts--H3N8 in horses and H1N1 in pigs-to determine how well these data recapitulate the known pattern of inter-host transmission. Although no mutations were fixed over the course of either experimental transmission chain, we show that some minor, transient alleles can provide evidence of host-to-host transmission and, importantly, can be distinguished from those that cannot.
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Affiliation(s)
- J Conrad Stack
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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42
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Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ, Ramirez-Gonzalez RH, Ormond D, Oliver K, Elton D, Mumford JA, Caccamo M, Kellam P, Grenfell BT, Holmes EC, Wood JLN. Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathog 2012; 8:e1002730. [PMID: 22693449 PMCID: PMC3364949 DOI: 10.1371/journal.ppat.1002730] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/19/2012] [Indexed: 12/21/2022] Open
Abstract
Influenza viruses are characterized by an ability to cross species boundaries and evade host immunity, sometimes with devastating consequences. The 2009 pandemic of H1N1 influenza A virus highlights the importance of pigs in influenza emergence, particularly as intermediate hosts by which avian viruses adapt to mammals before emerging in humans. Although segment reassortment has commonly been associated with influenza emergence, an expanded host-range is also likely to be associated with the accumulation of specific beneficial point mutations. To better understand the mechanisms that shape the genetic diversity of avian-like viruses in pigs, we studied the evolutionary dynamics of an Eurasian Avian-like swine influenza virus (EA-SIV) in naïve and vaccinated pigs linked by natural transmission. We analyzed multiple clones of the hemagglutinin 1 (HA1) gene derived from consecutive daily viral populations. Strikingly, we observed both transient and fixed changes in the consensus sequence along the transmission chain. Hence, the mutational spectrum of intra-host EA-SIV populations is highly dynamic and allele fixation can occur with extreme rapidity. In addition, mutations that could potentially alter host-range and antigenicity were transmitted between animals and mixed infections were commonplace, even in vaccinated pigs. Finally, we repeatedly detected distinct stop codons in virus samples from co-housed pigs, suggesting that they persisted within hosts and were transmitted among them. This implies that mutations that reduce viral fitness in one host, but which could lead to fitness benefits in a novel host, can circulate at low frequencies. The latest human influenza pandemic highlights the ability of influenza viruses to jump species barriers and emerge in new hosts, as well as the role of pigs in generating viruses with pandemic potential. The mutational power of influenza virus, caused by intrinsically error-prone viral polymerases, has been directly linked to viral emergence, as adaptive mutations present in the reservoir host are likely to be key to the evolution of sustained transmission in new hosts. Hence, studying how mutations are generated, maintained and transmitted in and among pigs is critical to understanding how novel viruses could emerge. Here we characterized the evolution and mutational spectra of influenza virus populations within naïve and vaccinated pigs linked by natural transmission, by analyzing multiple viral sequences obtained at different times post-infection. We show that the genetic make-up of influenza viruses in pigs is highly dynamic: the frequency of particular mutations, including those that could potentially alter host specificity or result in vaccine escape, fluctuated markedly, including one rapid fixation event. We also show that co-infections are common and multiple viruses – even defective ones – were transmitted between pigs despite being vaccinated. Our results provide empirical evidence of the complex dynamics of influenza viral populations in pigs and provide insight on the evolutionary basis of RNA viral emergence.
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Affiliation(s)
- Pablo R. Murcia
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrizia Battista
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy Lloyd
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - Gregory J. Baillie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Doug Ormond
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Karen Oliver
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Debra Elton
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - Jennifer A. Mumford
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mario Caccamo
- The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Pennsylvania, United States of America
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Pennsylvania, United States of America
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, United States of America
| | - James L. N. Wood
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Baker KS, Todd S, Marsh G, Fernandez-Loras A, Suu-Ire R, Wood JLN, Wang LF, Murcia PR, Cunningham AA. Co-circulation of diverse paramyxoviruses in an urban African fruit bat population. J Gen Virol 2011; 93:850-856. [PMID: 22205718 PMCID: PMC3542712 DOI: 10.1099/vir.0.039339-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bats constitute a reservoir of zoonotic infections and some bat paramyxoviruses are capable of cross-species transmission, often with fatal consequences. Determining the level of viral diversity in reservoir populations is fundamental to understanding and predicting viral emergence. This is particularly relevant for RNA viruses where the adaptive mutations required for cross-species transmission can be present in the reservoir host. We report the use of non-invasively collected, pooled, neat urine samples as a robust sample type for investigating paramyxoviruses in bat populations. Using consensus PCR assays we have detected a high incidence and genetic diversity of novel paramyxoviruses in an urban fruit bat population over a short period of time. This may suggest a similarly unique relationship between bats and the members of the family Paramyxoviridae as proposed for some other viral families. Additionally, the high rate of bat–human contact at the study site calls for the zoonotic potential of the detected viruses to be investigated further.
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Affiliation(s)
- K S Baker
- Cambridge Infectious Diseases Consortium, University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - S Todd
- CSIRO Australian Animal Health Laboratories, Portarlington Road, East Geelong, VIC 3219, Australia
| | - G Marsh
- CSIRO Australian Animal Health Laboratories, Portarlington Road, East Geelong, VIC 3219, Australia
| | - A Fernandez-Loras
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - R Suu-Ire
- Wildlife Division of the Forestry Commission, Accra, Ghana
| | - J L N Wood
- Cambridge Infectious Diseases Consortium, University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB3 0ES, UK
| | - L F Wang
- CSIRO Australian Animal Health Laboratories, Portarlington Road, East Geelong, VIC 3219, Australia
| | - P R Murcia
- University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Garscube Estate, Bearsden Road, Glasgow G61 1QH, UK
| | - A A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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McKinley TJ, Murcia PR, Gog JR, Varela M, Wood JLN. A Bayesian approach to analyse genetic variation within RNA viral populations. PLoS Comput Biol 2011; 7:e1002027. [PMID: 21483482 PMCID: PMC3068928 DOI: 10.1371/journal.pcbi.1002027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
The development of modern and affordable sequencing technologies has allowed the study of viral populations to an unprecedented depth. This is of particular interest for the study of within-host RNA viral populations, where variation due to error-prone polymerases can lead to immune escape, antiviral resistance and adaptation to new host species. Methods to sequence RNA virus genomes include reverse transcription (RT) and polymerase chain reaction (PCR). RT-PCR is a molecular biology technique widely used to amplify DNA from an RNA template. The method itself relies on the in vitro synthesis of copy DNA from RNA followed by multiple cycles of DNA amplification. However, this method introduces artefactual errors that can act as confounding factors when the sequence data are analysed. Although there are a growing number of published studies exploring the intra- and inter-host evolutionary dynamics of RNA viruses, the complexity of the methods used to generate sequences makes it difficult to produce probabilistic statements about the likely sources of observed sequence variants. This complexity is further compounded as both the depth of sequencing and the length of the genome segment of interest increase. Here we develop a bayesian method to characterise and differentiate between likely structures for the background viral population. This approach can then be used to identify nucleotide sites that show evidence of change in the within-host viral population structure, either over time or relative to a reference sequence (e.g. an inoculum or another source of infection), or both, without having to build complex evolutionary models. Identification of these sites can help to inform the design of more focussed experiments using molecular biology tools, such as site-directed mutagenesis, to assess the function of specific amino acids. We illustrate the method by applying to datasets from experimental transmission of equine influenza, and a pre-clinical vaccine trial for HIV-1.
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Affiliation(s)
- Trevelyan J McKinley
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
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Murcia PR, Wood JLN. Equine influenza virus: a jumping virus that races with Thoroughbred horses and greyhounds. Vet J 2010; 189:3-4. [PMID: 21123098 DOI: 10.1016/j.tvjl.2010.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 10/25/2010] [Indexed: 11/26/2022]
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Nunes SF, Murcia PR, Tiley LS, Brown IH, Tucker AW, Maskell DJ, Wood JLN. An ex vivo swine tracheal organ culture for the study of influenza infection. Influenza Other Respir Viruses 2010; 4:7-15. [PMID: 20021502 PMCID: PMC4941949 DOI: 10.1111/j.1750-2659.2009.00119.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background The threat posed by swine influenza viruses with potential to transmit from pig populations to other hosts, including humans, requires the development of new experimental systems to study different aspects of influenza infection. Ex vivo organ culture (EVOC) systems have been successfully used in the study of both human and animal respiratory pathogens. Objectives We aimed to develop an air interface EVOC using pig tracheas in the study of influenza infection demonstrating that tracheal explants can be effectively maintained in organ culture and support productive influenza infection. Methods Tracheal explants were maintained in the air interface EVOC system for 7 days. Histological characteristics were analysed with different staining protocols and co‐ordinated ciliary movement on the epithelial surface was evaluated through a bead clearance assay. Explants were infected with a swine H1N1 influenza virus. Influenza infection of epithelial cells was confirmed by immunohistochemistry and viral replication was quantified by plaque assays and real‐time RT‐PCR. Results Histological analysis and bead clearance assay showed that the tissue architecture of the explants was maintained for up to 7 days, while ciliary movement exhibited a gradual decrease after 4 days. Challenge with swine H1N1 influenza virus showed that the EVOC tracheal system shows histological changes consistent with in vivo influenza infection and supported productive viral replication over multiple cycles of infection. Conclusion The air interface EVOC system using pig trachea described here constitutes a useful biological tool with a wide range of applications in the study of influenza infection.
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Affiliation(s)
- Sandro F Nunes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Murcia PR, Delhon G, González MJ, Vilas M, Ramos-Vara JA, De Las Heras M, Nordhausen RW, Uzal FA. Cluster of cases of malignant schwannoma in cattle. Vet Rec 2008; 163:331-5. [PMID: 18791208 DOI: 10.1136/vr.163.11.331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Between 1998 and 2001, several cases of ataxia and paresis followed by recumbency and death were reported in cows from different farms in a restricted area of the Argentinian Patagonia. Five cases of this cluster were studied and a diagnosis of malignant schwannoma was established. Electron microscopy (em) of tumour samples from three of the animals revealed intracytoplasmic or interstitial structures resembling retroviral particles. Attempts to isolate a viral agent from the tumours were unsuccessful but the epidemiological data and the em findings suggest a viral aetiology.
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Affiliation(s)
- P R Murcia
- Virology Department, School of Veterinary Sciences, University of Buenos Aires, Buenos Aires, Argentina
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Abstract
The host has developed during evolution a variety of "restriction factors" to fight retroviral infections. We investigated the mechanisms of a unique viral block acting at late stages of the retrovirus replication cycle. The sheep genome is colonized by several copies of endogenous retroviruses, known as enJSRVs, which are highly related to the oncogenic jaagsiekte sheep retrovirus (JSRV). enJS56A1, one of the enJSRV proviruses, can act as a restriction factor by blocking viral particles release of the exogenous JSRV. We show that in the absence of enJS56A1 expression, the JSRV Gag (the retroviral internal structural polyprotein) targets initially the pericentriolar region, in a dynein and microtubule-dependent fashion, and then colocalizes with the recycling endosomes. Indeed, by inhibiting the endocytosis and trafficking of recycling endosomes we hampered JSRV exit from the cell. Using a variety of approaches, we show that enJS56A1 and JSRV Gag interact soon after synthesis and before pericentriolar/recycling endosome targeting of the latter. The transdominant enJS56A1 induces intracellular Gag accumulation in microaggregates that colocalize with the aggresome marker GFP-250 but develop into bona fide aggresomes only when the proteasomal machinery is inhibited. The data argue that dominant-negative proteins can modify the overall structure of Gag multimers/viral particles hampering the interaction of the latter with the cellular trafficking machinery.
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Affiliation(s)
- Frederick Arnaud
- Institute of Comparative Medicine, University of Glasgow Veterinary School, 464 Bearsden Road, Glasgow, G61 1QH Scotland, United Kingdom
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Murcia PR, Arnaud F, Palmarini M. The transdominant endogenous retrovirus enJS56A1 associates with and blocks intracellular trafficking of Jaagsiekte sheep retrovirus Gag. J Virol 2006; 81:1762-72. [PMID: 17135320 PMCID: PMC1797599 DOI: 10.1128/jvi.01859-06] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sheep genome harbors approximately 20 endogenous retroviruses (enJSRVs) highly related to the exogenous Jaagsiekte sheep retrovirus (JSRV). One of the enJSRV loci, enJS56A1, acts as a unique restriction factor by blocking JSRV in a transdominant fashion at a late stage of the retroviral cycle. To better understand the molecular basis of this restriction (termed JLR, for JSRV late restriction), we functionally characterized JSRV and enJS56A1 Gag proteins. We identified the putative JSRV Gag membrane binding and late domains and determined their lack of involvement in JLR. In addition, by using enJS56A1 truncation mutants, we established that the entire Gag protein is necessary to restrict JSRV exit. By using differentially tagged viruses, we observed, by confocal microscopy, colocalization between JSRV and enJS56A1 Gag proteins. By coimmunoprecipitation and molecular complementation analyses, we also revealed intracellular association and likely coassembly between JSRV and enJS56A1 Gag proteins. Interestingly, JSRV and enJS56A1 Gag proteins showed distinct intracellular targeting: JSRV exhibited pericentrosomal accumulation of Gag staining, while enJS56A1 Gag did not accumulate in this region. Furthermore, the number of cells displaying pericentrosomal JSRV Gag was drastically reduced in the presence of enJS56A1. We identified amino acid residue R21 in JSRV Gag as the primary determinant of centrosome targeting. We concluded that JLR is dependent on a Gag-Gag interaction between enJS56A1 and JSRV leading to altered cellular localization of the latter.
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Affiliation(s)
- Pablo R Murcia
- Institute of Comparative Medicine, University of Glasgow Veterinary School, 464 Bearsden Road, Glasgow G61 1QH, Scotland
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Uzal FA, Delhon G, Murcia PR, De las Heras M, Luján L, Fernández Miyakawa ME, Morris WE, Gonzalez MJ. Ovine pulmonary adenomatosis in Patagonia, Argentina. Vet Res Commun 2004; 28:159-70. [PMID: 14992245 DOI: 10.1023/b:verc.0000012110.49600.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An outbreak of pulmonary adenomatosis (OPA) occurred in sheep in Patagonia, Argentina's southernmost region. On the affected farm, nine animals died over a 6-month period with pulmonary lesions of OPA. In all cases, the histology of the lungs was characterized by proliferation of cuboideal and prismatic cells lining the alveoli. Inflammatory exudates and accumulation of alveolar macrophages were marked in most cases, but in six of the cases there was no excess fluid in the airways. The presence of the Jaagsiekte retrovirus was demonstrated in the lungs by immunocytochemistry and PCR. To the best of our knowledge, this is the first report of OPA in Patagonia.
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Affiliation(s)
- F A Uzal
- Animal Health Unit, The National Institute of Agricultural Technology, Bariloche, Argentina
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