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Shin GE, Lee KK, Ku BK, Oh SH, Jang SH, Kang B, Jeoung HY. Prevalence of viral agents causing swine reproductive failure in Korea and the development of multiplex real-time PCR and RT-PCR assays. Biologicals 2024; 86:101763. [PMID: 38641502 DOI: 10.1016/j.biologicals.2024.101763] [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: 05/26/2023] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 04/21/2024] Open
Abstract
This study aimed to investigate the prevalence of viral agents causing reproductive failure in pigs in Korea. In addition, two types of multiplex real-time PCR (mqPCR) were developed for the simultaneous detection of Aujeszky's disease virus (ADV) and porcine parvovirus (PPV) in mqPCR and encephalomyocarditis virus (EMCV) and Japanese encephalitis virus (JEV) in reverse transcription mqPCR (mRT-qPCR). A total of 150 aborted fetus samples collected from 2020 to 2022 were analyzed. Porcine reproductive and respiratory syndrome virus was the most prevalent (49/150 32.7%), followed by porcine circovirus type 2 (31/150, 20.7%), and PPV1 (7/150, 4.7%), whereas ADV, EMCV, and JEV were not detected. The newly developed mqPCR and mRT-qPCR could simultaneously detect and differentiate with high sensitivities and specificities. When applied to aborted fetuses, the newly developed mqPCR for PPV was 33.3% more sensitivities than the previously established diagnostic method. Amino acid analysis of the VP2 sequences of PPV isolates revealed considerable similarity to the highly pathogenic Kresse strain. This study successfully evaluated the prevalence of viral agents causing reproductive failure among swine in Korea, the developed mqPCR and mRT-qPCR methods could be utilized as effective and accurate diagnostic methods for the epidemiological surveillance of ADV, PPV, EMCV, and JEV.
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Affiliation(s)
- Go-Eun Shin
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Kyoung-Ki Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Bok-Kyung Ku
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Su Hong Oh
- Mediandiagnostics, Chuncheon, 24399, Gangwon-do, Republic of Korea.
| | - Sang-Ho Jang
- Mediandiagnostics, Chuncheon, 24399, Gangwon-do, Republic of Korea.
| | - Bokyu Kang
- Mediandiagnostics, Chuncheon, 24399, Gangwon-do, Republic of Korea.
| | - Hye-Young Jeoung
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
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Pegu SR, Deb R, Das PJ, Sengar GS, Yadav AK, Rajkhowa S, Paul S, Gupta VK. Development of multiplex PCR assay for simultaneous detection of African swine fever, porcine circo and porcine parvo viral infection from clinical samples. Anim Biotechnol 2023; 34:1883-1890. [PMID: 35343866 DOI: 10.1080/10495398.2022.2053698] [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] [Indexed: 11/01/2022]
Abstract
A diagnostic method for simultaneously detecting and distinguishing African Swine Fever (ASF), porcine circovirus type 2 (PCV2), and porcine parvovirus (PPV) in clinical specimens is critical for differential diagnosis, monitoring, and control in the field. Three primer pairs were designed and used to create a multiplex PCR assay. In addition, 356 porcine post mortem tissue samples from various parts of India's North Eastern region were tested by the developed multiplex PCR assay to demonstrate its accuracy. Using the designed primers, each of the ASF, PCV2 and PPV target genes was amplified, but no other porcine virus genes were detected. The assay's limit of detection was 102 copies/µl of PCV2, PPV, or ASFV. The detection of PCV2, PPV, and ASF in postmortem tissue samples revealed that they are co-circulating in India's North-Eastern region. The percentage positivity (PP) for PCV2, PPV and ASF single infection were 7.02% (25/356), 3.93% (14/356), and 3.37% (12/356), respectively, while the PP for PCV2& PPV co-infection was 2.80% (10/356), ASF & PCV2 co infection was 1.4% (5/356) and the ASF, PPV& PCV2 co-infection was1.40% (5/356). The results also indicate that the ASF can infect pigs alongside PCV and PPV.
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Affiliation(s)
| | - Rajib Deb
- ICAR-National Research Centre on Pig, Guwahati, Assam
| | | | | | | | | | - Souvik Paul
- ICAR-National Research Centre on Pig, Guwahati, Assam
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Flores-Contreras EA, Carrasco-González JA, Linhares DCL, Corzo CA, Campos-Villalobos JI, Henao-Díaz A, Melchor-Martínez EM, Iqbal HMN, González-González RB, Parra-Saldívar R, González-González E. Emergent Molecular Techniques Applied to the Detection of Porcine Viruses. Vet Sci 2023; 10:609. [PMID: 37888561 PMCID: PMC10610968 DOI: 10.3390/vetsci10100609] [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: 07/28/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | | | - Daniel C. L. Linhares
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Cesar A. Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA;
| | | | | | - Elda M. Melchor-Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Reyna Berenice González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Everardo González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
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Maity HK, Samanta K, Deb R, Gupta VK. Revisiting Porcine Circovirus Infection: Recent Insights and Its Significance in the Piggery Sector. Vaccines (Basel) 2023; 11:1308. [PMID: 37631876 PMCID: PMC10457769 DOI: 10.3390/vaccines11081308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
Porcine circovirus (PCV), a member of the Circoviridae family within the genus Circovirus, poses a significant economic risk to the global swine industry. PCV2, which has nine identified genotypes (a-i), has emerged as the predominant genotype worldwide, particularly PCV2d. PCV2 has been commonly found in both domestic pigs and wild boars, and sporadically in non-porcine animals. The virus spreads among swine populations through horizontal and vertical transmission routes. Despite the availability of commercial vaccines for controlling porcine circovirus infections and associated diseases, the continuous genotypic shifts from a to b, and subsequently from b to d, have maintained PCV2 as a significant pathogen with substantial economic implications. This review aims to provide an updated understanding of the biology, genetic variation, distribution, and preventive strategies concerning porcine circoviruses and their associated diseases in swine.
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Affiliation(s)
- Hemanta Kumar Maity
- Department of Avian Science, Faculty of Veterinary & Animal Science, West Bengal University of Animal & Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Kartik Samanta
- Department of Avian Science, Faculty of Veterinary & Animal Science, West Bengal University of Animal & Fishery Sciences, Kolkata 700037, West Bengal, India
| | - Rajib Deb
- ICAR-National Research Center on Pig, Rani, Guwahati 781131, Assam, India
| | - Vivek Kumar Gupta
- ICAR-National Research Center on Pig, Rani, Guwahati 781131, Assam, India
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Li M, Lv Y, Cui D, Xu Y, Lin M, Zhang X, Wang Y, Shen C, Xie J. Development and clinical validation of a one-step pentaplex real-time reverse transcription PCR assay for detection of hepatitis virus B, C, E, Treponema pallidum, and a human housekeeping gene. BMC Infect Dis 2023; 23:358. [PMID: 37231355 DOI: 10.1186/s12879-023-08240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND With the safety of blood transfusion being a major public health concern, the development of a rapid, sensitive, specific, and cost-effective multiplex PCR assay for simultaneous detection of hepatitis B virus(HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and Treponema pallidum(T. pallidum) in blood is crucial. METHODS Five primer pairs and probes were designed towards conserved regions of target genes and used to establish a one-step pentaplex real-time reverse transcription PCR(qRT-PCR) assay for simultaneous detection of HBV, HCV, HEV, T. pallidum, and RNase P(housekeeping gene), providing sample quality check. The clinical performance of the assay was further determined with 2400 blood samples from blood donors and patients in Zhejiang province, and compared the results with commercial singleplex qPCR and serological assays. RESULTS The 95% limit of detection(LOD) of HBV, HCV, HEV, and T. pallidum were 7.11 copies/µL, 7.65 copies/µL, 8.45 copies/µL, and 9.06 copies/µL, respectively. Moreover, the assay has good specificity and precision. Compared to the singleplex qPCR assay, the novel assay for detecting HBV, HCV, HEV, and T. pallidum presented 100% clinical sensitivity, specificity, and consistency. Several discrepant results between serological and pentaplex qRT-PCR assays were found. Of 2400 blood samples, there were 2(0.08%) HBsAg positive samples, 3(0.13%) anti-HCV positive samples, 29(1.21%) IgM anti-HEV positive samples and 6(0.25%) anti-T. pallidum positive samples proven negative in nucleic acid detection. 1(0.04%) HBV DNA positive sample and 1(0.04%) HEV RNA positive sample were detected negative by serological testing. CONCLUSIONS The developed pentaplex qRT-PCR is the first assay on simultaneous, sensitive, specific, and reproducible detection of HBV, HCV, HEV, T. pallidum, and RNase P in a single tube. It could detect pathogens in blood during the window period of infection and is a good tool for effectively screening blood donors and early clinical diagnosis.
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Affiliation(s)
- Miaomiao Li
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yan Lv
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yushan Xu
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Mengjiao Lin
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | | | - Yongjun Wang
- Key Laboratory of Blood Safety Research of Zhejiang Province, Zhejiang Province Blood Center, Hangzhou, 310052, China
| | - Cuifen Shen
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China.
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Wang J, Zhu X, Yin D, Cai C, Liu H, Yang Y, Guo Z, Yin L, Shen X, Dai Y, Pan X. Rapid and Easy-Read Porcine Circovirus Type 4 Detection with CRISPR-Cas13a-Based Lateral Flow Strip. Microorganisms 2023; 11:microorganisms11020354. [PMID: 36838319 PMCID: PMC9967505 DOI: 10.3390/microorganisms11020354] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
First identified as a new circovirus in Hunan Province in China in 2019, porcine circovirus (PCV4) is now widely detected in other Chinese provinces and South Korea. In recent years, the virus has threatened pig health and operations in the pig industry. Hence, early PCV4 detection and regular surveillance are required to control the spread of infection and prevent collateral damage to the industry. Due to PCV4 being difficult to isolate in vitro, molecular detection methods, such as conventional PCR and real-time PCR, and serological assays are currently the main methods used for the detection of PCV4 infection. However, they are time-consuming, labor-intensive, and complex and require professional personnel. To facilitate rapid pen-side PCV4 diagnoses, we used clustered regularly interspaced short palindromic repeats (CRISPR) and Cas13a technology to develop a quick testing kit. Five recombinase-aided amplification (RPA) primer sets were designed based on the conserved PCV4-Cap gene nucleotide region, which were used to determine several key lateral flow strip (LFD) characteristics (sensitivity, specificity, and accuracy). The results showed that the RPA-Cas13a-LFD reaction could detect PCV4 within 1.5 h in genomic DNA harboring a minimum of a single copy. Furthermore, the assay showed good specificity and absence of cross-reactivity with PCV2, PCV3, or other porcine viruses. When we tested 15 clinical samples, a high accuracy was also recorded. Therefore, we successfully developed a detection assay that was simple, fast, accurate, and suitable for on-site PCV4 testing.
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Affiliation(s)
- Jieru Wang
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojie Zhu
- China Institute of Veterinary Drug Control, Beijing 100000, China
| | - Dongdong Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chang Cai
- China-Australian Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China
| | - Hailong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Zishi Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xuehuai Shen
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Yin Dai
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence: (Y.D.); (X.P.)
| | - Xiaocheng Pan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Sciences, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence: (Y.D.); (X.P.)
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Parthiban S, Ramesh A, Dhinakar Raj G, Karuppannan AK, Hemalatha S, Parthiban M, Ravishankar C, Senthilkumar K, Balasubramaniyam D. Molecular evidence of porcine circovirus 3 infection in swine: first report in southern India. Virusdisease 2022; 33:284-290. [PMID: 36277416 PMCID: PMC9481802 DOI: 10.1007/s13337-022-00778-8] [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: 05/09/2022] [Accepted: 07/02/2022] [Indexed: 11/29/2022] Open
Abstract
The present study examined 434 field samples including serum (n = 273), swabs from natural orifices (n = 52) and postmortem tissue samples (n = 109) from both suspected and asymptomatic swine from Andhra Pradesh, Karnataka, Kerala, Pondicherry, Tamil Nadu, and Telangana states in southern India. All the samples were processed for molecular screening of PCV3 by specific PCR assay. Overall molecular positivity rate of PCV3 was found to be 0.7% in southern India with one sample positive from each state of Tamil Nadu, Kerala and Telangana. All the three PCR positive PCV3 samples are detected from reproductive failures and were processed and propagated in PK15 cell line for virus isolation. Out of 3 samples processed, one (INDKL9PK76) PCV3 isolate could be obtained in this study and it was confirmed by specific PCR at third and fifth passage levels. Sequencing of PCV3 positive PCR amplicon (INDKL9PK76) revealed 1004 nucleotides and BLAST analysis confirmed partial sequence of the PCV3 genome. The aligned contig sequence was submitted to GenBank under the accession number of MW627201. PCV3 sequence in this study revealed 99% homology with PCV3 isolates from Europe and China. Phylogentic analysis of the PCV3 isolate-INDKL9PK76 sequence along with established PCV3 genotypes revealed clustering within PCV3 genotypes. Characterization of PCV3 (INDKL9PK76) isolate based on deduced amino acid composition of PCV3-capsid protein revealed "A" (alanine) and "R" (arginine) at 24th and 27th residues respectively confirming the incidence of PCV3a genotype. This study evidences PCV3 associated reproductive failure in domestic pigs for the first time in southern India.
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Affiliation(s)
- S. Parthiban
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College Campus, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600 007 India
| | - A. Ramesh
- Vaccine Research Centre-Viral Vaccines, CAHS, MMC, Chennai, 600 051 India
| | - G. Dhinakar Raj
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College Campus, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600 007 India
| | | | - S. Hemalatha
- Department of Veterinary Pathology, MVC, Chennai, 600 007 India
| | - M. Parthiban
- Department of Animal Biotechnology, Faculty of Basic Sciences, Madras Veterinary College Campus, Tamil Nadu Veterinary and Animal Sciences University, Chennai, 600 007 India
| | - Chintu Ravishankar
- Department of Veterinary Microbiology, COVAS, Kerala Veterinary and Animal Sciences University, Pookode, India
| | - K. Senthilkumar
- Post Graduate Research Institute in Animal Sciences, Kattupakkam, 603 203 India
| | - D. Balasubramaniyam
- Post Graduate Research Institute in Animal Sciences, Kattupakkam, 603 203 India
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The Prevalence and Genetic Diversity of PCV3 and PCV2 in Colombia and PCV4 Survey during 2015–2016 and 2018–2019. Pathogens 2022; 11:pathogens11060633. [PMID: 35745487 PMCID: PMC9228467 DOI: 10.3390/pathogens11060633] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Four genotypes of circovirus have been recognized in swine, with PCV2 and PCV3 being the most associated with clinical manifestations, while PCV4 does not have a defined disease. In addition, PCV2 is associated with different syndromes grouped as diseases associated with porcine circovirus (PCVAD), while PCV3 causes systemic and reproductive diseases. In the present study, we retrospectively detected PCV2, PCV3, and PCV4 in Colombia during two periods: A (2015–2016) and B (2018–2019). During period A, we evaluated stool pools from the 32 Colombian provinces, finding a higher prevalence of PCV3 compared to PCV2 as well as PCV2/PCV3 co-infection. Furthermore, we determined that PCV3 had been circulating since 2015 in Colombia. Regarding period B, we evaluated sera pools and tissues from abortions and stillborn piglets from the five provinces with the highest pig production. The highest prevalence found was for PCV3 in tissues followed by sera pools, while PCV2 was lower and only in sera pools. In addition, PCV2/PCV3 co-infection in sera pools was also found for this period. The complete genome sequences of PCV3 and PCV3-ORF2 placed the Colombian isolates within clade 1 as the majority in the world. For PCV2, the predominant genotype currently in Colombia is PCV2d. Likewise, in some PCV3-ORF2 sequences, a mutation (A24V) was found at the level of the Cap protein, which could be involved in PCV3 immunogenic recognition. Regarding PCV4, retrospective surveillance showed that there is no evidence of the presence of this virus in Colombia.
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Five years of porcine circovirus 3: what have we learned about the clinical disease, immune pathogenesis, and diagnosis. Virus Res 2022; 314:198764. [DOI: 10.1016/j.virusres.2022.198764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/24/2022]
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Zhang J, Li M, Ou Y, Chen D, Ding Y, Zhang W, Li Y, Hou Q, Li X, Zhou L, Podgorska K, Zaberezhny AD, Szczotka-Bochniarz A, Liu Y, Wang Y. Development and Clinical Validation of a Potential Penside Colorimetric Loop-Mediated Isothermal Amplification Assay of Porcine Circovirus Type 3. Front Microbiol 2022; 12:758064. [PMID: 35095787 PMCID: PMC8790240 DOI: 10.3389/fmicb.2021.758064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine circovirus type 3 (PCV3), a novel circovirus, imposes great burdens on the global pig industry. The penside tests for detecting PCV3 are critical for assessing the epidemiological status and working out disease prevention and control programs due to the unavailability of a commercial vaccine. A one-step molecular assay based on visual loop-mediated isothermal amplification (vLAMP) was developed for simple and rapid detection of PCV3. We compared its sensitivity and specificity with TaqMan quantitative real-time polymerase chain reaction (qPCR) and applied the developed assay in the epidemiological study of (n = 407) pooled swine sera collected from almost the entire mainland China during the years 2017–2018. We also explored the feasibility of the vLAMP assay for detecting raw samples without a prior DNA isolation step to expand its application capability. Results showed that the vLAMP assay could reliably detect the PCV3 cap gene with a detection limit of 10 DNA copies equal to that of the Taqman qPCR assay. In the epidemiological study, the PCV3 positive detection rate for 407 swine pooled sera detected by the vLAMP assay was 37.35% (152/407), whereas it was 39.01% (159/407) for Taqman qPCR. For the detection method without genome extraction, the results kept satisfactory specificity (100%) but displayed lower sensitivity (100% for CT < 32), indicating the direct detection is not sensitive enough to discriminate the samples with low viral loads. The one-step vLAMP is a convenient, rapid, and cost-effective diagnostic for penside detection and will enable the epidemiological surveillance of PCV3, which has widely spread in mainland China.
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Affiliation(s)
- Jie Zhang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Miaomiao Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yunwen Ou
- Animal Disease Prevention and Control Center of Kaijiang County, Dazhou, China
| | - Danian Chen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yaozhong Ding
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Weibing Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yanjun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qian Hou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Luoyi Zhou
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Katarzyna Podgorska
- Department of Swine Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Alexei D Zaberezhny
- Federal State Budgetary Institution, All-Russian Research and Technological Institute of Biological Industry (VNITIBP), Moscow, Russia
| | | | - Yongsheng Liu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yang Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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11
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Manessis G, Mourouzis C, Griol A, Zurita-Herranz D, Peransi S, Sanchez C, Giusti A, Gelasakis AI, Bossis I. Integration of Microfluidics, Photonic Integrated Circuits and Data Acquisition and Analysis Methods in a Single Platform for the Detection of Swine Viral Diseases. Animals (Basel) 2021; 11:ani11113193. [PMID: 34827925 PMCID: PMC8614420 DOI: 10.3390/ani11113193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The control of several swine viral diseases relies mainly on evidence-based prevention protocols due to the lack of effective treatments or vaccines. To design these protocols, laboratory investigation of viral infections is critical to confirm their occurrence and determine their epizootiology. However, laboratory confirmation of certain swine viral diseases is a time-consuming and labor-intensive process, requiring scientific personnel with relevant expertise. Point-of-Care (POC) diagnostics are tests and devices that provide clinically relevant information on-site, facilitating decision-makers to swiftly take countermeasures for disease control. In the present study, novel photonic biosensors were integrated into a single, automated POC device that can record and analyze changes in the sensors’ refractive index, allowing the detection of Porcine Parvovirus (PPV) and Porcine Circovirus 2 (PCV-2) in oral fluids within 75 min. The objective of this work was to validate this device using reference and field samples (oral fluids). The system was able to detect PPV and PCV-2 in oral fluid samples satisfactorily. The device can be directly deployed in farms for the fast diagnosis of these diseases, contributing to farm biosecurity. Abstract Viral diseases challenge the health and welfare of pigs and undermine the sustainability of swine farms. Their efficient control requires early and reliable diagnosis, highlighting the importance of Point of Care (POC) diagnostics in veterinary practice. The objective of this study was to validate a novel POC system that utilizes Photonic Integrated Circuits (PICs) and microfluidics to detect swine viral pathogens using oral fluids and Porcine Parvovirus (PPV) and Porcine Circovirus 2 (PCV-2) as proofs of concept. The sensitivity and specificity of the device were calculated for both viruses, and Receiver Operating Characteristic (ROC) curves were drawn. PPV had an Area Under Curve (AUC) value of 0.820 (95% CI: 0.760 to 0.880, p < 0.0001), and its optimal efficiency threshold of detection shifts was equal to 4.5 pm (68.6% sensitivity, 77.1% specificity and Limit of Detection (LOD) value 106 viral copies/mL). PCV-2 had an AUC value of 0.742 (95% CI: 0.670 to 0.815, p < 0.0001) and an optimal efficiency threshold of shifts equal to 6.5 pm (69.5% sensitivity, 70.3% specificity and LOD 3.3 × 105 copies/mL). In this work, it was proven that PICs can be exploited for the detection of swine viral diseases. The novel device can be directly deployed on farms as a POC diagnostics tool.
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Affiliation(s)
- Georgios Manessis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, Agricultural University of Athens (AUA), Iera Odos 75 Str., 11855 Athens, Greece; (G.M.); (A.I.G.)
| | - Christos Mourouzis
- CyRIC, Cyprus Research and Innovation Centre Ltd., 28th Octovriou Ave 72, Off. 301, Engomi, Nicosia 2414, Cyprus; (C.M.); (A.G.)
| | - Amadeu Griol
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n Building 8F, 46022 Valencia, Spain; (A.G.); (D.Z.-H.)
| | - David Zurita-Herranz
- Nanophotonics Technology Center, Universitat Politècnica de València, Camino de Vera s/n Building 8F, 46022 Valencia, Spain; (A.G.); (D.Z.-H.)
| | - Sergio Peransi
- Lumensia Sensors S.L., Camino de Vera, s/n, K-Access, Building 8F 3th-Floor, 46022 Valencia, Spain; (S.P.); (C.S.)
| | - Carlos Sanchez
- Lumensia Sensors S.L., Camino de Vera, s/n, K-Access, Building 8F 3th-Floor, 46022 Valencia, Spain; (S.P.); (C.S.)
| | - Alessandro Giusti
- CyRIC, Cyprus Research and Innovation Centre Ltd., 28th Octovriou Ave 72, Off. 301, Engomi, Nicosia 2414, Cyprus; (C.M.); (A.G.)
| | - Athanasios I. Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, Agricultural University of Athens (AUA), Iera Odos 75 Str., 11855 Athens, Greece; (G.M.); (A.I.G.)
| | - Ioannis Bossis
- Laboratory of Animal Husbandry, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Correspondence: ; Tel./Fax: +30-2310991739
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12
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Kaiser FK, Wiedemann A, Kühl B, Menke L, Beineke A, Baumgärtner W, Wohlsein P, Rigbers K, Becher P, Peters M, Osterhaus ADME, Ludlow M. Swinepox Virus Strains Isolated from Domestic Pigs and Wild Boar in Germany Display Altered Coding Capacity in the Terminal Genome Region Encoding for Species-Specific Genes. Viruses 2021; 13:v13102038. [PMID: 34696467 PMCID: PMC8538704 DOI: 10.3390/v13102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Swinepox virus (SWPV) is a globally distributed swine pathogen that causes sporadic cases of an acute poxvirus infection in domesticated pigs, characterized by the development of a pathognomonic proliferative dermatitis and secondary ulcerations. More severe disease with higher levels of morbidity and mortality is observed in congenitally SWPV-infected neonatal piglets. In this study, we investigated the evolutionary origins of SWPV strains isolated from domestic pigs and wild boar. Analysis of whole genome sequences of SWPV showed that at least two different virus strains are currently circulating in Germany. These were more closely related to a previously characterized North American SWPV strain than to a more recent Indian SWPV strain and showed a variation in the SWPV-specific genome region. A single nucleotide deletion in the wild boar (wb) SWPV strain leads to the fusion of the SPV019 and SPV020 open reading frames (ORFs) and encodes a new hypothetical 113 aa protein (SPVwb020-019). In addition, the domestic pig (dp) SWPV genome contained a novel ORF downstream of SPVdp020, which encodes a new hypothetical 71aa protein (SPVdp020a). In summary, we show that SWPV strains with altered coding capacity in the SWPV specific genome region are circulating in domestic pig and wild boar populations in Germany.
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Affiliation(s)
- Franziska K. Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (L.M.); (A.D.M.E.O.)
| | - Anastasia Wiedemann
- Institute for Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (A.W.); (P.B.)
| | - Bianca Kühl
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (B.K.); (A.B.); (W.B.); (P.W.)
| | - Laura Menke
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (L.M.); (A.D.M.E.O.)
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (B.K.); (A.B.); (W.B.); (P.W.)
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (B.K.); (A.B.); (W.B.); (P.W.)
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (B.K.); (A.B.); (W.B.); (P.W.)
| | - Kerstin Rigbers
- Chemisches und Veterinäruntersuchungsamt Karlsruhe, 76187 Karlsruhe, Germany;
| | - Paul Becher
- Institute for Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (A.W.); (P.B.)
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany;
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (L.M.); (A.D.M.E.O.)
| | - Martin Ludlow
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (L.M.); (A.D.M.E.O.)
- Correspondence: ; Tel.: +49-51-1953-6112
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13
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Chen S, Zhang L, Li X, Niu G, Ren L. Recent Progress on Epidemiology and Pathobiology of Porcine Circovirus 3. Viruses 2021; 13:v13101944. [PMID: 34696373 PMCID: PMC8538958 DOI: 10.3390/v13101944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/27/2022] Open
Abstract
The recently discovered porcine circovirus 3 (PCV3) belongs to the Circovirus genus of the Circoviridae family together with the other three PCVs, PCV1, PCV2, and PCV4. As reported, PCV3 can infect pig, wild boar, and several other intermediate hosts, resulting in single or multiple infections in the affected animal. The PCV3 infection can lead to respiratory diseases, digestive disorders, reproductive disorders, multisystemic inflammation, and immune responses. Up to now, PCV3 infection, as well as the disease caused by PCV3, has been reported in many swine farms worldwide with high positive rates, which indicates that the virus may be another important pathogen in the swine industry. Therefore, we reviewed the current progress on epidemiology and pathobiology of PCV3, which may provide the latest knowledge of the virus and PCV3-related diseases.
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14
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Bian Z, Cai R, Jiang Z, Song S, Li Y, Chu P, Zhang K, Yang D, Gou H, Li C. Single Multiple Cross Displacement Amplification for Rapid and Real-Time Detection of Porcine Circovirus 3. Front Vet Sci 2021; 8:726723. [PMID: 34540937 PMCID: PMC8448386 DOI: 10.3389/fvets.2021.726723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2016, a novel porcine circovirus, PCV3, has been infecting pigs, causing significant economic losses to the pig industry. In recent years, the infection rate of PCV3 has been increasing, and thus rapid and accurate detection methods for PCV3 are essential. In this study, we established a novel probe-based single multiple cross displacement amplification (P-S-MCDA) method for PCV3. The method was termed as P-S-MCDA. The P-S-MCDA uses seven primers to amplify the capsid gene, and the assay can be performed at 60°C for 30 min, greatly shortening the reaction time. The results of P-S-MCDA can not only be monitored in real time through fluorescence signals but also be determined by observing the fluorescence of the reaction tubes using a smartphone-based cassette. This method demonstrated good specificity and the same sensitivity as qPCR, with a minimum detection limit of 10 copies. In 139 clinical samples, the coincidence rate with qPCR was 100%. The P-S-MCDA can be widely applied in PCV3 detection in laboratories or in rural areas.
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Affiliation(s)
- Zhibiao Bian
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Rujian Cai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Zhiyong Jiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Yan Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Pinpin Chu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Kunli Zhang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Dongxia Yang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Hongchao Gou
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
| | - Chunling Li
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, China.,Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China.,Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou, China
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15
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Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing. Viruses 2021; 13:v13081608. [PMID: 34452472 PMCID: PMC8402840 DOI: 10.3390/v13081608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
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16
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Yang K, Dong L, Duan Z, Guo R, Zhou D, Liu Z, Liang W, Liu W, Yuan F, Gao T, Tian Y. Expression profile of long non-coding RNAs in porcine lymphnode response to porcine circovirus type 2 infection. Microb Pathog 2021; 158:105118. [PMID: 34339795 DOI: 10.1016/j.micpath.2021.105118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022]
Abstract
Porcine circovirus type 2 (PCV2) can cause various clinical diseases in pigs, resulting in huge losses for the pig farms all over the world. In order to develop a new strategy to control PCV2, it is essential to understand its mechanisms firstly, especially PCV2 interferes with the host's innate immunity. In the present study, lncRNA and mRNA expression profiles in porcine lymphnode response to PCV2 infection were deeply sequenced and analyzed. 3271 novel lncRNAs were identified in all. 1898 mRNAs and 282 lncRNAs showed differential expression between control and PCV2-infected groups. The bioinformatics analysis including lncRNA-mRNA co-expression network construction, as well as GO and KEGG pathway analysis focused on the DEGs was carried out. The results indicated that lncRNAs might participate in PCV2 infection-induced the pathogenesis of immunosuppression through regulating the host's immune responses, biological regulation, response to stimulus, cellular component organization or biogenesis and metabolism. And these differentially expressed lncRNAs might play important roles in response to PCV2 infection in the host's innate immune system. These findings provided a large-scale survey of dysregulated lncRNAs after PCV2 infection, especially the lncRNAs responded to host's innate immune within the lymphnode. This study will provide a novel insight into the lncRNAs' functions and the possible immunosuppressive mechanism induced by PCV2 infection. However, further research will be required to verify the characteristic function of the dysregulated lncRNAs.
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Affiliation(s)
- Keli Yang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China; Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Wuhan, 430064, Hubei, PR China.
| | - Ling Dong
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhengying Duan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Rui Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Danna Zhou
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Zewen Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Wan Liang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Wei Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Ting Gao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China
| | - Yongxiang Tian
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Ministry of Agriculture and Rural Affairs; Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, 430064, PR China.
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17
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Pathogenic Characterization of a Porcine Circovirus Type 3 Isolate from Heilongjiang, China. DISEASE MARKERS 2021; 2021:9434944. [PMID: 34257749 PMCID: PMC8253634 DOI: 10.1155/2021/9434944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/30/2021] [Indexed: 12/23/2022]
Abstract
The clinical outcome of porcine circovirus 3 (PCV3) infection is still controversial. Herein, a novel PCV3 isolate (PCV3-China/DB-1/2017) with the molecular characterization of 24A and 27K in the Cap protein was used to inoculate three-week-old cesarean-derived, colostrum-deprived piglets. The nine PCV3 DB-1 inoculated piglets exhibited no obvious clinical symptoms or macroscopic lesions. PCV3 displayed a broad histotropism, including the heart, liver, spleen, lung, kidney, brain, lymph nodes, and tonsil, and the lungs and lymph nodes contained a higher quantity of viral genomes compared to that of the other organs. From 7 days after PCV3 DB-1 inoculation, the piglets showed obvious IgG antibody responses against PCV3 rCap-VLPs. The cumulative results demonstrated that PCV3 trend to low pathogenicity.
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18
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Nan P, Wen D, Opriessnig T, Zhang Q, Yu X, Jiang Y. Novel universal primer-pentaplex PCR assay based on chimeric primers for simultaneous detection of five common pig viruses associated with diarrhea. Mol Cell Probes 2021; 58:101747. [PMID: 34116142 DOI: 10.1016/j.mcp.2021.101747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/18/2022]
Abstract
Viral pathogens associated with diarrhea in pigs include porcine circovirus 2 (PCV2), porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus A (RVA) and C (RVC) among others. In this study, a novel universal primer-based pentaplex PCR (UP-M-PCR) assay was developed for simultaneous detection and differentiation of these five viruses. The assay uses a short-cycle multiplex amplification by chimeric primers (CP), which are virus specific, with a tail added at the 5' end of the universal primer (UP), followed by universal amplification using UPs and a regular cycle amplification. Five universal primers with CPs (UP1-5) were designed and evaluated in an UP-based single PCR (UP-S-PCR). All five UPs were found to work efficiently and UP2 exhibited the best performance. After system optimizations, the analytical sensitivity of the UP-M-PCR, using plasmids containing the specific viral target fragments, was 5 copies/reaction for each of the five viruses irrespective of presence of a single or multiple viruses in the reaction. No cross-reaction was observed with other non-target viruses. When 273 fecal samples from clinically healthy pigs were tested, the assay sensitivity was 90.9-100%, the specificity was 98.0-100%, and the agreement rate with the UP-S-PCR was 98.5-99.6% with a Kappa value being 0.95-0.98. In summary, the UP-M-PCR developed here is a rapid and highly sensitive and specific detection method that can be used to demonstrate mixed infections in pigs with diarrhea.
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Affiliation(s)
- Pei Nan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Dan Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Qiuya Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xiaoya Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
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19
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Park KH, Chae C. The prevalence of porcine circovirus type 2e (PCV2e) in Korean slaughter pig lymph nodes when compared with other PCV2 genotypes. Transbound Emerg Dis 2021; 68:3043-3047. [PMID: 33406315 DOI: 10.1111/tbed.13975] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/12/2020] [Accepted: 01/01/2021] [Indexed: 12/18/2022]
Abstract
The objective of this study was to determine the prevalence of porcine circovirus type 2e (PCV2e) over other PCV2 genotypes (a, b, c and d) from the lymph nodes of 1,550 randomly selected slaughter pigs. Samples were obtained at a rate of five samples per farm from 310 farms between January 2018 and May 2020. Of the 1,550 lymph node samples, PCV2 DNA was detected in 762 (49.20%) samples. Among the 762 PCV2 DNA-positive samples, a single PCV2 genotype was detected in 744 samples, while multiple PCV2 genotypes were only detected in 18 samples. Of the 744 single infection cases, PCV2d was the most prevalent with 709 cases, followed by PCV2b (15 cases), PCV2a (14 cases) and PCV2e (6 cases). Of the 18 multiple infection cases, PCV2a+PCV2d was the most prevalent (7 cases) followed by PCV2b+PCV2d (3 cases), PCV2b+PCV2e (3 cases), PCV2a+PCV2b+PCV2d (3 cases) and PCV2a+PCV2b (2 cases). No PCV2c was detected in any of the single or multiple infection cases. The results of prevalence identified PCV2d as the current dominant genotype, while the newly emerging PCV2e maintained the lowest prevalence among the evaluated swine farms.
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Affiliation(s)
- Kee Hwan Park
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Chanhee Chae
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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20
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Chen N, Xiao Y, Li X, Li S, Xie N, Yan X, Li X, Zhu J. Development and application of a quadruplex real-time PCR assay for differential detection of porcine circoviruses (PCV1 to PCV4) in Jiangsu province of China from 2016 to 2020. Transbound Emerg Dis 2020; 68:1615-1624. [PMID: 32931644 DOI: 10.1111/tbed.13833] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/17/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022]
Abstract
To date, four species of porcine circoviruses (PCVs), including PCV1-4, have been reported to exist in the clinical cases. Fast and effective differential detection is critical to monitor the infection and co-infection status of PCVs for adopting reliable control strategies. However, currently available methods cannot simultaneously differentiate the four species of PCV strains. In this study, a quadruplex real-time PCR assay based on TaqMan probes was developed for differential detection of PCV1-4. The new quadruplex real-time PCR assay exhibited satisfied specificity, sensitivity, repeatability and reproducibility. In addition, the new assay was applied to the detection of 120 clinical samples collected from 2016 to 2020 in Jiangsu province of China and compared with previously reported PCV1-4 singleplex conventional PCR assays. Based on the clinical performance, the results from the quadruplex real-time PCR and conventional PCR assays showed 100% agreement. A total of 47 samples were detected as PCV positive by the quadruplex real-time PCR assay, including 1, 2, 1 samples were co-infected with PCV1 and PCV4, PCV2 and PCV3, PCV2 and PCV4, respectively. Full-length ORF2 sequencing and phylogenetic analysis supported the real-time PCR results that 5, 34, 8 and 4 of the 51 PCV sequences were PCV1, PCV2, PCV3 and PCV4, respectively. This study provides a promising alternative tool for rapid differential detection of PCVs and confirms the coexistence of all species of PCV1-4 strains in Jiangsu province in recent years.
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Affiliation(s)
- Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, P.R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Comparative Medicine Research Institute, Yangzhou University, Yangzhou, P.R. China
| | - Yanzhao Xiao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Xinshuai Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Shubin Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Ningjun Xie
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Xilin Yan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China
| | - Xiangdong Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, P.R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Comparative Medicine Research Institute, Yangzhou University, Yangzhou, P.R. China
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, P.R. China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou, P.R. China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.,Comparative Medicine Research Institute, Yangzhou University, Yangzhou, P.R. China
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Development of a SYBR green I-based duplex real-time PCR assay for detection of pseudorabies virus and porcine circovirus 3. Mol Cell Probes 2020; 53:101593. [PMID: 32387303 DOI: 10.1016/j.mcp.2020.101593] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/28/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023]
Abstract
In the present study, a specific and reliable duplex SYBR green I-based quantitative real-time polymerase chain reaction assay was established to detect pseudorabies virus (PRV) and porcine circovirus 3 (PCV3) simultaneously. Viral genomes of PRV and PCV3 in one specimen were identified by their different melting temperatures with melting peaks at 87 °C and 81 °C for PRV and PCV3 respectively, whilst other non-targeted swine pathogens exhibited no fluorescent signals. The assay displayed a high degree of linearity (R2 > 0.997), and the limits of detection were 37.8 copies/μL, 30.6 copies/μL and 60 copies/μL for PRV, PCV3 and the mixture of two recombinant plasmids, respectively. It had good repeatability and reproducibility, and the coefficients of variation in intra-batch and inter-batch assays were all less than 2.0%. In this research, the duplex assay was further evaluated using 117 clinical tissue specimens from diseased pigs in the field. The results revealed the infection rates of PRV and PCV3 were 23.08% (27/117) and 55.56% (65/117) respectively, and PRV and PCV3 co-infection rate was 14.53% (17/117). The assay could be utilized as a diagnostic tool with specificity, sensitivity, and reliability for molecular epidemiological surveillance of PRV and PCV3.
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