1
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Welker C, Huang J, Elmadhoun O, Esmaeilzadeh S, Mookadam F, Ramakrishna H. Morbidity Following Pulmonary Embolism Hospitalization- Contributing Factors and Outcomes. J Cardiothorac Vasc Anesth 2024; 38:1239-1243. [PMID: 38402062 DOI: 10.1053/j.jvca.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Affiliation(s)
- Carson Welker
- Division of Anesthesia and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Jeffrey Huang
- Division of Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Omar Elmadhoun
- Division of Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Sarvie Esmaeilzadeh
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - Farouk Mookadam
- Emeritus member, Department of Cardiovascular Medicine, Mayo Clinic, Scottsdale, AZ
| | - Harish Ramakrishna
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN.
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2
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Establishing an In Vitro System to Assess How Specific Antibodies Drive the Evolution of Foot-and-Mouth Disease Virus. Viruses 2022; 14:v14081820. [PMID: 36016442 PMCID: PMC9412381 DOI: 10.3390/v14081820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Viruses can evolve to respond to immune pressures conferred by specific antibodies generated after vaccination and/or infection. In this study, an in vitro system was developed to investigate the impact of serum-neutralising antibodies upon the evolution of a foot-and-mouth disease virus (FMDV) isolate. The presence of sub-neutralising dilutions of specific antisera delayed the onset of virus-induced cytopathic effect (CPE) by up to 44 h compared to the untreated control cultures. Continued virus passage with sub-neutralising dilutions of these sera resulted in a decrease in time to complete CPE, suggesting that FMDV in these cultures adapted to escape immune pressure. These phenotypic changes were associated with three separate consensus-level non-synonymous mutations that accrued in the viral RNA-encoding amino acids at positions VP266, VP280 and VP1155, corresponding to known epitope sites. High-throughput sequencing also identified further nucleotide substitutions within the regions encoding the leader (Lpro), VP4, VP2 and VP3 proteins. While association of the later mutations with the adaptation to immune pressure must be further verified, these results highlight the multiple routes by which FMDV populations can escape neutralising antibodies and support the application of a simple in vitro approach to assess the impact of the humoral immune system on the evolution of FMDV and potentially other viruses.
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3
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Brown E, Freimanis G, Shaw AE, Horton DL, Gubbins S, King D. Characterising Foot-and-Mouth Disease Virus in Clinical Samples Using Nanopore Sequencing. Front Vet Sci 2021; 8:656256. [PMID: 34079833 PMCID: PMC8165188 DOI: 10.3389/fvets.2021.656256] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains. At present, sequencing of FMD virus (FMDV) relies upon the time-consuming transport of samples to well-resourced laboratories. The Oxford Nanopore Technologies' MinION portable sequencer has the potential to allow sequencing in remote, decentralised laboratories closer to the outbreak location. In this study, we investigated the utility of the MinION to generate sequence data of sufficient quantity and quality for the characterisation of FMDV serotypes O, A, Asia 1. Prior to sequencing, a universal two-step RT-PCR was used to amplify parts of the 5′UTR, as well as the leader, capsid and parts of the 2A encoding regions of FMDV RNA extracted from three sample matrices: cell culture supernatant, tongue epithelial suspension and oral swabs. The resulting consensus sequences were compared with reference sequences generated on the Illumina MiSeq platform. Consensus sequences with an accuracy of 100% were achieved within 10 and 30 min from the start of the sequencing run when using RNA extracted from cell culture supernatants and tongue epithelial suspensions, respectively. In contrast, sequencing from swabs required up to 2.5 h. Together these results demonstrated that the MinION sequencer can be used to accurately and rapidly characterise serotypes A, O, and Asia 1 of FMDV using amplicons amplified from a variety of different sample matrices.
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Affiliation(s)
- Emma Brown
- yaDepartment of Transmission Biology, The Pirbright Institute, Woking, United Kingdom.,Faculty of Health and Medical Science, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Graham Freimanis
- Department of Bioinformatics, Sequencing & Proteomics, The Pirbright Institute, Woking, United Kingdom
| | - Andrew E Shaw
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Woking, United Kingdom
| | - Daniel L Horton
- Faculty of Health and Medical Science, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Simon Gubbins
- yaDepartment of Transmission Biology, The Pirbright Institute, Woking, United Kingdom
| | - David King
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Woking, United Kingdom.,Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, Stag Hill campus, University of Surrey, Guildford, United Kingdom
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4
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King DJ, Freimanis G, Lasecka-Dykes L, Asfor A, Ribeca P, Waters R, King DP, Laing E. A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations. Viruses 2020; 12:E1187. [PMID: 33092085 PMCID: PMC7594041 DOI: 10.3390/v12101187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
High-throughput sequencing such as those provided by Illumina are an efficient way to understand sequence variation within viral populations. However, challenges exist in distinguishing process-introduced error from biological variance, which significantly impacts our ability to identify sub-consensus single-nucleotide variants (SNVs). Here we have taken a systematic approach to evaluate laboratory and bioinformatic pipelines to accurately identify low-frequency SNVs in viral populations. Artificial DNA and RNA "populations" were created by introducing known SNVs at predetermined frequencies into template nucleic acid before being sequenced on an Illumina MiSeq platform. These were used to assess the effects of abundance and starting input material type, technical replicates, read length and quality, short-read aligner, and percentage frequency thresholds on the ability to accurately call variants. Analyses revealed that the abundance and type of input nucleic acid had the greatest impact on the accuracy of SNV calling as measured by a micro-averaged Matthews correlation coefficient score, with DNA and high RNA inputs (107 copies) allowing for variants to be called at a 0.2% frequency. Reduced input RNA (105 copies) required more technical replicates to maintain accuracy, while low RNA inputs (103 copies) suffered from consensus-level errors. Base errors identified at specific motifs identified in all technical replicates were also identified which can be excluded to further increase SNV calling accuracy. These findings indicate that samples with low RNA inputs should be excluded for SNV calling and reinforce the importance of optimising the technical and bioinformatics steps in pipelines that are used to accurately identify sequence variants.
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Affiliation(s)
- David J. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Graham Freimanis
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Lidia Lasecka-Dykes
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Amin Asfor
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical sciences, School of Veterinary Medicine, University of Surrey, Guilford GU2 7XH, UK
| | - Paolo Ribeca
- Biomathematics and Statistics Scotland, Edinburgh, Midlothian EH9 3FD, UK;
| | - Ryan Waters
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Donald P. King
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK; (D.J.K.); (G.F.); (L.L.-D.); (A.A.); (R.W.); (D.P.K.)
| | - Emma Laing
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
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5
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Fish I, Stenfeldt C, Palinski RM, Pauszek SJ, Arzt J. Into the Deep (Sequence) of the Foot-and-Mouth Disease Virus Gene Pool: Bottlenecks and Adaptation during Infection in Naïve and Vaccinated Cattle. Pathogens 2020; 9:pathogens9030208. [PMID: 32178297 PMCID: PMC7157448 DOI: 10.3390/pathogens9030208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) infects hosts as a population of closely related viruses referred to as a quasispecies. The behavior of this quasispecies has not been described in detail in natural host species. In this study, virus samples collected from vaccinated and non-vaccinated cattle up to 35 days post-experimental infection with FMDV A24-Cruzeiro were analyzed by deep-sequencing. Vaccination induced significant differences compared to viruses from non-vaccinated cattle in substitution rates, entropy, and evidence for adaptation. Genomic variation detected during early infection reflected the diversity inherited from the source virus (inoculum), whereas by 12 days post infection, dominant viruses were defined by newly acquired mutations. Mutations conferring recognized fitness gain occurred and were associated with selective sweeps. Persistent infections always included multiple FMDV subpopulations, suggesting distinct foci of infection within the nasopharyngeal mucosa. Subclinical infection in vaccinated cattle included very early bottlenecks associated with reduced diversity within virus populations. Viruses from both animal cohorts contained putative antigenic escape mutations. However, these mutations occurred during later stages of infection, at which time transmission is less likely to occur. This study improves upon previously published work by analyzing deep sequences of samples, allowing for detailed characterization of FMDV populations over time within multiple hosts.
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Affiliation(s)
- Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN 37830, USA
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M. Palinski
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Steven J. Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient, NY 11957, USA; (I.F.); (C.S.); (R.M.P.); (S.J.P.)
- Correspondence:
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6
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Orton RJ, Wright CF, King DP, Haydon DT. Estimating viral bottleneck sizes for FMDV transmission within and between hosts and implications for the rate of viral evolution. Interface Focus 2019; 10:20190066. [PMID: 31897294 DOI: 10.1098/rsfs.2019.0066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
RNA viruses exist as populations of closely related genomes, characterized by a high diversity of low-frequency variants. As viral genomes from one population disperse to establish new sites of replication, the fate of these low-frequency variants depends to a large extent on the size of the founding population. Focusing on foot-and-mouth disease virus (FMDV) we conjecture that variants are more likely to be transmitted through wide bottlenecks, but more likely to approach fixation in new populations following narrow bottlenecks; therefore, the longer-term rate of accumulation of 'nearly neutral' variants at high frequencies is likely to be inversely related to the bottleneck size. We examine this conjecture in vivo by estimating bottleneck sizes relating 'parent' and 'daughter' populations observed at different scales ranging from within host to between host (within the same herd, and in different herds) using a previously established method. Within hosts, we find bottleneck sizes to range from 5 to 20 viral genomes between populations transmitted from the pharynx to the serum, and from 4 to 54 between serum and lesion populations. Between hosts, we find bottleneck sizes to range from 2 to 39, suggesting inter-host bottlenecks are of a similar size to intra-host bottlenecks. We establish a statistically significant negative relationship between the probability of genomic consensus level change and bottleneck size, and present a simple sampling model that captures this empirical relationship. We also present a novel in vitro experiment to investigate the impact of bottleneck size on the frequency of mutations within FMDV populations, demonstrate that variant frequency in a population increases more rapidly during small population passages, and provide evidence for positive selection during the passage of large populations.
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Affiliation(s)
- Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | | | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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7
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Baazizi R, Mimoune N, Mokhefi ME, Raza M, Chahed A, Hussain T. Knowledge and behavior of cattle and sheep owners and herders regarding foot-and-mouth disease in Northern Algeria. Vet World 2019; 12:1285-1290. [PMID: 31641309 PMCID: PMC6755404 DOI: 10.14202/vetworld.2019.1285-1290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Foot-and-mouth disease (FMD) has been occurring in Algeria since 2014, when an outbreak was announced in Setif, a district in the eastern region of the country. The problem was apparently resolved with the help of vaccination. However, in 2015, 2016, and 2018, FMD recurred. The veterinary authorities and media educated breeders on how to recognize the clinical signs and how to report the disease. This study aimed to evaluate the knowledge and recognition of FMD by farmers and breeders. Moreover, an assessment of the behavior of cattle and sheep owners and herders following FMD cases is examined. Materials and Methods: A cross-sectional survey was conducted from June to October 2018 to evaluate the perception of cattle and sheep owners and breeders regarding FMD in the Northern regions of Algeria, using questionnaires. Results: One hundred questionnaires were distributed; 71 were collected. Data showed that all the responders claimed to know about the disease, while more than half of the owners/herders claimed that they knew the clinical symptoms of FMD and mentioned fever, hypersalivation, lameness, and vesicles. Fewer than half (42%) (30/71) took some measures to prevent the disease, while more than half (58%) (41/71) did not take any measures in 2018. No one claimed to have reported the disease to authorities in 2018, while more than half had done so in 2014. Conclusion: It appears that experienced farmers recognized the clinical signs of FMD, while an academic background was not conclusively necessary for the identification of the clinical signs of the disease. Concerning the assessment of risk-associated behavior in the event of FMD occurrence, the responses of the breeders were not significantly different from those of risk-associated behaviors in the event of an epidemic. Farmers and breeders expressed similarity in terms of communicating the appearance of the disease in their livestock; the majority of them seemed to be aware of the importance of reporting the disease to local authorities, especially in 2014, when the disease first occurred. This behavior is encouraged by refund and technical assistance policies by the veterinary authorities, but in 2018, no disease was reported due to fear of slaughtering and economic loss.
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Affiliation(s)
- Ratiba Baazizi
- Department of Clinic, National Veterinary High School, ENSV, Algiers, Algeria
| | - Nora Mimoune
- Department of Clinic, National Veterinary High School, ENSV, Algiers, Algeria
| | - M'Hamed El Mokhefi
- Department of Clinic, National Veterinary High School, ENSV, Algiers, Algeria
| | - Muslim Raza
- Department of Quantitative Methods, School of Business and Economics, University of Management and Technology, Lahore, Pakistan
| | - Amina Chahed
- Department of Clinic, National Veterinary High School, ENSV, Algiers, Algeria
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
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8
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Cortey M, Ferretti L, Pérez-Martín E, Zhang F, de Klerk-Lorist LM, Scott K, Freimanis G, Seago J, Ribeca P, van Schalkwyk L, Juleff ND, Maree FF, Charleston B. Persistent Infection of African Buffalo (Syncerus caffer) with Foot-and-Mouth Disease Virus: Limited Viral Evolution and No Evidence of Antibody Neutralization Escape. J Virol 2019; 93:e00563-19. [PMID: 31092573 PMCID: PMC6639274 DOI: 10.1128/jvi.00563-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
African buffaloes (Syncerus caffer) are the principal "carrier" hosts of foot-and-mouth disease virus (FMDV). Currently, the epithelia and lymphoid germinal centers of the oropharynx have been identified as sites for FMDV persistence. We carried out studies in FMDV SAT1 persistently infected buffaloes to characterize the diversity of viruses in oropharyngeal epithelia, germinal centers, probang samples (oropharyngeal scrapings), and tonsil swabs to determine if sufficient virus variation is generated during persistence for immune escape. Most sequencing reads of the VP1 coding region of the SAT1 virus inoculum clustered around 2 subpopulations differing by 22 single-nucleotide variants of intermediate frequency. Similarly, most sequences from oropharynx tissue clustered into two subpopulations, albeit with different proportions, depending on the day postinfection (dpi). There was a significant difference between the populations of viruses in the inoculum and in lymphoid tissue taken at 35 dpi. Thereafter, until 400 dpi, no significant variation was detected in the viral populations in samples from individual animals, germinal centers, and epithelial tissues. Deep sequencing of virus from probang or tonsil swab samples harvested prior to postmortem showed less within-sample variability of VP1 than that of tissue sample sequences analyzed at the same time. Importantly, there was no significant difference in the ability of sera collected between 14 and 400 dpi to neutralize the inoculum or viruses isolated at later time points in the study from the same animal. Therefore, based on this study, there is no evidence of escape from antibody neutralization contributing to FMDV persistent infection in African buffalo.IMPORTANCE Foot-and-mouth disease virus (FMDV) is a highly contagious virus of cloven-hoofed animals and is recognized as the most important constraint to international trade in animals and animal products. African buffaloes (Syncerus caffer) are efficient carriers of FMDV, and it has been proposed that new virus variants are produced in buffalo during the prolonged carriage after acute infection, which may spread to cause disease in livestock populations. Here, we show that despite an accumulation of low-frequency sequence variants over time, there is no evidence of significant antigenic variation leading to immune escape. Therefore, carrier buffalo are unlikely to be a major source of new virus variants.
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Affiliation(s)
- Martí Cortey
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Luca Ferretti
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | - Fuquan Zhang
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | - Katherine Scott
- Agricultural Research Council of South Africa, Onderstepoort Veterinary Institute-Transboundary Animal Disease Section (OVI-TAD), Vaccine and Diagnostic Development Programme, Onderstepoort, Gauteng, South Africa
| | | | - Julian Seago
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | - Paolo Ribeca
- The Pirbright Institute, Woking, Surrey, United Kingdom
| | | | | | - Francois F Maree
- Agricultural Research Council of South Africa, Onderstepoort Veterinary Institute-Transboundary Animal Disease Section (OVI-TAD), Vaccine and Diagnostic Development Programme, Onderstepoort, Gauteng, South Africa
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9
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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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10
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Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C. The evolution of a super-swarm of foot-and-mouth disease virus in cattle. PLoS One 2019; 14:e0210847. [PMID: 31022193 PMCID: PMC6483180 DOI: 10.1371/journal.pone.0210847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.
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Affiliation(s)
- Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Shannon L Johnson
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Patrick S Chain
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Devendra K Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America.,Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
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11
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Lau MSY, Grenfell BT, Worby CJ, Gibson GJ. Model diagnostics and refinement for phylodynamic models. PLoS Comput Biol 2019; 15:e1006955. [PMID: 30951528 PMCID: PMC6469796 DOI: 10.1371/journal.pcbi.1006955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/17/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022] Open
Abstract
Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Development of such tools is essential for model criticism, refinement, and calibration. The idea of utilising latent residuals for model assessment has already been exploited in general spatio-temporal epidemiological settings. Specifically, by proposing appropriately designed non-centered, re-parameterizations of a given epidemiological process, one can construct latent residuals with known sampling distributions which can be used to quantify evidence of model mis-specification. In this paper, we extend this idea to formulate a novel model-diagnostic framework for phylodynamic models. Using simulated examples, we show that our framework may effectively detect a particular form of mis-specification in a phylodynamic model, particularly in the event of superspreading. We also exemplify our approach by applying the framework to a dataset describing a local foot-and-mouth (FMD) outbreak in the UK, eliciting strong evidence against the assumption of no within-host-diversity in the outbreak. We further demonstrate that our framework can facilitate model calibration in real-life scenarios, by proposing a within-host-diversity model which appears to offer a better fit to data than one that assumes no within-host-diversity of FMD virus. Integrated modelling of conventional epidemiological data and modern genomic data (i.e. phylodynamics) has made significant progress in recent years, due to the ever-increasing availability of genomic data and development of statistical methods. However, there is a lack of tools for carrying out effective diagnostics for phylodynamic models. We propose a novel model diagnostic framework that involves a latent residual process which is a priori independent of model assumptions and which can be used to quantify, and reveal the nature of, model inadequacy. Our results suggest that our framework may systematically detect deviation from a particular model assumption and greatly facilitate subsequent model calibration.
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Affiliation(s)
- Max S. Y. Lau
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- * E-mail:
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- Fogarty International Center, National Institute of Health, Bethesda, MD, USA
| | | | - Gavin J. Gibson
- Maxwell Institute for Mathematical Sciences, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
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12
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Arzt J, Fish I, Pauszek SJ, Johnson SL, Chain PS, Rai DK, Rieder E, Goldberg TL, Rodriguez LL, Stenfeldt C. The evolution of a super-swarm of foot-and-mouth disease virus in cattle. PLoS One 2019; 14:e0210847. [PMID: 31022193 DOI: 10.1101/512178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/05/2019] [Indexed: 05/21/2023] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious viral disease that severely impacts global food security and is one of the greatest constraints on international trade of animal products. Extensive viral population diversity and rapid, continuous mutation of circulating FMD viruses (FMDVs) pose significant obstacles to the control and ultimate eradication of this important transboundary pathogen. The current study investigated mechanisms contributing to within-host evolution of FMDV in a natural host species (cattle). Specifically, vaccinated and non-vaccinated cattle were infected with FMDV under controlled, experimental conditions and subsequently sampled for up to 35 days to monitor viral genomic changes as related to phases of disease and experimental cohorts. Consensus-level genomic changes across the entire FMDV coding region were characterized through three previously defined stages of infection: early, transitional, and persistent. The overall conclusion was that viral evolution occurred via a combination of two mechanisms: emergence of full-genomic minority haplotypes from within the inoculum super-swarm, and concurrent continuous point mutations. Phylogenetic analysis indicated that individuals were infected with multiple distinct haplogroups that were pre-existent within the ancestral inoculum used to infect all animals. Multiple shifts of dominant viral haplotype took place during the early and transitional phases of infection, whereas few shifts occurred during persistent infection. Overall, this work suggests that the establishment of the carrier state is not associated with specific viral genomic characteristics. These insights into FMDV population dynamics have important implications for virus sampling methodology and molecular epidemiology.
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Affiliation(s)
- Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Ian Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Steven J Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Shannon L Johnson
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Patrick S Chain
- Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Devendra K Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Greenport, NY, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN, United States of America
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13
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Jamal SM, Belsham GJ. Molecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus. INFECTION GENETICS AND EVOLUTION 2018; 59:84-98. [PMID: 29412184 DOI: 10.1016/j.meegid.2018.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 02/07/2023]
Abstract
Foot-and-mouth disease virus (FMDV) is responsible for one of the most economically important infectious diseases of livestock. The virus spreads very easily and continues to affect many countries (mainly in Africa and Asia). The risks associated with the introduction of FMDV result in major barriers to trade in animals and their products. Seven antigenically distinct forms of the virus are known, called serotypes, but serotype C has not been detected anywhere for many years and may now be extinct. The serotypes have been further divided into topotypes (except for serotype Asia-1 viruses, which comprise a single topotype), genotypes, lineages and sub-lineages, which are usually restricted to specific geographical regions. However, sometimes, trans-regional spread of some strains occurs. Due to the error-prone replication of the RNA genome, the virus continuously evolves and new strains frequently arise (e.g. with modified antigenicity). Using nucleotide sequencing technologies, this rapid evolution of the viral genome can be followed. This allows the tracing of virus transmission pathways within an outbreak of disease if (near) full-length genome sequences can be generated. Furthermore, the movement of distinct virus lineages, from one country to another can be analyzed. Some important examples of the spread of new strains of FMD virus are described.
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Affiliation(s)
- Syed M Jamal
- Department of Biotechnology, University of Malakand, Chakdara, Dir (L), Khyber Pakhtunkhwa, Pakistan
| | - Graham J Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark.
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Understanding the transmission of foot-and-mouth disease virus at different scales. Curr Opin Virol 2017; 28:85-91. [PMID: 29245054 DOI: 10.1016/j.coviro.2017.11.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/23/2017] [Accepted: 11/28/2017] [Indexed: 12/23/2022]
Abstract
Foot-and-mouth disease (FMD) is highly infectious, but despite the large quantities of FMD virus released into the environment and the extreme susceptibility of host species to infection, transmission is not always predictable. Whereas virus spread in endemic settings is characterised by frequent direct and indirect animal contacts, incursions into FMD-free countries may be seeded by low-probability events such as fomite or wind-borne aerosol routes. There remains a void between data generated from small-scale experimental studies and our ability to reliably reconstruct transmission routes at different scales between farms, countries and regions. This review outlines recent transmission studies in susceptible host species, and considers new approaches that integrate virus genomics and epidemiological data to recreate and understand the spread of FMD.
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Nasheri N, Petronella N, Ronholm J, Bidawid S, Corneau N. Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach. Front Microbiol 2017; 8:73. [PMID: 28197136 PMCID: PMC5282449 DOI: 10.3389/fmicb.2017.00073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/11/2017] [Indexed: 01/14/2023] Open
Abstract
Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use a de novo assembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens.
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Affiliation(s)
- Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada
| | - Sabah Bidawid
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
| | - Nathalie Corneau
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada
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