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Luo T, Li K, Li C, Xia C, Gao C. Development of a triplex quantitative reverse transcription-polymerase chain reaction for the detection of porcine epidemic diarrhea virus, porcine transmissible gastroenteritis virus, and porcine rotavirus A. Front Microbiol 2024; 15:1390328. [PMID: 38800746 PMCID: PMC11117717 DOI: 10.3389/fmicb.2024.1390328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Porcine viral diarrhea is caused by many pathogens and can result in watery diarrhea, dehydration and death. Various detection methods, such as polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR), have been widely used for molecular diagnosis. We developed a triplex real-time quantitative reverse transcription PCR (qRT-PCR) for the simultaneous detection of three RNA viruses potentially associated with porcine viral diarrhea: porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and porcine rotavirus A (PoRVA). The triplex qRT-PCR had R2 values of 0.999 for the standard curves of PEDV, TGEV and PoRVA. Importantly, the limits of detection for PEDV, TGEV and PoRVA were 10 copies/μL. The specificity test showed that the triplex qRT-PCR detected these three pathogens specifically, without cross-reaction with other pathogens. In addition, the approach had good repeatability and reproducibility, with intra-and inter-assay coefficients of variation <1%. Finally, this approach was evaluated for its practicality in the field using 256 anal swab samples. The positive rates of PEDV, TGEV and PoRVA were 2.73% (7/256), 3.91% (10/256) and 19.14% (49/256), respectively. The co-infection rate of two or more pathogens was 2.73% (7/256). The new triplex qRT-PCR was compared with the triplex RT-PCR recommended by the Chinese national standard (GB/T 36871-2018) and showed 100% agreement for PEDV and TGEV and 95.70% for PoRVA. Therefore, the triplex qRT-PCR provided an accurate and sensitive method for identifying three potential RNA viruses for porcine viral diarrhea that could be applied to diagnosis, surveillance and epidemiological investigation.
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Affiliation(s)
| | | | | | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Caixia Gao
- State Key Laboratory for Animal Disease Control and Prevention, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Neujahr AC, Loy DS, Loy JD, Brodersen BW, Fernando SC. Rapid detection of high consequence and emerging viral pathogens in pigs. Front Vet Sci 2024; 11:1341783. [PMID: 38384961 PMCID: PMC10879307 DOI: 10.3389/fvets.2024.1341783] [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: 11/20/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction An increasing emergence of novel animal pathogens has been observed over the last decade. Viruses are a major contributor to the increased emergence and therefore, veterinary surveillance and testing procedures are greatly needed to rapidly and accurately detect high-consequence animal diseases such as Foot and Mouth Disease, Highly Pathogenic Avian Influenza, Classical Swine Fever, and African Swine Fever. The major detection methods for such diseases include real-time PCR assays and pathogen-specific antibodies among others. However, due to genetic drift or -shift in virus genomes, failure to detect such pathogens is a risk with devastating consequences. Additionally, the emergence of novel pathogens with no prior knowledge requires non-biased detection methods for discovery. Methods Utilizing enrichment techniques coupled with Oxford Nanopore Technologies MinION™ sequencing platform, we developed a sample processing and analysis pipeline to identify DNA and RNA viruses and bacterial pathogens from clinical samples. Results and discussion The sample processing and analysis pipeline developed allows the identification of both DNA and RNA viruses and bacterial pathogens simultaneously from a single tissue sample and provides results in less than 12 h. Preliminary evaluation of this method using surrogate viruses in different matrices and using clinical samples from animals with unknown disease causality, we demonstrate that this method can be used to simultaneously detect pathogens from multiple domains of life simultaneously with high confidence.
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Affiliation(s)
- Alison C. Neujahr
- Department of Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Duan S. Loy
- Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - John Dustin Loy
- Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Bruce W. Brodersen
- Nebraska Veterinary Diagnostic Center, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Samodha C. Fernando
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Food Science, University of Nebraska-Lincoln, Lincoln, NE, United States
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
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Kabir A, Ullah K, Ali Kamboh A, Abubakar M, Shafiq M, Wang L. The Pathogenesis of Foot-and-Mouth Disease Virus Infection: How the Virus Escapes from Immune Recognition and Elimination. Arch Immunol Ther Exp (Warsz) 2024; 72:aite-2024-0013. [PMID: 38910298 DOI: 10.2478/aite-2024-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/22/2024] [Indexed: 06/25/2024]
Abstract
Foot-and-mouth disease virus (FMDV) is a highly contagious and economically devastating pathogen that affects cloven-hoofed animals worldwide. FMDV infection causes vesicular lesions in the mouth, feet, and mammary glands, as well as severe systemic symptoms such as fever, salivation, and lameness. The pathogenesis of FMDV infection involves complex interactions between the virus and the host immune system, which determine the outcome of the disease. FMDV has evolved several strategies to evade immune recognition and elimination, such as antigenic variation, receptor switching, immune suppression, and subversion of innate and adaptive responses. This review paper summarizes the current knowledge on the pathogenesis of FMDV infection and the mechanisms of immune evasion employed by the virus. It also discusses the challenges and opportunities for developing effective vaccines and therapeutics against this important animal disease.
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Affiliation(s)
- Abdul Kabir
- 1Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh, Pakistan
| | - Kalim Ullah
- 2Laboratory of Human Virology and Oncology, Center of Pathogen Biology and Immunology, Institute of Basic Medical Research, Shantou University Medical College, Shantou, Guangdong, China
| | - Asghar Ali Kamboh
- 1Department of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University Tandojam, Sindh, Pakistan
| | - Muhammad Abubakar
- 3Department of Microbiology, National Veterinary Laboratories, NVL, Islamabad, Pakistan
| | - Muhammad Shafiq
- 4Department of Pharmacology, Research Institute of Clinical Pharmacy, Shantou University Medical College, Shantou, China
| | - Li Wang
- 5Department of Dermatology, Beijing University of Chinese Medicine Shenzhen Hospital, Longgang, Shenzen, China
- 6Department of Dermatology, Shenzhen University General Hospital, Shenzhen University, Shenzen, China
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4
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Ho KL, Ding J, Fan JS, Tsui WNT, Bai J, Fan SK. Digital Microfluidic Multiplex RT-qPCR for SARS-CoV-2 Detection and Variants Discrimination. MICROMACHINES 2023; 14:1627. [PMID: 37630161 PMCID: PMC10456927 DOI: 10.3390/mi14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
Continuous mutations have occurred in the genome of the SARS-CoV-2 virus since the onset of the COVID-19 pandemic. The increased transmissibility of the mutated viruses has not only imposed medical burdens but also prolonged the duration of the pandemic. A point-of-care (POC) platform that provides multitarget detection will help to track and reduce disease transmissions. Here we detected and discriminated three genotypes of SARS-CoV-2, including the wildtype and two variants of concern (VOCs), the Delta variant and Omicron variant, through reverse transcription quantitative polymerase chain reaction (RT-qPCR) on a digital microfluidics (DMF)-based cartridge. Upon evaluating with the RNA samples of Omicron variant, the DMF RT-qPCR presented a sensitivity of 10 copies/μL and an amplification efficiency of 96.1%, capable for clinical diagnosis. When spiking with SARS-CoV-2 RNA (wildtype, Delta variant, or Omicron variant) and 18S rDNA, the clinical analog samples demonstrated accurate detection and discrimination of different SARS-CoV-2 strains in 49 min.
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Affiliation(s)
- Kuan-Lun Ho
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jing Ding
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
| | - Jia-Shao Fan
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506, USA;
| | - Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA; (W.N.T.T.); (J.B.)
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Shih-Kang Fan
- Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506, USA; (K.-L.H.); (J.D.)
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5
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Fan Q, Xie Z, Wei Y, Zhang Y, Xie Z, Xie L, Huang J, Zeng T, Wang S, Luo S, Li M. Development of a visual multiplex fluorescent LAMP assay for the detection of foot-and-mouth disease, vesicular stomatitis and bluetongue viruses. PLoS One 2022; 17:e0278451. [PMID: 36480573 PMCID: PMC9731490 DOI: 10.1371/journal.pone.0278451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can be used to amplify target genes at a constant temperature, and it has several advantages, including convenience, specificity and sensitivity. However, due to the special interpretation methods of this technology for reaction results, all the previously reported LAMP detection methods have been restricted to identifying a single target, which limits the application of this technology. In this study, we modified conventional LAMP to include a quencher-fluorophore composite probe complementary to the F1c segment of the inner primer FIP; upon strand separation, a gain in the visible fluorescent signal was observed. The probes could be labeled with different fluorophores, showing different colors at the corresponding wavelengths. Therefore, this multiplex LAMP (mLAMP) assay can simultaneously detect 1-3 target sequences in a single LAMP reaction tube, and the results are more accurate and intuitive. In this study, we comprehensively demonstrated a single-reaction mLAMP assay for the robust detection of three cattle viruses without nonspecific amplification of other related pathogenic cattle viruses. The detection limit of this mLAMP assay was as low as 526-2477 copies/reaction for the recombinant plasmids. It is expected that this mLAMP assay can be widely used in clinical diagnosis.
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Affiliation(s)
- Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- * E-mail:
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
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6
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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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7
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Gao H, Chen YJ, Xu XQ, Xu ZY, Xu SJ, Xing JB, Liu J, Zha YF, Sun YK, Zhang GH. Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A. Front Microbiol 2022; 13:980862. [PMID: 36246286 PMCID: PMC9557172 DOI: 10.3389/fmicb.2022.980862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Senecavirus A (SVA) is a member of the genus Senecavirus in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss to the pig industry. However, the global transmission routes of SVA and its natural origins remain unclear. In this study, we processed representative SVA sequences from the GenBank database along with 10 newly isolated SVA strains from the field samples collected from our lab to explore the origins, population characteristics, and transmission patterns of SVA. The SVA strains were firstly systematically divided into eight clades including Clade I–VII and Clade Ancestor based on the maximum likelihood phylogenetic inference. Phylogeographic and phylodynamics analysis within the Bayesian statistical framework revealed that SVA originated in the United States in the 1980s and afterward spread to different countries and regions. Our analysis of viral transmission routes also revealed its historical spread from the United States and the risk of the global virus prevalence. Overall, our study provided a comprehensive assessment of the phylogenetic characteristics, origins, history, and geographical evolution of SVA on a global scale, unlocking insights into developing efficient disease management strategies.
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Affiliation(s)
- Han Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yong-jie Chen
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xiu-qiong Xu
- Guangdong Animal Health and Quarantine Office, Guangdong Animal Disease Prevention and Control Center, Guangzhou, China
| | - Zhi-ying Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Si-jia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jia-bao Xing
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yun-feng Zha
- Guangdong Animal Health and Quarantine Office, Guangdong Animal Disease Prevention and Control Center, Guangzhou, China
| | - Yan-kuo Sun
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Yan-kuo Sun,
| | - Gui-hong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Gui-hong Zhang,
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Dong J, Tsui WNT, Leng X, Fu J, Lohman M, Anderson J, Hamill V, Lu N, Porter EP, Gray M, Sebhatu T, Brown S, Pogranichniy R, Wang H, Noll L, Bai J. Development of a three-panel multiplex real-time PCR assay for simultaneous detection of nine canine respiratory pathogens. METHODS IN MICROBIOLOGY 2022; 199:106528. [PMID: 35753509 DOI: 10.1016/j.mimet.2022.106528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
Infectious respiratory disease is one of the most common diseases in dogs worldwide. Several bacterial and viral pathogens can serve as causative agents of canine infectious respiratory disease (CIRD), including Mycoplasma cynos, Mycoplasma canis, Bordetella bronchiseptica, canine adenovirus type 2 (CAdV-2), canine herpesvirus 1 (CHV-1), canine parainfluenza virus (CPIV), canine distemper virus (CDV), canine influenza virus (CIA) and canine respiratory coronavirus (CRCoV). Since these organisms cause similar clinical symptoms, disease diagnosis based on symptoms alone can be difficult. Therefore, a quick and accurate test is necessary to rapidly identify the presence and relative concentrations of causative CIRD agents. In this study, a multiplex real-time PCR panel assay was developed and composed of three subpanels for detection of the aforementioned pathogens. Correlation coefficients (R2) were >0.993 for all singleplex and multiplex real-time PCR assays with the exception of one that was 0.988; PCR amplification efficiencies (E) were between 92.1% and 107.8% for plasmid DNA, and 90.6-103.9% for RNA templates. In comparing singular and multiplex PCR assays, the three multiplex reactions generated similar R2 and E values to those by corresponding singular reactions, suggesting that multiplexing did not interfere with the detection sensitivities. The limit of detection (LOD) of the multiplex real-time PCR for DNA templates was 5, 2, 3, 1, 1, 1, 4, 24 and 10 copies per microliter for M. cynos, M. canis, B. brochiseptica, CAdV-2, CHV-1, CPIV, CDV, CIA and CRCoV, respectively; and 3, 2, 6, 17, 4 and 8 copies per microliter for CAdV-2, CHV-1, CPIV, CDV, CIA and CRCoV, respectively, when RNA templates were used for the four RNA viruses. No cross-detection was observed among the nine pathogens. For the 740 clinical samples tested, the newly designed PCR assay showed higher diagnostic sensitivity compared to an older panel assay; pathogen identities from selected samples positive by the new assay but undetected by the older assay were confirmed by Sanger sequencing. Our data showed that the new assay has higher diagnostic sensitivity while maintaining the assay's specificity, as compared to the older version of the panel assay.
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Affiliation(s)
- Junsheng Dong
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, China
| | - Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Xue Leng
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Jilin Agricultural University, Changchun, Jilin, China
| | - Jinping Fu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Molly Lohman
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Joseph Anderson
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Elizabeth Poulsen Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Mark Gray
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Tesfaalem Sebhatu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Roman Pogranichniy
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Heng Wang
- Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, China
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, United States.
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9
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Tsui WNT, Hamill V, Noll L, Lu N, Porter EP, Harbidge D, Cox E, Richardson C, Gray M, Sebhatu T, Goerl K, Brown S, Hanzlicek G, Retallick J, Bai J. Molecular detverection of SARS-CoV-2 and differentiation of Omicron and Delta variant strains. Transbound Emerg Dis 2022; 69:e1618-e1631. [PMID: 35218683 PMCID: PMC9115370 DOI: 10.1111/tbed.14497] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022]
Abstract
The SARS‐CoV‐2 virus is the causative agent of COVID‐19 and has undergone continuous mutations throughout the pandemic. The more transmissible Omicron variant has quickly spread and is replacing the Delta variant as the most prevalent strain globally, including in the United States. A new molecular assay that can detect and differentiate both the Delta and Omicron variants was developed. A collection of 660,035 SARS‐CoV‐2 full‐ or near‐full genomes, including 169,454 Delta variant and 24,202 Omicron variant strains, were used for primer and probe designs. In silico data analysis predicted an assay coverage of >99% of all strains, including >99% of the Delta and >99% of Omicron strains. The Omicron variant differential test was designed based on the Δ31‐33 aa deletion in the N‐gene, which is present in the original B.1.1.529 main genotype, BA.1, as well as in BA.2 and BA.3 subtypes. Therefore, the assay should detect the majority of all Omicron variant strains. Standard curves generated with human clinical samples indicated that the PCR amplification efficiencies were 104%, 90.7% and 90.4% for the Omicron, Delta, and non‐Delta/non‐Omicron wild‐type genotypes, respectively. Correlation coefficients of the standard curves were all >0.99. The detection limit of the assay was 14.3, 32.0, and 21.5 copies per PCR reaction for Omicron, Delta, and wild‐type genotypes, respectively. The assay was designed to specifically detect SAR‐CoV‐2 strains. Selected samples with Omicron, Delta and wild‐type genotypes identified by the RT‐qPCR assay were also confirmed by sequencing. The assay did not detect any animal coronavirus‐positive samples that were tested. Human nasal swab samples that previously tested positive (n = 182) or negative (n = 42) for SARS‐CoV‐2 by the ThermoFisher TaqPath COVID‐19 Combo Kit, produced the same result with the new assay. Among positive samples, 55.5% (101/182), 23.1% (42/182), and 21.4% (39/182) were identified as Omicron, Delta, and non‐Omicron/non‐Delta wild‐type genotypes, respectively.
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Affiliation(s)
- Wai Ning Tiffany Tsui
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Elizabeth Poulsen Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Donald Harbidge
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Emily Cox
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Claire Richardson
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Mark Gray
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Tesfaalem Sebhatu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States
| | - Kyle Goerl
- Lafene Health Center, Kansas State University, Manhattan, KS 66506, United States
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Gregg Hanzlicek
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jamie Retallick
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, United States.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, United States
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10
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Abade dos Santos FA, Carvalho CL, Parra F, Dalton KP, Peleteiro MC, Duarte MD. A Quadruplex qPCR for Detection and Differentiation of Classic and Natural Recombinant Myxoma Virus Strains of Leporids. Int J Mol Sci 2021; 22:ijms222112052. [PMID: 34769480 PMCID: PMC8584577 DOI: 10.3390/ijms222112052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 01/19/2023] Open
Abstract
A natural recombinant myxoma virus (referred to as ha-MYXV or MYXV-Tol08/18) emerged in the Iberian hare (Lepus granatensis) and the European rabbit (Oryctolagus cuniculus) in late 2018 and mid-2020, respectively. This new virus is genetically distinct from classic myxoma virus (MYXV) strains that caused myxomatosis in rabbits until then, by acquiring an additional 2.8 Kbp insert within the m009L gene that disrupted it into ORFs m009L-a and m009L-b. To distinguish ha-MYXV from classic MYXV strains, we developed a robust qPCR multiplex technique that combines the amplification of the m000.5L/R duplicated gene, conserved in all myxoma virus strains including ha-MYXV, with the amplification of two other genes targeted by the real-time PCR systems designed during this study, specific either for classic MYXV or ha-MYXV strains. The first system targets the boundaries between ORFs m009L-a and m009L-b, only contiguous in classic strains, while the second amplifies a fragment within gene m060L, only present in recombinant MYXV strains. All amplification reactions were validated and normalized by a fourth PCR system directed to a housekeeping gene (18S rRNA) conserved in eukaryotic organisms, including hares and rabbits. The multiplex PCR (mPCR) technique described here was optimized for Taqman® and Evagreen® systems allowing the detection of as few as nine copies of viral DNA in the sample with an efficiency > 93%. This real-time multiplex is the first fast method available for the differential diagnosis between classic and recombinant MYXV strains, also allowing the detection of co-infections. The system proves to be an essential and effective tool for monitoring the geographical spread of ha-MYXV in the hare and wild rabbit populations, supporting the management of both species in the field.
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Affiliation(s)
- Fábio A. Abade dos Santos
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.C.P.); (M.D.D.)
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33003 Oviedo, Spain; (F.P.); (K.P.D.)
- Correspondence: ; Tel.: +351-21-440-3500
| | - Carina L. Carvalho
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33003 Oviedo, Spain; (F.P.); (K.P.D.)
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33003 Oviedo, Spain; (F.P.); (K.P.D.)
| | - Maria C. Peleteiro
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.C.P.); (M.D.D.)
| | - Margarida D. Duarte
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal; (M.C.P.); (M.D.D.)
- Instituto Nacional de Investigação Agrária e Veterinária (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
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11
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Das A, Wang Y, Babiuk S, Bai J, Dodd K, Jia W. Development of multiplex real-time PCR assays for differential detection of capripoxvirus, parapoxvirus and foot-and-mouth disease virus. Transbound Emerg Dis 2021; 69:1326-1337. [PMID: 33837669 DOI: 10.1111/tbed.14099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022]
Abstract
This study reports the development of multiplex real-time PCR assays for differential detection of capripoxvirus (CaPV), parapoxvirus (PaPV) and foot-and-mouth disease virus (FMDV) in sheep, goats and cattle. Three multiplex assays were developed, a capripox (CaP) rule-out assay for simultaneous detection and differentiation of CaPV and PaPV, a FMD rule-out assay for simultaneous detection and differentiation of FMDV and PaPV, and a FMD/CaP rule-out assay for simultaneous detection and differentiation of CaPV, PaPV and FMDV. All multiplex assays included β-actin gene ACTB as an internal positive control to monitor PCR inhibition and accuracy of nucleic acid extractions. The optimized assays were highly specific to the target viruses (CaPV, PaPV and FMDV) with no cross-reactivity against other viruses that cause similar clinical signs. Using positive control plasmids as template, the limit of detection (LOD) of the multiplex assays were estimated as 2 CaPV, 7 PaPV and 15 FMDV copies per assay. The amplification efficiency (AE) and correlation coefficient (R2 ), estimated from the standard curves (Ct vs. log10 template dilution), were 94%-106% and >0.99, respectively, for CaP and FMD rule-out assays, 96%-116% (AE) and >0.98 (R2 ), respectively, for CaP/FMD rule-out assays and 91%-102% and >0.99, respectively, for the corresponding singleplex assays. The diagnostic sensitivity (DSe) of the multiplex assays was assessed on 35 CaPV and 39 FMDV clinical specimens from experimentally infected (CS-E) animals, and 29 CaPV (LSDV), 28 FMDV and 36 PaPV clinical specimens from naturally infected (CS-N) animals; all tested positive (DSe 100%) except two CS-E FMDV specimens that were tested negative by FMD rule-out and the corresponding singleplex (FMDV) assays (37/39; DSe 95%). The newly developed multiplex assays offer a valuable tool for differential detection of clinically indistinguishable CaPV, PaPV and FMDV in suspected animals and animals with mixed infections.
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Affiliation(s)
- Amaresh Das
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Kimberly Dodd
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Wei Jia
- Foreign Animal Disease Diagnostic Laboratory, NVSL, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
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12
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Guo Z, Li K, Qiao S, Chen XX, Deng R, Zhang G. Development and evaluation of duplex TaqMan real-time PCR assay for detection and differentiation of wide-type and MGF505-2R gene-deleted African swine fever viruses. BMC Vet Res 2020; 16:428. [PMID: 33167979 PMCID: PMC7654620 DOI: 10.1186/s12917-020-02639-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/23/2020] [Indexed: 01/10/2023] Open
Abstract
Background African swine fever (ASF) is the most important disease to the pigs and cause serious economic losses to the countries with large-scale swine production. Vaccines are recognized as the most useful tool to prevent and control ASF virus (ASFV) infection. Currently, the MGF505 and MGF360 gene-deleted ASFVs or combined with CD2v deletion were confirmed to be the most promising vaccine candidates. Thus, it is essential to develop a diagnosis method to discriminate wide-type strain from the vaccines used. Results In this study, we established a duplex TaqMan real-time PCR based on the B646L gene and MGF505-2R gene. The sequence alignment showed that the targeted regions of primers and probes are highly conserved in the genotype II ASFVs. The duplex real-time assay can specifically detect B646L and MGF505-2R gene single or simultaneously without cross-reaction with other porcine viruses tested. The limit of detection was 5.8 copies and 3.0 copies for the standard plasmids containing B646L and MGF505-2R genes, respectively. Clinical samples were tested in parallel by duplex real-time PCR and a commercial ASFV detection kit. The detection results of these two assays against B646L gene were well consistent. Conclusion We successfully developed and evaluated a duplex TaqMan real-time PCR method which can effectively distinguish the wide type and MGF505 gene-deleted ASFVs. It would be a useful tool for the clinical diagnosis and control of ASF.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, People's Republic of China
| | - Kunpeng Li
- ZhengZhou ZhongDao Biotechnology Co., Ltd, Zhengzhou, People's Republic of China
| | - Songlin Qiao
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, People's Republic of China
| | - Xin-Xin Chen
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, People's Republic of China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, People's Republic of China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, People's Republic of China. .,College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, People's Republic of China.
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13
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Liu F, Wang Q, Huang Y, Wang N, Shan H. A 5-Year Review of Senecavirus A in China since Its Emergence in 2015. Front Vet Sci 2020; 7:567792. [PMID: 33134352 PMCID: PMC7561413 DOI: 10.3389/fvets.2020.567792] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022] Open
Abstract
Senecavirus A (SVA), previously known as Seneca Valley virus, is classified into the genus Senecavirus in the family Picornaviridae. This virus can cause vesicular disease and epidemic transient neonatal losses in swine. Typical clinical signs include vesicular and/or ulcerative lesions on the snout, oral mucosa, coronary bands and hooves. SVA emerged in Guangdong Province of China in 2015, and thereafter gradually spread into other provinces, autonomous regions and municipalities (P.A.M.s). Nowadays more than half of the P.A.M.s have been affected by SVA, and asymptomatic infection has occurred in some areas. The phylogenetic analysis shows that China isolates are clustered into five genetic branches, implying a fast evolutionary speed since SVA emergence in 2015. This review presented current knowledge concerning SVA infection in China, including its history, epidemiology, evolutionary characteristics, diagnostics and vaccines.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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14
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Wang Y, Noll L, Porter E, Stoy C, Dong J, Anderson J, Fu J, Pogranichniy R, Woodworth J, Peddireddi L, Bai J. Development of a differential multiplex real-time PCR assay for porcine circovirus type 2 (PCV2) genotypes PCV2a, PCV2b and PCV2d. J Virol Methods 2020; 286:113971. [PMID: 32926893 PMCID: PMC7486290 DOI: 10.1016/j.jviromet.2020.113971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/18/2022]
Abstract
A multiplex real-time PCR (mqPCR) is developed for PCV2a, 2b, and 2d differentiations. Sequencing of 74 strains confirmed genotyping results generated by the mqPCR. The mqPCR did not detect any non-target swine pathogens included in this study. This genotyping assay is recommended following a general PCV2 diagnostic testing.
A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for detection and differentiation of porcine circovirus type 2 (PCV2) genotypes, PCV2a, PCV2b and PCV2d. Single nucleotide polymorphism in primers or probes was deployed for different genotype detections, while conserved sequence in the 3' end of a primer and in the middle of a probe was used for the targeted genotype. In silico analysis of 2601 PCV2 ORF2 sequences showed that the predicted strain coverage of the assay was 93.4 % (409/438) for PCV2a, 95.1 % (1161/1221) for PCV2b and 93.6 % (882/942) for PCV2d strains. The PCR amplification efficiencies were 94.5 %, 100.2 %, and 99.2 % for PCV2a, PCV2b and PCV2d, respectively, with correlation coefficients >0.995 for all genotypes. The limits of detection (LOD) were 1.58 × 10−4 TCID50/mL for PCV2a, 5.62 × 10−4 TCID50/mL for PCV2b, and 3.16 × 10−3 TCID50/mL for PCV2d. Sanger sequencing of 74 randomly selected PCV2 positive clinical samples confirmed the genotypes of strains identified by the mqPCR. Validation with clinical samples co-positive for target and non-target pathogens demonstrated that the mqPCR assay specifically detected targeted viruses without cross reacting to each other or to other common porcine viruses.
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Affiliation(s)
- Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Colin Stoy
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Junsheng Dong
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Joe Anderson
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Jinping Fu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Roman Pogranichniy
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Jason Woodworth
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS, USA
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA; Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA.
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15
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Wang Y, Yim-Im W, Porter E, Lu N, Anderson J, Noll L, Fang Y, Zhang J, Bai J. Development of a bead-based assay for detection and differentiation of field strains and four vaccine strains of type 2 porcine reproductive and respiratory syndrome virus (PRRSV-2) in the USA. Transbound Emerg Dis 2020; 68:1414-1423. [PMID: 32816334 DOI: 10.1111/tbed.13808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) remains one of the most economically devastating diseases in swine population in the United States of America. Due to high mutation rate of the PRRS virus (PRRSV) genome, it is difficult to develop an accurate diagnostic assay with high strain coverage. Differentiation of field strains from the four vaccines that have been used in the USA, namely Ingelvac PRRS MLV, Ingelvac ATP, Fostera PRRS and Prime Pac PRRS, adds an additional challenge. It is difficult to use current real-time PCR systems to detect and differentiate the field strains from the vaccine strains. Luminex xTAG technology allows us to detect more molecular targets in a single reaction with a cost similar to a single real-time PCR reaction. By analysing all available 678 type 2 PRRSV (PRRSV-2) complete genome sequences, including the 4 vaccine strains, two pairs of detection primers were designed targeting the conserved regions of ORF4-ORF7, with strain coverage of 98.8% (670/678) based on in silico analysis. The virus strains sharing ≥98% identity of the complete genomes with the vaccine strains were considered vaccine or vaccine-like strains. One pair of primers for each vaccine strain were designed targeting the nsp2 region. In silico analysis showed the assay matched 94.7% (54/57) of Ingelvac PRRS® MLV (MLV) strain and the MLV-like strains, and 100% of the other three vaccine strains. Analytical sensitivity of the Luminex assay was one to two logs lower than that of the reverse transcription real-time PCR assay. Evaluated with 417 PRRSV-2 positive clinical samples, 95% were detected by the Luminex assay. Compared to ORF5 sequencing results, the Luminex assay detected 92.4% (73/79) of MLV strains, 78.3% (18/23) of Fostera strains and 50% (2/4) of ATP strains. None of the 472 samples were the Prime Pac strain tested by either ORF5 sequencing or the Luminex assay.
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Affiliation(s)
- Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Wannarat Yim-Im
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Nanyan Lu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Bioinformatics Center, Kansas State University, Manhattan, KS, USA
| | - Joe Anderson
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Ying Fang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
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16
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Wang Y, Xu L, Noll L, Stoy C, Porter E, Fu J, Feng Y, Peddireddi L, Liu X, Dodd KA, Jia W, Bai J. Development of a real-time PCR assay for detection of African swine fever virus with an endogenous internal control. Transbound Emerg Dis 2020; 67:2446-2454. [PMID: 32306531 DOI: 10.1111/tbed.13582] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/22/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023]
Abstract
Real-time PCR assays are highly sensitive, specific and rapid techniques for the identification of ASF virus (ASFV) (Section 3.8, OIE Terrestrial Manual, 2019). Although an ASFV p72 gene-based real-time PCR assay (a.k.a. the Zsak assay) (Journal of Clinical Microbiology, 2005, 43, 112) has been widely used for ASFV detection, several more ASFV whole genome sequences have become available in the 15 years since the design of the Zsak assay. In this study, we developed a new ASFV p72 gene-based real-time PCR after analysis of all currently available sequences of the p72 gene and multiplexed the new assay with a modified Zsak assay aiming to have a broader coverage of ASFV strain/isolates. To reduce false-negative detections, porcine house-keeping gene, beta actin (ACTB), was applied as an internal control. Eight ACTB sequences from the GenBank and 61 partial ACTB sequences generated in this study, and 1,012 p72 sequences from the GenBank and 23 p72 sequences generated at FADDL, were used for ACTB and ASFV primer and probe designs, respectively, to ensure broader host and ASFV coverage. Multiplexing ACTB in the reaction did not affect ASFV amplification. The multiplex assay was evaluated for strain/isolate coverage, sensitivity and specificity. The in silico analysis showed high ASFV strain/isolate coverage: 98.4% (978/994) of all p72 sequences currently available. The limit of detection (LOD) was 6 plasmid copies or 0.1-1 TCID50 /ml of ASFV isolates per reaction. Only targeted ASFV isolates and the viruses in the positive clinical samples were detected, indicating that the assay is highly specific (100% specificity). The test results of 26 ASFV isolates with different country origins showed that this newly developed multiplex assay performed better than the Zsak assay that has been widely accepted and used worldwide, indicating that it may be used as an alternative assay for ASFV detection.
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Affiliation(s)
- Yin Wang
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Lizhe Xu
- Foreign Animal Disease Diagnostic Laboratory, NVSL, VS, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Lance Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Colin Stoy
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Elizabeth Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Jinping Fu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Yuan Feng
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA
| | - Lalitha Peddireddi
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Xuming Liu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Kimberly A Dodd
- Foreign Animal Disease Diagnostic Laboratory, NVSL, VS, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Wei Jia
- Foreign Animal Disease Diagnostic Laboratory, NVSL, VS, APHIS, USDA, Plum Island Animal Disease Center, Orient, NY, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, USA.,Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
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