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Xu L, Berninger A, Lakin SM, O’Donnell V, Pierce JL, Pauszek SJ, Barrette RW, Faburay B. Direct RNA Sequencing of Foot-and-mouth Disease Virus Genome Using a Flongle on MinION. Bio Protoc 2024; 14:e5017. [PMID: 38948261 PMCID: PMC11211080 DOI: 10.21769/bioprotoc.5017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024] Open
Abstract
Foot-and-mouth disease (FMD) is a severe and extremely contagious viral disease of cloven-hoofed domestic and wild animals, which leads to serious economic losses to the livestock industry globally. FMD is caused by the FMD virus (FMDV), a positive-strand RNA virus that belongs to the genus Aphthovirus, within the family Picornaviridae. Early detection and characterization of FMDV strains are key factors to control new outbreaks and prevent the spread of the disease. Here, we describe a direct RNA sequencing method using Oxford Nanopore Technology (ONT) Flongle flow cells on MinION Mk1C (or GridION) to characterize FMDV. This is a rapid, low cost, and easily deployed point of care (POC) method for a near real-time characterization of FMDV in endemic areas or outbreak investigation sites. Key features • Saves ~35 min of the original protocol time by omitting the reverse transcription step and lowers the costs of reagents and consumables. • Replaces the GridION flow cell from the original protocol with the Flongle, which saves ~90% on the flow cell cost. • Combines the NGS benchwork with a modified version of our African swine fever virus (ASFV) fast analysis pipeline to achieve FMDV characterization within minutes. Graphical overview Schematic of direct RNA sequencing of foot-and-mouth disease virus (FMDV) process, which takes ~50 min from extracted RNA to final loading, modified from the ONT SQK-RNA002 protocol (Version: DRS_9080_v2_revO_14Aug2019).
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Affiliation(s)
- Lizhe Xu
- Foreign Animal Disease Diagnostic Laboratory (FADDL), National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Plum Island, New York, NY, USA
| | - Amy Berninger
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Steven M. Lakin
- FADDL, National Bio- and Agro-defense Facility (NBAF), United States Department of Agriculture, Manhattan, KS, USA
| | - Vivian O’Donnell
- Foreign Animal Disease Diagnostic Laboratory (FADDL), National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Plum Island, New York, NY, USA
| | - Jim L. Pierce
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Steven J. Pauszek
- Foreign Animal Disease Diagnostic Laboratory (FADDL), National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Plum Island, New York, NY, USA
| | - Roger W. Barrette
- Foreign Animal Disease Diagnostic Laboratory (FADDL), National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Plum Island, New York, NY, USA
| | - Bonto Faburay
- Foreign Animal Disease Diagnostic Laboratory (FADDL), National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Plum Island Animal Disease Center, Plum Island, New York, NY, USA
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Gunasekara U, Bertram MR, Van Long N, Minh PQ, Chuong VD, Perez A, Arzt J, VanderWaal K. Phylogeography as a Proxy for Population Connectivity for Spatial Modeling of Foot-and-Mouth Disease Outbreaks in Vietnam. Viruses 2023; 15:v15020388. [PMID: 36851602 PMCID: PMC9958845 DOI: 10.3390/v15020388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023] Open
Abstract
Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independence amongst case counts across spatial units. Structured spatial effects capture correlations in case counts amongst neighboring provinces arising from shared risk factors or population connectivity. For highly mobile populations, spatial adjacency is an imperfect measure of connectivity due to long-distance movement, but we often lack data on host movements. Phylogeographic models inferring routes of viral dissemination across a region could serve as a proxy for patterns of population connectivity. The objective of this study was to investigate whether the effects of population connectivity in space-time regressions of case counts were better captured by spatial adjacency or by inferences from phylogeographic analyses. To compare these two approaches, we used foot-and-mouth disease virus (FMDV) outbreak data from across Vietnam as an example. We identified that accounting for virus movement through phylogeographic analysis serves as a better proxy for population connectivity than spatial adjacency in spatial-temporal risk models. This approach may contribute to design surveillance activities in countries lacking movement data.
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Affiliation(s)
- Umanga Gunasekara
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Miranda R. Bertram
- Foreign Animal Disease Research Unit, USDA-ARS, Plum Island Animal Disease Center, Southold, NY 11957, USA
| | - Nguyen Van Long
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Phan Quang Minh
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Vo Dinh Chuong
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Andres Perez
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, USDA-ARS, Plum Island Animal Disease Center, Southold, NY 11957, USA
- Correspondence: (J.A.); (K.V.)
| | - Kimberly VanderWaal
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
- Correspondence: (J.A.); (K.V.)
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Chen W, Wang W, Wang X, Li Z, Wu K, Li X, Li Y, Yi L, Zhao M, Ding H, Fan S, Chen J. Advances in the differential molecular diagnosis of vesicular disease pathogens in swine. Front Microbiol 2022; 13:1019876. [PMID: 36386633 PMCID: PMC9641196 DOI: 10.3389/fmicb.2022.1019876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV), Senecavirus A (SVA) and swine vesicular disease virus (SVDV) are members of the family Picornaviridae, which can cause similar symptoms - vesicular lesions in the tissues of the mouth, nose, feet, skin and mucous membrane of animals. Rapid and accurate diagnosis of these viruses allows for control measures to prevent the spread of these diseases. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR are traditional and reliable methods for pathogen detection, while their amplification reaction requires a thermocycler. Isothermal amplification methods including loop-mediated isothermal amplification and recombinase polymerase amplification developed in recent years are simple, rapid and do not require specialized equipment, allowing for point of care diagnostics. Luminex technology allows for simultaneous detection of multiple pathogens. CRISPR-Cas diagnostic systems also emerging nucleic acid detection technologies which are very sensitivity and specificity. In this paper, various nucleic acid detection methods aimed at vesicular disease pathogens in swine (including FMDV, SVA and SVDV) are summarized.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Weijun Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xinyan Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
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Genome Sequences of Foot-and-Mouth Disease Virus SAT2 Strains Purified from Coinfected Cape Buffalo in Kenya. Microbiol Resour Announc 2022; 11:e0058522. [PMID: 36094207 PMCID: PMC9584222 DOI: 10.1128/mra.00585-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) SAT2 sequences were acquired from Cape buffalo in Kenya in 2016, from either primary passage (n = 38) or plaque purification of dually SAT1/SAT2-infected samples (n = 61). All samples were derived from asymptomatic animals. These sequences contribute to our understanding of FMDV diversity in reservoirs and during subclinical FMDV infections.
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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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Outbreaks of Foot-and-Mouth Disease in Burundi, East Africa, in 2016, Caused by Different Serotypes. Viruses 2022; 14:v14051077. [PMID: 35632817 PMCID: PMC9143720 DOI: 10.3390/v14051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Burundi is a small, densely populated country in the African Great Lakes region. In March 2016, several hundreds of cattle were reported with vesicular lesions, suggesting foot-and-mouth disease (FMD). Epithelial samples, saliva, and blood were collected in six of the affected provinces spread over the country. The overall seroprevalence of FMD virus (FMDV) in the affected herds, as determined by antibodies against FMDV non-structural proteins, was estimated at 87%. Antibodies against FMDV serotypes O (52%), A (44%), C (19%), SAT1 (36%), SAT2 (58%), and SAT3 (23%) were detected across the provinces. FMDV genome was detected in samples from five of the six provinces using rRT-PCR. FMDV was isolated from samples from three provinces: in Cibitoke province, serotypes A and SAT2 were isolated, while in Mwaro and Rutana provinces, only serotype SAT2 was isolated. In Bururi and Cankuzo provinces, the serological profile suggested a recent incursion with serotype SAT2, while in Bubanza province, the serological profile suggested past incursions with serotype O and possibly serotype SAT1. The phylogenetic assessments showed the presence of topotypes A/Africa/G-I and SAT2/IV, similarly to previously characterized virus strains from other countries in the region, suggesting a transboundary origin and necessitating a regional approach for vaccination and control of FMD.
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Genome of Bovine Viral Diarrhea Virus (BVDV) Contaminating a Continuous LFBK-α Vβ 6 Cell Line. Microbiol Resour Announc 2022; 11:e0116721. [PMID: 35112907 PMCID: PMC8812309 DOI: 10.1128/mra.01167-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here, we report the genome of bovine viral diarrhea virus 1 (BVDV-1) contaminating a continuous fetal bovine kidney cell line. The cell line (LFBK-αVβ6) is used for the rapid isolation and serotyping of foot-and-mouth disease virus (FMDV). The sequence contains the full polyprotein-coding sequence and partial untranslated regions (UTRs).
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Use of Slaughterhouses as Sentinel Points for Genomic Surveillance of Foot-and-Mouth Disease Virus in Southern Vietnam. Viruses 2021; 13:v13112203. [PMID: 34835007 PMCID: PMC8624567 DOI: 10.3390/v13112203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022] Open
Abstract
The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate the sampling of clinically healthy livestock at slaughterhouses as a strategy for genomic FMDV surveillance. Serum samples (n = 11,875) and oropharyngeal fluid (OPF) samples (n = 5045) were collected from clinically healthy cattle and buffalo on farms in eight provinces in southern and northern Vietnam (2015-2019) to characterize viral diversity. Outbreak sequences were collected between 2009 and 2019. In two slaughterhouses in southern Vietnam, 1200 serum and OPF samples were collected from clinically healthy cattle and buffalo (2017 to 2019) as a pilot study on the use of slaughterhouses as sentinel points in surveillance. FMDV VP1 sequences were analyzed using discriminant principal component analysis and time-scaled phylodynamic trees. Six of seven serotype-O and -A clusters circulating in southern Vietnam between 2017-2019 were detected at least once in slaughterhouses, sometimes pre-dating outbreak sequences associated with the same cluster by 4-6 months. Routine sampling at slaughterhouses may provide a timely and efficient strategy for genomic surveillance to identify circulating and emerging FMDV strains.
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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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Abstract
We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019. We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019.
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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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Omondi GP, Gakuya F, Arzt J, Sangula A, Hartwig E, Pauszek S, Smoliga G, Brito B, Perez A, Obanda V, VanderWaal K. The role of African buffalo in the epidemiology of foot-and-mouth disease in sympatric cattle and buffalo populations in Kenya. Transbound Emerg Dis 2020; 67:2206-2221. [PMID: 32303117 DOI: 10.1111/tbed.13573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/12/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Quantitative knowledge on the contribution of African buffalo to the epidemiology of foot-and-mouth disease virus (FMDV) in East Africa is lacking, and this information is essential for the design of control programs in the region. The objective of this study was to investigate the epidemiology of FMDV in buffalo, including the role of buffalo in the circulation of FMDV in livestock populations. We collected blood and oropharyngeal fluids from 92 wild buffalo and 98 sympatric cattle in central Kenya and sequenced the virus' VP1 coding region. We show that FMDV has a high seroprevalence in buffalo (~77%) and targeted cattle (~93%). In addition, we recovered 80 FMDV sequences from buffalo, all of which were serotype SAT1 and SAT2, and four serotype O and A sequences from sympatric cattle. Notably, six individual buffalo were co-infected with both SAT1 and SAT2. Amongst sympatric buffalo and cattle, the fact that no SAT1 or 2 sequences were found in cattle suggests that transmission of FMDV from buffalo to sympatric cattle is rare. Similarly, there was no evidence that serotype O and A sequences found in cattle were transmitted to buffalo. However, viruses from FMDV outbreaks in cattle elsewhere in Kenya were closely related to SAT1 and SAT2 viruses found in buffalo in this study, suggesting that FMDV in cattle and buffalo do not constitute independently evolving populations. We also show that fine-scale geographic features, such as rivers, influence the circulation of FMDV in buffalo and that social segregation amongst sympatric herds may limit between-herd transmission. These results significantly advance our understanding of the ecology and molecular epidemiology of FMDV at wildlife-livestock interfaces in East Africa and will help to inform the design of control and surveillance strategies for this disease in the region.
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Affiliation(s)
- George P Omondi
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Ahadi Veterinary Resource Center, Nairobi, Kenya
| | - Francis Gakuya
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Jonathan Arzt
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | | | - Ethan Hartwig
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Steven Pauszek
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - George Smoliga
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Barbara Brito
- Plum Island Animal Disease Center, Foreign Animal Disease Research Unit, ARS, USDA, NY, USA
| | - Andres Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, Kenya
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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Genome Sequences of Seven Foot-and-Mouth Disease Virus Isolates Reveal Diversity in the O/ME-SA/Ind2001 Lineage in India between 1997 and 2009. Microbiol Resour Announc 2020; 9:9/16/e00287-20. [PMID: 32299883 PMCID: PMC7163021 DOI: 10.1128/mra.00287-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the genome sequences of seven foot-and-mouth disease (FMD) virus (FMDV) isolates collected in India between 1997 and 2009. The strains represented four sublineages within the O/ME-SA/Ind2001 lineage. These viruses provide insights into FMDV diversity and evolution in India and may influence future control measures, including vaccine selections.
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Wang H, Xin X, Zheng C, Shen C. Single-Cell Analysis of Foot-and-Mouth Disease Virus. Front Microbiol 2020; 11:361. [PMID: 32194538 PMCID: PMC7066083 DOI: 10.3389/fmicb.2020.00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/18/2020] [Indexed: 11/25/2022] Open
Abstract
With the rapid development of single-cell technologies, the mechanisms underlying viral infections and the interactions between hosts and viruses are starting to be explored at the single-cell level. The foot-and-mouth-disease (FMD) virus (FMDV) causes an acute and persistent infection that can result in the break-out of FMD, which can have serious effects on animal husbandry. Single-cell techniques have emerged as powerful approaches to analyze virus infection at the resolution of individual cells. In this review, the existing single-cell studies examining FMDV will be systematically summarized, and the central themes of these studies will be presented.
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Affiliation(s)
- Hailong Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiu Xin
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Congyi Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Chao Shen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.,China Center for Type Culture Collection, Wuhan University, Wuhan, China
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15
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Foot-and-Mouth Disease Virus Serotype O/CATHAY Genome Sequences from Five Outbreaks in Vietnam, 2017 to 2019. Microbiol Resour Announc 2020; 9:9/5/e01315-19. [PMID: 32001559 PMCID: PMC6992863 DOI: 10.1128/mra.01315-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We report the genomes of five foot-and-mouth disease viruses (FMDVs) from distinct provinces in Vietnam. All five viruses were grouped within the O/CATHAY topotype. Sequences contain the full polyprotein coding sequence and partial untranslated regions. These genomes provide critical data on the spread and evolution of FMDVs in the region. We report the genomes of five foot-and-mouth disease viruses (FMDVs) from distinct provinces in Vietnam. All five viruses were grouped within the O/CATHAY topotype. Sequences contain the full polyprotein coding sequence and partial untranslated regions. These genomes provide critical data on the spread and evolution of FMDVs in the region.
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16
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Ehizibolo DO, Fish IH, Brito B, Bertram MR, Ardo A, Ularamu HG, Lazarus DD, Wungak YS, Nwosuh CI, Smoliga GR, Hartwig EJ, Pauszek SJ, Dickmu S, Abdoulkadiri S, Arzt J. Characterization of transboundary foot-and-mouth disease viruses in Nigeria and Cameroon during 2016. Transbound Emerg Dis 2020; 67:1257-1270. [PMID: 31880066 DOI: 10.1111/tbed.13461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 10/26/2019] [Accepted: 12/16/2019] [Indexed: 11/29/2022]
Abstract
Continuous surveillance for foot-and-mouth disease (FMD) in endemic settings such as West Africa is imperative to support improved local and regional control plans, with the long-term goal of regional eradication. This paper describes the genetic characterization of FMD viruses (FMDV) obtained from outbreaks in Nigeria (n = 45) and Cameroon (n = 15) during 2016 and from archival samples (n = 3) retrieved from a 2014 outbreak in Nigeria. These viruses were analysed in the context of previously published FMDV sequences from the region. Four FMDV serotypes: O, A, SAT1 and SAT2, were detected. Phylogenetic analyses of the VP1 coding sequences indicate the continuity of FMDV serotype O East Africa-3 (O/EA-3), serotype A AFRICA genotype G-IV (A/AFRICA/G-IV) and serotype South African Territories (SAT) 2 lineage VII (SAT2/VII). The FMDV SAT1 topotype X (SAT1/X), which emerged in Nigeria in 2015, continued to be associated with outbreaks in the region during 2016, and SAT1 is reported for the first time from Cameroon. Additionally, a re-emergence or re-introduction of the serotype O West Africa (O/WA) topotype in Nigeria is described herein. Our findings indicate a consistent, pan-serotypic relationship between FMDV strains detected in Cameroon and Nigeria. Additionally, FMDV strains from West Africa obtained in this study were genetically related to those occurring in East and North Africa. These phylogenetic relationships suggest that animal movements (pastoralism and/or trade) are important factors for virus spread across the African continent. These data provide critical baselines which are a necessary component of Stages 0 and 1 of the Progressive Control Pathway of FMD (PCP-FMD). Specifically, characterizing the existing virus strains (risk) provides the basis for the comprehensive risk-based control plan which is the requisite criteria for Nigeria's transition to Stage 2 of PCP-FMD, and for coordinated regional control of FMD.
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Affiliation(s)
| | - Ian H Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA.,Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, USA
| | - Barbara Brito
- The ithree Institute, University of Technology Sydney, Ultimo, Australia
| | - Miranda R Bertram
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA.,Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, USA
| | - Abdullahi Ardo
- Virology Division, National Veterinary Research Institute, Vom, Nigeria
| | | | - David D Lazarus
- Virology Division, National Veterinary Research Institute, Vom, Nigeria
| | - Yiltawe S Wungak
- Virology Division, National Veterinary Research Institute, Vom, Nigeria
| | - Chika I Nwosuh
- Virology Division, National Veterinary Research Institute, Vom, Nigeria
| | - George R Smoliga
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA
| | - Ethan J Hartwig
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA
| | - Steven James Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA
| | - Simon Dickmu
- Laboratoire National Vétérinaire (LANAVET), Garoua, Cameroon
| | | | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY, USA
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17
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Jamal SM, Nazem Shirazi MH, Ozyoruk F, Parlak U, Normann P, Belsham GJ. Evidence for multiple recombination events within foot-and-mouth disease viruses circulating in West Eurasia. Transbound Emerg Dis 2019; 67:979-993. [PMID: 31758840 DOI: 10.1111/tbed.13433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
Phylogenetic studies on foot-and-mouth disease viruses (FMDVs) circulating in the West Eurasian region have largely focused on the genomic sequences encoding the structural proteins that determine the serotype. The present study has compared near-complete genome sequences of FMDVs representative of the viruses that circulate in this region. The near-complete genome sequences (ca. 7,600 nt) were generated from multiple overlapping RT-PCR products. These amplicons were from FMDVs belonging to serotypes O, A and Asia-1, including members of the O-PanAsia-II and the A-Iran05 lineages, and of Group-II and Group-VII (Sindh-08) within serotype Asia-1, which are currently predominant and widespread in West Eurasia. These new sequences were analysed together with other sequences obtained from GenBank. Comparison of different regions of the FMDVs genomes revealed evidence for multiple, inter-serotypic, recombination events between FMDVs belonging to the serotypes O, A and Asia-1. It is concluded from the present study that dramatic changes in virus sequences can occur in the field through recombination between different FMDV genomes. These analyses provide information about the ancestry of the serotype O, A and Asia-1 FMDVs that are currently circulating within the West Eurasian region.
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Affiliation(s)
- Syed M Jamal
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | | | | | | | - Preben Normann
- National Veterinary Institute, Technical University of Denmark, Lindholm, Denmark
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, Denmark
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18
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Genome Sequences of 18 Foot-and-Mouth Disease Virus Outbreak Strains of Serotype O Sublineage Ind2001d from India, 2013 to 2014. Microbiol Resour Announc 2019; 8:8/33/e00776-19. [PMID: 31416875 PMCID: PMC6696650 DOI: 10.1128/mra.00776-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the full polyprotein-coding sequences and partial untranslated regions (UTRs) of 18 foot-and-mouth disease (FMD) viruses from 4 outbreaks in India in 2013 and 2014. All strains grouped within the O/ME-SA/Ind2001d sublineage. These genomes update knowledge of FMD virus (FMDV) diversity in South Asia and may contribute to molecular epidemiology studies and vaccine selections.
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19
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Mwiine FN, Velazquez-Salinas L, Ahmed Z, Ochwo S, Munsey A, Kenney M, Lutwama JJ, Maree FF, Lobel L, Perez AM, Rodriguez LL, VanderWaal K, Rieder E. Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross-sectional surveillance study in cattle between 2014 and 2017. Transbound Emerg Dis 2019; 66:2011-2024. [PMID: 31127983 DOI: 10.1111/tbed.13249] [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] [Received: 05/25/2018] [Revised: 04/20/2019] [Accepted: 04/30/2019] [Indexed: 01/08/2023]
Abstract
Here, we report the results of a cross-sectional study designed to monitor the circulation and genetic diversity of foot and mouth disease virus (FMDV) in Uganda between 2014 and 2017. In this study, 13,614 sera and 2,068 oral-pharyngeal fluid samples were collected from cattle and analysed to determine FMDV seroprevalence, circulating serotypes and their phylogenetic relationships. Circulation of FMDV was evidenced by the detection of antibodies against non-structural proteins of FMDV or viral isolations in all districts sampled in Uganda. Sequence analysis revealed the presence of FMDV serotypes A, O, SAT 1 and SAT 2. FMDVs belonging to serotype O, isolated from 21 districts, were the most prevalent and were classified into six lineages within two East African topotypes, namely EA-1 and EA-2. Serotype A viruses belonging to the Africa G-I topotype were isolated from two districts. SAT 1 viruses grouped within topotypes I and IV and SAT 2 viruses within topotypes VII, IV and X were isolated from six and four districts respectively. Phylogenetic analysis of SAT 1 and SAT 2 sequences from cattle clustered with historical sequences from African buffalo, indicating possible interspecies transmission at the wildlife-livestock interface. In some cases, Uganda viruses also shared similarities to viral strains recovered from other regions in East Africa. This 3-year study period provides knowledge about the geographical distribution of FMDV serotypes isolated in Uganda and insights into the genetic diversity of the multiple serotypes circulating in the country. Knowledge of circulating FMDV viruses will assist in antigenic matching studies to devise improved FMDV control strategies with vaccination and vaccine strain selection for Uganda.
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Affiliation(s)
- Frank Norbert Mwiine
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Lauro Velazquez-Salinas
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota.,Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Zaheer Ahmed
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Sylvester Ochwo
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Anna Munsey
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Mary Kenney
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Julius J Lutwama
- Department of Emerging and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francois F Maree
- Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, South Africa
| | - Leslie Lobel
- Department of Virology and Developmental Genetics, Ben Gurion University, Beer Sheva, Israel
| | - Andres M Perez
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Luis L Rodriguez
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
| | - Kimberly VanderWaal
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, Department of Agriculture Plum Island Animal Disease Center, ARS, USDA, Greenport, New York
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20
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First Detection and Genome Sequence of Senecavirus A in Vietnam. Microbiol Resour Announc 2019; 8:MRA01247-18. [PMID: 30687818 PMCID: PMC6346150 DOI: 10.1128/mra.01247-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/11/2018] [Indexed: 11/29/2022] Open
Abstract
In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first complete genome of a senecavirus A isolate collected from pigs in Kon Tum Province, Vietnam. In 2018, senecavirus A was detected for the first time in Vietnam. This report contains the first complete genome of a senecavirus A isolate collected from pigs in Kon Tum Province, Vietnam. This novel incursion has substantial implications for regional control of vesicular transboundary diseases.
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21
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Bertram MR, Bravo de Rueda C, Garabed R, Dickmu Jumbo S, Moritz M, Pauszek S, Abdoulkadiri S, Rodriguez LL, Arzt J. Molecular Epidemiology of Foot-and-Mouth Disease Virus in the Context of Transboundary Animal Movement in the Far North Region of Cameroon. Front Vet Sci 2018; 5:320. [PMID: 30619901 PMCID: PMC6301994 DOI: 10.3389/fvets.2018.00320] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Abstract
Transboundary movement of animals is an important mechanism for foot-and-mouth disease virus (FMDV) spread in endemic regions, such as Cameroon. Several transboundary animal trade routes cross the Far North Region of Cameroon, and cattle moved on foot along these routes often come in contact with native (sedentary and transhumant) herds. The purpose of this study was to investigate the role of transboundary trade cattle in the epidemiology of FMDV in the Far North Region of Cameroon. A total of 582 oropharyngeal fluid (OPF) samples were collected from asymptomatic transboundary trade cattle at official border check points and 57 vesicle epithelial tissues were collected from clinically affected native cattle in the Far North Region of Cameroon during 2010-2014. Viral protein 1 (VP1) coding sequences were obtained from 6 OPF samples from transboundary cattle (4 serotype O, 2 serotype SAT2) and 19 epithelial tissue samples from native cattle (7 serotype O, 3 serotype SAT2, 9 serotype A). FMDV serotype O viruses belonged to two topotypes (East Africa-3 and West Africa), and phylogenetic analyses suggested a pattern of continuous transmission in the region. Serotype SAT2 viruses belonged to a single topotype (VII), and phylogenetic analysis suggested a pattern of repeated introductions of different SAT2 lineages in the region. Serotype A viruses belonged to topotype AFRICA/G-IV, and the pattern of transmission was unclear. Spearman rank correlation analysis of VP1 coding sequences obtained in this study from transboundary and native cattle showed a positive correlation between genetic distance and time for serotype O (ρ = 0.71, p = 0.003) and between genetic distance and geographic distance for serotype SAT2 (ρ = 0.54, p = 0.1). These data suggest that transboundary trade cattle participate in the transmission of FMDV in the Far North Region of Cameroon, however the dynamics and direction of transmission could not be determined in this study. Results of this study contribute to the understanding of transboundary FMDV epidemiology in Central Africa and will help to inform control programs in Cameroon and in the region.
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Affiliation(s)
- Miranda R. Bertram
- Foreign Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Plum Island Animal Disease Center (PIADC), Greenport, NY, United States
- Research Participation Program, Plum Island Animal Disease Center, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Carla Bravo de Rueda
- Foreign Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Plum Island Animal Disease Center (PIADC), Greenport, NY, United States
- Research Participation Program, Plum Island Animal Disease Center, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Rebecca Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, United States
| | | | - Mark Moritz
- Department of Anthropology, The Ohio State University, Columbus, OH, United States
| | - Steven Pauszek
- Foreign Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Plum Island Animal Disease Center (PIADC), Greenport, NY, United States
| | | | - Luis L. Rodriguez
- Foreign Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Plum Island Animal Disease Center (PIADC), Greenport, NY, United States
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Agricultural Research Service, Department of Agriculture, Plum Island Animal Disease Center (PIADC), Greenport, NY, United States
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22
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Farooq U, Ahmed Z, Naeem K, Bertram M, Brito B, Stenfeldt C, Pauszek SJ, LaRocco M, Rodriguez L, Arzt J. Characterization of naturally occurring, new and persistent subclinical foot‐and‐mouth disease virus infection in vaccinated Asian buffalo in Islamabad Capital Territory, Pakistan. Transbound Emerg Dis 2018; 65:1836-1850. [DOI: 10.1111/tbed.12963] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/08/2018] [Accepted: 06/28/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Umer Farooq
- Animal Health Program National Agricultural Research Center Islamabad Pakistan
| | - Zaheer Ahmed
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
- Oak Ridge Institute for Science and Education (ORISE) Oak Ridge Tennessee
| | - Khalid Naeem
- Animal Health Program National Agricultural Research Center Islamabad Pakistan
| | - Miranda Bertram
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
- Oak Ridge Institute for Science and Education (ORISE) Oak Ridge Tennessee
| | - Barbara Brito
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
- Oak Ridge Institute for Science and Education (ORISE) Oak Ridge Tennessee
| | - Carolina Stenfeldt
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
- Department of Veterinary Population Medicine University of Minnesota St. Paul Minnesota
| | - Steven J. Pauszek
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
| | - Michael LaRocco
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
| | - Luis Rodriguez
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
| | - Jonathan Arzt
- Agricultural Research Service Plum Island Animal Disease Center Orient Point New York
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23
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Bertram MR, Delgado A, Pauszek SJ, Smoliga GR, Brito B, Stenfeldt C, Hartwig EJ, Jumbo SD, Abdoulmoumini M, Oliva Marie AA, Salhine R, Rodriguez LL, Garabed R, Arzt J. Effect of vaccination on cattle subclinically infected with foot-and-mouth disease virus in Cameroon. Prev Vet Med 2018; 155:1-10. [PMID: 29786519 DOI: 10.1016/j.prevetmed.2018.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/18/2022]
Abstract
Foot-and-mouth disease (FMD) is one of the most contagious and economically important livestock diseases worldwide. Four serotypes of FMD virus (FMDV; O, A, SAT1, SAT2) circulate in Cameroon, and a trivalent inactivated vaccine against the three most common serotypes (O, A, SAT2) was recently introduced in 2014. The objective of this study was to characterize vaccine performance in cattle under natural hyperendemic conditions in the Adamawa region of Cameroon. Vaccinated cattle (n = 50) and non-vaccinated controls (n = 100) were monitored by serum and oropharyngeal fluid (OPF) sample collection through a 12-month period. Anti-FMDV non-structural protein (anti-NSP) seroprevalence increased from 59.3% (89/150) at the beginning of the study to 85.8% (103/120) at the end of the study, and FMDV RNA was found in 28% (42/150) of animals overall, despite detection of clinical signs of FMD in only 6 non-vaccinated animals. Viral sequence analysis indicated that subclinical infections of FMDV serotypes O and A were present within the study herds during the study period, which was reflected by an overall increase of anti-NSP seroprevalence during the study. There was no association between vaccination status and seroconversion or prevalence of FMDV RNA in OPF. Younger cattle had higher odds of detection of FMDV RNA in OPF, but older animals were more likely to be seropositive. This study suggests vaccination of herds previously exposed to FMDV may help to limit clinical signs and reduce economic losses caused by FMDV. These findings also suggest that subclinical circulation of FMDV occurs in hyperendemic regions regardless of vaccination.
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Affiliation(s)
- Miranda R Bertram
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA; Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, USA
| | - Amy Delgado
- Monitoring and Modeling, Center for Epidemiology and Animal Health, APHIS, USDA, Fort Collins, CO, USA
| | - Steven J Pauszek
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA
| | - George R Smoliga
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA
| | - Barbara Brito
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA; Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, USA
| | - Carolina Stenfeldt
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA; STEMMA Laboratory, Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Ethan J Hartwig
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA
| | | | - Mamoudou Abdoulmoumini
- School of Science and Veterinary Medicine, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Amba Abona Oliva Marie
- School of Science and Veterinary Medicine, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Robert Salhine
- School of Science and Veterinary Medicine, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Luis L Rodriguez
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA
| | - Rebecca Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Jonathan Arzt
- USDA/ARS Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, P.O. Box 848, Greenport, NY, USA.
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24
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Dill V, Beer M, Hoffmann B. Simple, quick and cost-efficient: A universal RT-PCR and sequencing strategy for genomic characterisation of foot-and-mouth disease viruses. J Virol Methods 2017; 246:58-64. [PMID: 28442328 DOI: 10.1016/j.jviromet.2017.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 04/07/2017] [Accepted: 04/18/2017] [Indexed: 02/02/2023]
Abstract
Foot-and-mouth disease (FMD) is a major contributor to poverty and food insecurity in Africa and Asia, and it is one of the biggest threats to agriculture in highly developed countries. As FMD is extremely contagious, strategies for its prevention, early detection, and the immediate characterisation of outbreak strains are of great importance. The generation of whole-genome sequences enables phylogenetic characterisation, the epidemiological tracing of virus transmission pathways and is supportive in disease control strategies. This study describes the development and validation of a rapid, universal and cost-efficient RT-PCR system to generate genome sequences of FMDV, reaching from the IRES to the end of the open reading frame. The method was evaluated using twelve different virus strains covering all seven serotypes of FMDV. Additionally, samples from experimentally infected animals were tested to mimic diagnostic field samples. All primer pairs showed a robust amplification with a high sensitivity for all serotypes. In summary, the described assay is suitable for the generation of FMDV sequences from all serotypes to allow immediate phylogenetic analysis, detailed genotyping and molecular epidemiology.
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Affiliation(s)
- V Dill
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - M Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - B Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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25
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Knight-Jones TJD, Robinson L, Charleston B, Rodriguez LL, Gay CG, Sumption KJ, Vosloo W. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 4 - Diagnostics. Transbound Emerg Dis 2016; 63 Suppl 1:42-8. [DOI: 10.1111/tbed.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - L. L. Rodriguez
- Plum Island Animal Disease Center; ARS; USDA; Greenport NY USA
| | - C. G. Gay
- Agricultural Research Service; USDA; National Program 103-Animal Health; Beltsville MD USA
| | - K. J. Sumption
- European Commission for the Control of FMD (EuFMD); FAO; Rome Italy
| | - W. Vosloo
- Australian Animal Health Laboratory; CSIRO-Biosecurity Flagship; Geelong VIC Australia
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26
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Lemire KA, Rodriguez YY, McIntosh MT. Alkaline hydrolysis to remove potentially infectious viral RNA contaminants from DNA. Virol J 2016; 13:88. [PMID: 27260412 PMCID: PMC4893296 DOI: 10.1186/s12985-016-0552-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/30/2016] [Indexed: 11/10/2022] Open
Abstract
Background Diagnostics and research of high-consequence animal disease agents is often limited to laboratories with a high level of biosecurity that restrict the transport of biological material. Often, sharing of DNA with external partners is needed to support diagnostics, forensics, or research. Even in the absence of virus, RNA from positive-sense single stranded RNA (+ssRNA) viruses that may contaminate otherwise purified DNA preparations continues to pose a threat due to its potential to be infectious via direct translation to yield viral proteins. While the risk of animal infection or accidental reconstitution and release of a virus from RNA is very low, the high impact of an animal disease event associated with the accidental release of some + ssRNA viruses, such as classical swine fever or foot-and-mouth disease viruses, necessitates the precaution of having procedures to ensure the complete inactivation of viruses and + ssRNA viral genomes. RNA and DNA are differentially susceptible to enzymatic degradations; however, such procedures are susceptible to unintended DNA damage and/or failure due to enzyme or cofactor instabilities. Therefore, we describe the development and verification of a robust and simple chemical and physical method to selectively degrade RNA from purified DNA preparations. The procedure employs incubation of DNA in 0.25 N sodium hydroxide at 65 °C for 1 h followed by neutralization and boiling for 10 min to hydrolyze contaminating RNA and inactivate animal disease viruses from DNA preparations. Additional critical quality control elements include use of a synthetic control RNA (SCR) and an SCR-specific real-time RT-PCR to track effectiveness of the procedure in a parallel treated control sample, and a pH check of reagents to ensure proper neutralization of alkaline conditions. Results The new procedure reduced intact RNA beyond the limit of detection by realtime RT-PCR and inactivated viruses by in vitro culture infectivity assays. Conclusions Treated DNA, while denatured, remains suitable for most common molecular biology procedures including PCR, transformation of E. coli, and molecular sequencing. The procedure ensures not only the inactivation of a variety of viruses but also the degradation through hydrolysis of potentially contaminating infectious + ssRNA viral genomes.
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Affiliation(s)
- Karissa A Lemire
- Foreign Animal Disease Diagnostic Laboratory, NVSL, STAS, VS, APHIS, USDA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY, 11944-0848, USA
| | - Yelitza Y Rodriguez
- Foreign Animal Disease Diagnostic Laboratory, NVSL, STAS, VS, APHIS, USDA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY, 11944-0848, USA
| | - Michael T McIntosh
- Foreign Animal Disease Diagnostic Laboratory, NVSL, STAS, VS, APHIS, USDA, Plum Island Animal Disease Center, PO Box 848, Greenport, NY, 11944-0848, USA.
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Ludi A, Ahmed Z, Pomeroy LW, Pauszek SJ, Smoliga GR, Moritz M, Dickmu S, Abdoulkadiri S, Arzt J, Garabed R, Rodriguez LL. Serotype Diversity of Foot-and-Mouth-Disease Virus in Livestock without History of Vaccination in the Far North Region of Cameroon. Transbound Emerg Dis 2016; 63:e27-38. [PMID: 24735162 PMCID: PMC4499489 DOI: 10.1111/tbed.12227] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Indexed: 11/28/2022]
Abstract
Little information is available about the natural cycle of foot-and-mouth disease (FMD) in the absence of control measures such as vaccination. Cameroon presents a unique opportunity for epidemiological studies because FMD vaccination is not practiced. We carried out a prospective study including serological, antigenic and genetic aspects of FMD virus (FMDV) infections among different livestock production systems in the Far North of Cameroon to gain insight into the natural ecology of the virus. We found serological evidence of FMDV infection in over 75% of the animals sampled with no significant differences of prevalence observed among the sampled groups (i.e. market, sedentary, transboundary trade and mobile). We also found antibodies reactive to five of the seven FMDV serotypes (A, O, SAT1, SAT2 and SAT3) among the animals sampled. Finally, we were able to genetically characterize viruses obtained from clinical and subclinical FMD infections in Cameroon. Serotype O viruses grouped into two topotypes (West and East Africa). SAT2 viruses grouped with viruses from Central and Northern Africa, notably within the sublineage causing the large epidemic in Northern Africa in 2012, suggesting a common origin for these viruses. This research will guide future interventions for the control of FMD such as improved diagnostics, guidance for vaccine formulation and epidemiological understanding in support of the progressive control of FMD in Cameroon.
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Affiliation(s)
- A. Ludi
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
- Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
| | - Z. Ahmed
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
- Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
| | - L. W. Pomeroy
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - S. J. Pauszek
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
| | - G. R. Smoliga
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
| | - M. Moritz
- Department of Anthropology, The Ohio State University, Columbus, OH, USA
| | - S. Dickmu
- Laboratoire National Veterinaire, Lanavet, Garoua, Cameroon
| | | | - J. Arzt
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
| | - R. Garabed
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, USA
- Public Health Preparedness for Infectious Disease Program, The Ohio State University, Columbus, OH, USA
| | - L. L. Rodriguez
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, NY, USA
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A novel parainfluenza virus type 3 (PIV3) identified from goat herds with respiratory diseases in eastern China. Vet Microbiol 2014; 174:100-6. [PMID: 25236986 PMCID: PMC7117102 DOI: 10.1016/j.vetmic.2014.08.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/25/2014] [Accepted: 08/25/2014] [Indexed: 11/24/2022]
Abstract
Parainfluenza virus type 3 (PIV3) is one of the most important viral respiratory pathogens for humans and for many animals, but goat infection has been rarely reported. Starting in Aug 2013, goats in the Jiangsu and Anhui provinces of eastern China suffered severe respiratory diseases. In order to identify the causative agent, numerous related pathogens were tested with RT-PCR or PCR. A unique PIV3 strain was detected in most of the clinical nasal swabs or serum samples. The virus was isolated on MDBK cells and characterized by RT-PCR, nucleotide sequence analysis and hemagglutination test. The entire M and F gene coding regions, HN, 5'-UTR-N and L gene fragments were amplified using pairs of degenerate primers. Nucleotide, amino acid sequence alignments and phylogenetic analyses based on these genes indicated that the goat-derived PIV3 strain was distinct from previously reported BPIV3 genotypes and HPIV3 strains. The novel isolate, named JS2013, might be a potentially new member of the respirovirus genus. Goats were experimentally infected with JS2013 culture. The virus-inoculated goats displayed coughing and nasal discharges that were related to respiratory diseases. Viremia and virus shedding were detected during 4-10 days post-inoculation (dpi). Virus-specific HI antibodies became positive from 14 dpi. This is the first report of the detection of PIV3 from Chinese goat herds and genetic and pathogenetic characterization of the novel goat-derived PIV3.
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Comparison of test methodologies for foot-and-mouth disease virus serotype A vaccine matching. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:674-83. [PMID: 24623625 DOI: 10.1128/cvi.00034-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Vaccination has been one of the most important interventions in disease prevention and control. The impact of vaccination largely depends on the quality and suitability of the chosen vaccine. To determine the suitability of a vaccine strain, antigenic matching is usually studied by in vitro analysis. In this study, we performed three in vitro test methods to determine which one gives the lowest variability and the highest discriminatory capacity. Binary ethylenimine inactivated vaccines, prepared from 10 different foot-and-mouth disease (FMD) virus serotype A strains, were used to vaccinate cattle (5 animals for each strain). The antibody titers in blood serum samples 3 weeks postvaccination (w.p.v.) were determined by a virus neutralization test, neutralization index test, and liquid-phase blocking enzyme-linked immunosorbent assay (ELISA). The titers were then used to calculate relationship coefficient (r1) values. These r1 values were compared to the genetic lineage using receiver operating characteristic (ROC) analysis. In the two neutralization test methods, the median titers observed against the test strains differed considerably, and the sera of the vaccinated animals did not always show the highest titers against their respective homologous virus strains. When the titers were corrected for test strain effect (scaling), the variability (standard error of the mean per vaccinated group) increased because the results were on a different scale, but the discriminatory capacity improved. An ROC analysis of the r1 value calculated on both observed and scaled titers showed that only r1 values of the liquid-phase blocking ELISA gave a consistent statistically significant result. Under the conditions of the present study, the liquid-phase blocking ELISA showed less variation and still had a higher discriminatory capacity than the other tests.
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Kumar Verm A, Dhama K, Chakrabort S, Kumar A, Tiwari R, Rahal A, . M, Vir Singh S. Strategies for Combating and Eradicating Important Infectious Diseases of Animals with Particular Reference to India: Present and Future Perspectives. ACTA ACUST UNITED AC 2014. [DOI: 10.3923/ajava.2014.77.106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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