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Ye H, Wang X, Zhou L, Ge X, Gao P, Han J, Guo X, Wen K, Zhang Y, Yang H. Development of a triplex RT-RAA-LFA assay for the rapid differential diagnosis of porcine epidemic diarrhea virus, porcine deltacoronavirus and transmissible gastroenteritis virus. Microb Pathog 2024; 195:106885. [PMID: 39182857 DOI: 10.1016/j.micpath.2024.106885] [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: 07/11/2024] [Revised: 08/13/2024] [Accepted: 08/23/2024] [Indexed: 08/27/2024]
Abstract
Porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV) and transmissible gastroenteritis virus (TGEV) are three clinically common coronaviruses causing diarrhea in pigs, with indistinguishable clinical signs and pathological changes. Rapid, portable and reliable differential diagnosis of these three pathogens is crucial for the prompt implementation of appropriate control measures. In this study, we developed a triplex nucleic acid assay that combines reverse transcription recombinase-aided amplification (RT-RAA) with lateral flow assay (LFA) by targeting the most conserved genomic region in the ORF1b genes of PEDV, PDCoV and TGEV. The entire detection process of the triplex RT-RAA-LFA assay included 10-min nucleic acid amplification at 42 °C and 5-min visual LFA readout at room temperature. The assay could specifically differentiate PEDV, PDCoV and TGEV without cross-reaction with any other major swine pathogens. Sensitivity analysis showed that the triplex RT-RAA-LFA assay was able to detect the viral RNA extracted from the spiked fecal samples with the minimum of 1 × 100 TCID50 PEDV, 1 × 104 TCID50 PDCoV, and 1 × 102 TCID50 TGEV per reaction, respectively. Further analysis showed that the 95 % detection limit (LOD) of triplex RT-RAA-LFA for PEDV, PDCoV, and TGEV were 22, 478, and 205 copies of recombinant plasmids per reaction, respectively. The diagnostic performance of triplex RT-RAA-LFA was compared with that of PEDV, PDCoV and TGEV respective commercial real-time RT-PCR kits by testing 114 clinical rectal swab samples in parallel. The total diagnostic coincidence rates of triplex RT-RAA-LFA with real-time RT-PCR kits of PEDV, PDCoV and TGEV were 100 %, 99.1 % and 99.1 %, respectively, and their Kappa values were 1.00, 0.958 and 0.936, respectively. Collectively, the RT-RAA-LFA assay is a powerful tool for the rapid, portable, visual, and synchronous differential diagnosis of PEDV, PDCoV, and TGEV.
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Affiliation(s)
- Huan Ye
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xiaonan Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety, Beijing Laboratory for Food Quality and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Lei Zhou
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xinna Ge
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Peng Gao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jun Han
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xin Guo
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Detection Technology for Animal Derived Food Safety, Beijing Laboratory for Food Quality and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yongning Zhang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Hanchun Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China; Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
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Kim JH, Park J, Lee DK, Kim WI, Lyoo YS, Park CK, Kim HR. Prevalence and Genetic Characterization of Porcine Respiratory Coronavirus in Korean Pig Farms. Animals (Basel) 2024; 14:1698. [PMID: 38891745 PMCID: PMC11171391 DOI: 10.3390/ani14111698] [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: 05/14/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Porcine respiratory coronavirus (PRCV) is a member of the species Alphacoronavirus 1 within the genus Alphacoronavirus of the family Coronaviridae. A few studies have been conducted on the prevalence of PRCV since its first identification in 1997, but there have been no recent studies on the prevalence and genetic characterization of the virus in Korea. In this study, the seroprevalence of PRCV was determined in Korean pig farms using a commercially available TGEV/PRCV differential enzyme-linked immunosorbent assay kit. The farm-level seroprevalence of PRCV was determined to be 68.6% (48/70), similar to previous reports in Korea, suggesting that PRCV is still circulating in Korean pig herds nationwide. Among the 20 PRCV-seropositive farms tested in this study, PRCV RNAs were detected in 17 oral fluid samples (28.3%) from nine farms (45.0%), while TGEV RNAs were not detected in any sample. To investigate the genetic characteristics of Korean PRCV strains, genetic and phylogenetic analyses were conducted on PRCV spike gene sequences obtained in this study. The three Korean PRCV strains (KPRCV2401, KPRCV2402, and KPRCV2403) shared 98.5-100% homology with each other and 96.2-96.6% and 91.6-94.5% homology with European and American strains, respectively. A 224-amino acid deletion was found in the S gene of both Korean and European PRCVs but not in that of American PRCVs, suggesting a European origin for Korean PRCVs. Phylogenetic analysis showed that Korean PRCVs are more closely related to European PRCVs than American PRCVs but clustered apart from both, suggesting that Korean PRCV has evolved independently since its emergence in Korean PRCVs. The results of this study will help expand knowledge on the epidemiology and molecular biology of PRCV currently circulating in Korea.
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Affiliation(s)
- Ju-Han Kim
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea; (J.-H.K.); (Y.S.L.)
- Swine Medical Corporation, Sunjin Bridge Lab, Icheon 17332, Republic of Korea
| | - Jonghyun Park
- Institute for Veterinary Biomedical Science, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea; (J.P.); (D.-K.L.); (C.-K.P.)
- DIVA Bio Incorporation, Daegu 41519, Republic of Korea
| | - Dong-Kyu Lee
- Institute for Veterinary Biomedical Science, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea; (J.P.); (D.-K.L.); (C.-K.P.)
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea;
| | - Young S. Lyoo
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea; (J.-H.K.); (Y.S.L.)
| | - Choi-Kyu Park
- Institute for Veterinary Biomedical Science, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea; (J.P.); (D.-K.L.); (C.-K.P.)
| | - Hye-Ryung Kim
- Institute for Veterinary Biomedical Science, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea; (J.P.); (D.-K.L.); (C.-K.P.)
- DIVA Bio Incorporation, Daegu 41519, Republic of Korea
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3
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Sovová K, Vašíčková P, Valášek V, Výravský D, Očenášková V, Juranová E, Bušová M, Tuček M, Bencko V, Mlejnková HZ. SARS-CoV-2 wastewater surveillance in the Czech Republic: Spatial and temporal differences in SARS-CoV-2 RNA concentrations and relationship to clinical data and wastewater parameters. WATER RESEARCH X 2024; 23:100220. [PMID: 38628304 PMCID: PMC11017050 DOI: 10.1016/j.wroa.2024.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
This study presents the results of systematic wastewater monitoring of SARS-CoV-2 RNA and basic wastewater parameters from four different wastewater treatment plants (WWTPs) in the Czech Republic over the 2020-2022 epidemic. Two-step reverse-transcription quantitative PCR targeting genes encoding the N and Nsp12 proteins was employed to detect SARS-CoV-2 RNA loading in 420 wastewater samples. The results obtained were used to evaluate the potential of wastewater analysis for describing the epidemiological situation in cities of different sizes and determining temporal differences based on the prevailing SARS-CoV-2 variant. Strong correlations between the number of active and hospitalised COVID-19 cases in each WWTP catchment area and the concentration of SARS-CoV-2 RNA detected in the wastewater clearly demonstrated the suitability of this wastewater-based epidemiological approach for WWTPs of different sizes and characteristics, despite differences in SARS-CoV-2 variant waves, with some WWTPs showing high predictive potential. This study demonstrated on the data from the Czech Republic that targeted systematic monitoring of wastewater provides sufficiently robust data for surveillance of viral loads in sample populations, and thus contributes to preventing the spread of infection and subsequent introduction of appropriate measures.
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Affiliation(s)
- Kateřina Sovová
- T. G. Masaryk Water Research Institute p.r.i., Brno Branch, Mojmírovo náměstí 16, 612 00 Brno, Czech Republic
| | - Petra Vašíčková
- Masaryk University, Faculty of Science, Kotlářská 267/2, 611 37 Brno, Czech Republic
| | - Vojtěch Valášek
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - David Výravský
- T. G. Masaryk Water Research Institute p.r.i., Brno Branch, Mojmírovo náměstí 16, 612 00 Brno, Czech Republic
| | - Věra Očenášková
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - Eva Juranová
- T. G. Masaryk Water Research Institute, Podbabská 30, 160 00 Prague, Czech Republic
| | - Milena Bušová
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
| | - Milan Tuček
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
| | - Vladimír Bencko
- Charles University, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Studničkova 7, 128 00 Prague, Czech Republic
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Zarouri A, Barnes AMT, Aboubakr H, Thekkudan Novi V, Dong Q, Nelson A, Goyal S, Abbas A. A high-performance polymer composite column for coronavirus nucleic acid purification. Sci Rep 2024; 14:1138. [PMID: 38212439 PMCID: PMC10784286 DOI: 10.1038/s41598-024-51671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% specificity). The high specificity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.
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Affiliation(s)
- Akli Zarouri
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Aaron M T Barnes
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota Medical School, 689 23rd Ave SE, Minneapolis, MN, USA
| | - Hamada Aboubakr
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Qiuchen Dong
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA
| | - Andrew Nelson
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota Twin Cities, 420 Delaware Street SE, Minneapolis, MN, USA
| | - Sagar Goyal
- Department of Veterinary Population Medicine, University of Minnesota Twin Cities, 1333 Gortner Ave., Saint Paul, MN, USA
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota Twin Cities, 2004 Folwell Ave, Saint Paul, MN, USA.
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5
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Zarouri A, Barnes AMT, Aboubakr H, Novi VT, Dong Q, Nelson A, Goyal S, Abbas A. A High-Performance Polymer Composite Column for Coronavirus Nucleic Acid Purification. RESEARCH SQUARE 2023:rs.3.rs-3261727. [PMID: 37674719 PMCID: PMC10479450 DOI: 10.21203/rs.3.rs-3261727/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% selectivity). The high selectivity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.
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Mattei M, Pintó RM, Guix S, Bosch A, Arenas A. Analysis of SARS-CoV-2 in wastewater for prevalence estimation and investigating clinical diagnostic test biases. WATER RESEARCH 2023; 242:120223. [PMID: 37354838 PMCID: PMC10265495 DOI: 10.1016/j.watres.2023.120223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/10/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Here we analyze SARS-CoV-2 genome copies in Catalonia's wastewater during the Omicron peak and develop a mathematical model to estimate the number of infections and the temporal relationship between reported and unreported cases. 1-liter samples from 16 wastewater treatment plants were collected and used in a compartmental epidemiological model. The average correlation between genome copies and reported cases was 0.85, with an average delay of 8.8 days. The model estimated that 53% of the population was infected, compared to the 19% reported cases. The under-reporting was highest in November and December 2021. The maximum genome copies shed in feces by an infected individual was estimated to range from 1.4×108 gc/g to 4.4×108 gc/g. Our framework demonstrates the potential of wastewater data as a leading indicator for daily new infections, particularly in contexts with low detection rates. It also serves as a complementary tool for prevalence estimation and offers a general approach for integrating wastewater data into compartmental models.
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Affiliation(s)
- Mattia Mattei
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, School of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Alex Arenas
- Departament d'Enginyeria Informàtica i Matemàtiques, Universitat Rovira i Virgili, 43007 Tarragona, Spain; Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 99354, USA.
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Lazov CM, Papetti A, Belsham GJ, Bøtner A, Rasmussen TB, Boniotti MB. Multiplex Real-Time RT-PCR Assays for Detection and Differentiation of Porcine Enteric Coronaviruses. Pathogens 2023; 12:1040. [PMID: 37624000 PMCID: PMC10457881 DOI: 10.3390/pathogens12081040] [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: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
It is important to be able to detect and differentiate between distinct porcine enteric coronaviruses that can cause similar diseases. However, the existence of naturally occurring recombinant coronaviruses such as swine enteric coronavirus (SeCoV) can give misleading results with currently used diagnostic methods. Therefore, we have developed and validated three duplex real-time quantitative RT-PCR assays for the simultaneous detection of, and differentiation between, porcine epidemic diarrhea virus (PEDV) and SeCoV. Transmissible gastroenteritis virus (TGEV) is also detected by two out of these three assays. In addition, a novel triplex assay was set up that was able to detect and differentiate between these alphacoronaviruses and the porcine deltacoronavirus (PDCoV). The validated assays have low limits of detection, close to 100% efficiency, and were able to correctly identify the presence of PEDV and SeCoV in 55 field samples, whereas 20 samples of other pathogens did not give a positive result. Implementing one or more of these multiplex assays into the routine diagnostic surveillance for PEDV will ensure that the presence of SeCoV, TGEV, and PDCoV will not go unnoticed.
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Affiliation(s)
- Christina M. Lazov
- DTU Institute of Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Alice Papetti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Thomas Bruun Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, IZSLER, Reparto Tecnologie Biologiche Applicate, Via Bianchi, 9, 25124 Brescia, Italy
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Development and Clinical Applications of a 5-Plex Real-Time RT-PCR for Swine Enteric Coronaviruses. Viruses 2022; 14:v14071536. [PMID: 35891517 PMCID: PMC9324624 DOI: 10.3390/v14071536] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 01/21/2023] Open
Abstract
A PEDV/PDCoV/TGEV/SADS-CoV/XIPC 5-plex real-time RT-PCR was developed and validated for the simultaneous detection and differentiation of four swine enteric coronaviruses (PEDV, PDCoV, TGEV and SADS-CoV) in one PCR reaction (XIPC serves as an exogenous internal positive control). The 5-plex PCR had excellent analytical specificity, analytical sensitivity, and repeatability based on the testing of various viral and bacterial pathogens, serial dilutions of virus isolates, and in vitro transcribed RNAs. The 5-plex PCR had comparable diagnostic performance to a commercial PEDV/TGEV/PDCoV reference PCR, based on the testing of 219 clinical samples. Subsequently, 1807 clinical samples collected from various U.S. states during 2019–2021 were tested by the 5-plex PCR to investigate the presence of SADS-CoV in U.S. swine and the frequency of detecting swine enteric CoVs. All 1807 samples tested negative for SADS-CoV. Among the samples positive for swine enteric CoVs, there was a low frequency of detecting TGEV, an intermediate frequency of detecting PDCoV, and a high frequency of detecting PEDV. Although there is no evidence of SADS-CoV presence in the U.S. at present, the availability of the 5-plex PCR will enable us to conduct ongoing surveillance to detect and differentiate these viruses in swine samples and other host species samples as some of these coronaviruses can cause cross-species infection.
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Carcereny A, Garcia-Pedemonte D, Martínez-Velázquez A, Quer J, Garcia-Cehic D, Gregori J, Antón A, Andrés C, Pumarola T, Chacón-Villanueva C, Borrego CM, Bosch A, Guix S, Pintó RM. Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. ENVIRONMENTAL RESEARCH 2022; 208:112720. [PMID: 35074352 PMCID: PMC8782736 DOI: 10.1016/j.envres.2022.112720] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/02/2022] [Accepted: 01/08/2022] [Indexed: 05/25/2023]
Abstract
Wastewater based epidemiology (WBE) offers an overview of the SARS-CoV-2 variants circulating among the population thereby serving as a proper surveillance method. The variant of concern (VOC) Alpha was first identified in September 2020 in the United Kingdom, and rapidly became dominant across Europe. Our objective was to elucidate the Alpha VOC outcompetition rate and identify mutations in the spike glycoprotein (S) gene, indicative of the circulation of the Alpha VOC and/or other variants in the population through wastewater analysis. In the period covered by this study (November 2020-April 2021), forteen wastewater treatment plants (WWTPs) were weekly sampled. The total number of SARS-CoV-2 genome copies per L (GC/L) was determined with a Real-Time qPCR, targeting the N gene. Surveillance of the Alpha VOC circulation was ascertained using a duplex RT-qPCR, targeting and discriminating the S gene. Our results showed that in a period of 6 weeks the Alpha VOC was present in all the studied WWTPs, and became dominant in 11 weeks on average. The outcompetition rates of the Alpha VOC were estimated, and their relationship with different parameters statistically analyzed. The rapid spread of the Alpha VOC was influenced by its initial input and by the previous circulation of SARS-COV-2 in the population. This latter point could be explained by its higher transmissibility, particularly advantadgeous when a certain degree of herd immunity exists. Moreover, the presence of signature mutations of SARS-COV-2 variants were established by deep-sequencing of the complete S gene. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified.
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Affiliation(s)
- Albert Carcereny
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - David Garcia-Pedemonte
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Adán Martínez-Velázquez
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Cristina Andrés
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | - Tomàs Pumarola
- Microbiology Department, Vall D'Hebron Institut de Recerca (VHIR), Vall D'Hebron Hospital Campus, Barcelona, Spain
| | | | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Susana Guix
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona Diagonal 643, 08028, Barcelona, Spain; Enteric Virus Laboratory, Institute of Nutrition and Food Safety (INSA), University of Barcelona, Spain.
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Carcereny A, Martínez-Velázquez A, Bosch A, Allende A, Truchado P, Cascales J, Romalde JL, Lois M, Polo D, Sánchez G, Pérez-Cataluña A, Díaz-Reolid A, Antón A, Gregori J, Garcia-Cehic D, Quer J, Palau M, Ruano CG, Pintó RM, Guix S. Monitoring Emergence of the SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:11756-11766. [PMID: 34397216 PMCID: PMC8404293 DOI: 10.1021/acs.est.1c03589] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 05/03/2023]
Abstract
Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2 has become dominant in several countries raising great concern. We developed a duplex real-time RT-qPCR assay to detect, discriminate, and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the ΔHV69/70 deletion, and used it to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). The B.1.1.7 variant was detected earlier than clinical epidemiological reporting by the local authorities, first in the southern city of Málaga (Andalucía) in week 20_52 (year_week), and multiple introductions during Christmas holidays were inferred in different parts of the country. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from wastewater treatment plants, which reached B.1.1.7 prevalences higher than 90% for ≥2 consecutive weeks showed that 8.1 ± 2.0 weeks were required for B.1.1.7 to become dominant. The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern as soon as they are identified by clinical sequencing and their integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.
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Affiliation(s)
- Albert Carcereny
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Adán Martínez-Velázquez
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Albert Bosch
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Ana Allende
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Pilar Truchado
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jenifer Cascales
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jesús L Romalde
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Marta Lois
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - David Polo
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Gloria Sánchez
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Alba Pérez-Cataluña
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Azahara Díaz-Reolid
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Andrés Antón
- Microbiology
Department, Vall d’Hebron Institut
de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital
Campus, Barcelona 08035, Spain
| | - Josep Gregori
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Damir Garcia-Cehic
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Josep Quer
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Margarita Palau
- General
Directorate of Public Health, Ministry of Health, Madrid 28014, Spain
| | - Cristina González Ruano
- Subdirección
General de Protección de las Aguas y Gestión de Riesgos,
Ministerio para la Transición Ecológica y el Reto Demográfico, Madrid 28071, Spain
| | - Rosa M Pintó
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Susana Guix
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
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11
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Mlejnkova H, Sovova K, Vasickova P, Ocenaskova V, Jasikova L, Juranova E. Preliminary Study of Sars-Cov-2 Occurrence in Wastewater in the Czech Republic. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E5508. [PMID: 32751749 PMCID: PMC7432771 DOI: 10.3390/ijerph17155508] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022]
Abstract
The virus SARS-CoV-2, which has caused the recent COVID-19 pandemic, may be present in the stools of COVID-19 patients. Therefore, we aimed to detect SARS-CoV-2 in wastewater for surveillance of SARS-CoV-2 in the population. Samples of untreated wastewater were collected from 33 wastewater treatment plants (WWTPs) of different sizes within the Czech Republic. SARS-CoV-2 RNA was concentrated from wastewater and viral RNA was determined using real-time reverse transcription polymerase chain reaction (RT-qPCR). SARS-CoV-2 RNA was detected in 11.6% of samples and more than 27.3% of WWTPs; in some of them, SARS-CoV-2 was detected repeatedly. Our preliminary results indicate that an epidemiology approach that focuses on the determination of SARS-CoV-2 in wastewater could be suitable for SARS-CoV-2 surveillance in the population.
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Affiliation(s)
- Hana Mlejnkova
- T. G. Masaryk Water Research Institute, Public Research Institution, Podbabska 2582/30, 160 00 Prague, Czech Republic; (H.M.); (V.O.); (L.J.); (E.J.)
| | - Katerina Sovova
- T. G. Masaryk Water Research Institute, Public Research Institution, Brno Branch, Mojmirovo namesti 16, 612 00 Brno, Czech Republic
| | - Petra Vasickova
- Veterinary Research Institute, Public Research Institution, Hudcova 296/70, 621 00 Brno, Czech Republic;
| | - Vera Ocenaskova
- T. G. Masaryk Water Research Institute, Public Research Institution, Podbabska 2582/30, 160 00 Prague, Czech Republic; (H.M.); (V.O.); (L.J.); (E.J.)
| | - Lucie Jasikova
- T. G. Masaryk Water Research Institute, Public Research Institution, Podbabska 2582/30, 160 00 Prague, Czech Republic; (H.M.); (V.O.); (L.J.); (E.J.)
| | - Eva Juranova
- T. G. Masaryk Water Research Institute, Public Research Institution, Podbabska 2582/30, 160 00 Prague, Czech Republic; (H.M.); (V.O.); (L.J.); (E.J.)
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12
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Rapid and efficient detection methods of pathogenic swine enteric coronaviruses. Appl Microbiol Biotechnol 2020; 104:6091-6100. [PMID: 32430534 PMCID: PMC7235545 DOI: 10.1007/s00253-020-10645-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/18/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023]
Abstract
Abstract Porcine enteric coronaviruses (CoVs) cause highly contagious enteric diarrhea in suckling piglets. These COV infections are characterized by clinical signs of vomiting, watery diarrhea, dehydration, and high morbidity and mortality, resulting in significant economic losses and tremendous threats to the pig farming industry worldwide. Because the clinical manifestations of pigs infected by different CoVs are similar, it is difficult to differentiate between the specific pathogens. Effective high-throughput detection methods are powerful tools used in the prevention and control of diseases. The immune system of piglets is not well developed, so serological methods to detect antibodies against these viruses are not suitable for rapid and early detection. This paper reviews various PCR-based methods used for the rapid and efficient detection of these pathogenic CoVs in swine intestines. Key points Swine enteric coronaviruses (CoVs) emerged and reemerged in past years. Enteric CoVs infect pigs at all ages with high mortality rate in suckling pigs. Rapid and efficient detection methods are needed and critical for diagnosis.
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13
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Blanco A, Abid I, Al-Otaibi N, Pérez-Rodríguez FJ, Fuentes C, Guix S, Pintó RM, Bosch A. Glass Wool Concentration Optimization for the Detection of Enveloped and Non-enveloped Waterborne Viruses. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:184-192. [PMID: 30903596 PMCID: PMC7090506 DOI: 10.1007/s12560-019-09378-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/13/2019] [Indexed: 05/15/2023]
Abstract
An extremely affordable virus concentration method based on adsorption-elution to glass wool and subsequent reconcentration through polyethylene glycol 6000 (PEG) precipitation was optimized to recover not only non-enveloped viruses but also enveloped viruses. Hepatitis A virus (HAV) and transmissible gastroenteritis virus (TGEV) were employed as surrogates for naked and enveloped viruses, respectively, to set up the methodology. Initial experimentation in small-volume samples showed that both types of particles readily adsorbed to the positively charged glass wool but were poorly detached from it through standard elution with 0.05 M glycine with 3% of beef extract buffer, pH 9.5, with elution efficiencies of 7.2% and 2.6%, for HAV and TGEV, respectively. To improve the recovery of enveloped viruses, several modifications in the elution were assayed: increasing the elution pH, extending glass wool and eluent contact time, adding a detergent, or performing the elution by recirculation or under agitation. Considering practicability and performance, recircularization of the eluent at pH 11.0 for 20 min was the elution procedure of choice, with efficiencies of 25.7% and 18.8% for HAV and TGEV in 50 L of water. Additionally, employing 20% PEG instead of 10% for virus reconcentration improved recoveries up to 47% and 51%, respectively. The optimized procedure was applied to detect naturally occurring HAV and coronaviruses in surface water of Wadi Hanifa, Riyadh. HAV was detected in 38% of the samples, while one sample was positive for an alphacoronavirus. This cheap virus detection system enables the comprehensive surveillance of viruses present in water samples.
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Affiliation(s)
- Albert Blanco
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Islem Abid
- Botany and Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Nawal Al-Otaibi
- Botany and Microbiology Department, Science College, King Saud University, Riyadh, Saudi Arabia
| | - Francisco José Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Cristina Fuentes
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.
- Institute of Nutrition and Food Safety (INSA·UB), University of Barcelona, Barcelona, Spain.
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14
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Simultaneous detection of five pig viruses associated with enteric disease in pigs using EvaGreen real-time PCR combined with melting curve analysis. J Virol Methods 2019; 268:1-8. [PMID: 30844408 DOI: 10.1016/j.jviromet.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/02/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
Abstract
In recent years, a series of porcine diarrhea viruses such as porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), rotaviruses of group A (RVA), rotaviruses of group C (RVC), and porcine circovirus 2 (PCV2) caused enormous economic losses all over the world. While any of these viruses is capable to cause disease alone, there is often concurrent infection with more than one virus on pig farms. In this study, a multiplex real-time PCR method based on EvaGreen fluorescent dye and melting curve analysis was established to simultaneously detect these five viruses in a single closed tube. Five distinct melt peaks were obtained with different melting temperature (Tm) value corresponding to each of the five viruses. This method was highly sensitive to detect and distinguish TGEV, RVA, RVC, PEDV and PCV2 with the limits of detection ranging from 5 to 50 copies/μL. The intra-assay and inter-assay reproducibility were good with coefficient of variation of Tm and cycle threshold values less than 0.32% and 2.86%, respectively. Testing of 90 field samples by the single and multiplex real-time PCR assays demonstrated a concordance of 91.1%. Thus, the EvaGreen multiplex real-time PCR is a rapid, sensitive and low-cost diagnostic tool for differential detection and routine surveillance of TGEV, RVA, RVC, PEDV and PCV2 in pigs.
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15
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Liu G, Jiang Y, Opriessnig T, Gu K, Zhang H, Yang Z. Detection and differentiation of five diarrhea related pig viruses utilizing a multiplex PCR assay. J Virol Methods 2019; 263:32-37. [DOI: 10.1016/j.jviromet.2018.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/05/2018] [Accepted: 10/12/2018] [Indexed: 01/16/2023]
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16
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Wang J, Wang J, Zhang R, Liu L, Shi R, Han Q, Yuan W. Rapid detection of transmissible gastroenteritis virus in swine small intestine samples using real-time reverse transcription recombinase polymerase amplification. J Virol Methods 2018; 256:85-88. [PMID: 29550352 PMCID: PMC7113865 DOI: 10.1016/j.jviromet.2018.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/10/2018] [Accepted: 03/13/2018] [Indexed: 11/30/2022]
Abstract
A rapid and specific real-time reverse-transcription recombinase polymerase amplification assay (RT-RPA) was developed to detect the transmissible gastroenteritis virus (TGEV) in this study. The primers and exo probe were designed to be specific for a portion of spike (S) gene conserved in TGEV, but absent in the closely related porcine respiratory coronavirus (PRCV). The amplification was performed at 40 °C for 20 min. The assay could only detect the TGEV, and there was no cross-reaction with other pathogens tested. Using the in vitro transcribed TGEV RNA as template, the limit of detection of the developed RT-RPA was 100 copies per reaction. The assay performance was evaluated by testing 76 clinical samples by RT-RPA and a real-time RT-PCR. Fourteen samples were TGEV RNA positive in RT-RPA (18.4%, 14/76), which were also positive in the real-time RT-PCR. The diagnostic agreement between the two assays was 100% (76/76). The R2 value of RT-RPA and real-time RT-PCR was 0.959 by linear regression analysis. The developed RT-RPA assay provides a useful alternative tool for rapid, simple and reliable detection of TGEV in resource-limited diagnostic laboratories and on-site facilities.
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Affiliation(s)
- Jinfeng Wang
- Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China; Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China
| | - Jianchang Wang
- Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China; Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China
| | - Ruoxi Zhang
- Hebei Animal Disease Control Center, Shijiazhuang 050050, China
| | - Libing Liu
- Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China; Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China
| | - Ruihan Shi
- Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang 050051, China; Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang 050051, China
| | - Qingan Han
- Hebei Animal Disease Control Center, Shijiazhuang 050050, China
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China.
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17
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Goecke NB, Hjulsager CK, Kongsted H, Boye M, Rasmussen S, Granberg F, Fischer TK, Midgley SE, Rasmussen LD, Angen Ø, Nielsen JP, Jorsal SE, Larsen LE. No evidence of enteric viral involvement in the new neonatal porcine diarrhoea syndrome in Danish pigs. BMC Vet Res 2017; 13:315. [PMID: 29115952 PMCID: PMC5678564 DOI: 10.1186/s12917-017-1239-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate whether the syndrome New Neonatal Porcine Diarrhoea Syndrome (NNPDS) is associated with a viral aetiology. Four well-managed herds experiencing neonatal diarrhoea and suspected to be affected by NNPDS were included in a case-control set up. A total of 989 piglets were clinically examined on a daily basis. Samples from diarrhoeic and non-diarrhoeic piglets at the age of three to seven days were selected for extensive virological examination using specific real time polymerase chain reactions (qPCRs) and general virus detection methods. RESULTS A total of 91.7% of the animals tested positive by reverse transcription qPCR (RT-qPCR) for porcine kobuvirus 1 (PKV-1) while 9% and 3% were found to be positive for rotavirus A and porcine teschovirus (PTV), respectively. The overall prevalence of porcine astrovirus (PAstV) was 75% with 69.8% of the PAstV positive pigs infected with PAstV type 3. No animals tested positive for rotavirus C, coronavirus (TGEV, PEDV and PRCV), sapovirus, enterovirus, parechovirus, saffoldvirus, cosavirus, klassevirus or porcine circovirus type 2 (PCV2). Microarray analyses performed on a total of 18 animals were all negative, as were eight animals examined by Transmission Electron Microscopy (TEM). Using Next Generation de novo sequencing (de novo NGS) on pools of samples from case animals within all herds, PKV-1 was detected in four herds and rotavirus A, rotavirus C and PTV were detected in one herd each. CONCLUSIONS Our detailed analyses of piglets from NNPDS-affected herds demonstrated that viruses did not pose a significant contribution to NNPDS. However, further investigations are needed to investigate if a systemic virus infection plays a role in the pathogenesis of NNPDS.
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Affiliation(s)
- N B Goecke
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.
| | - C K Hjulsager
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - H Kongsted
- Pig Research Centre, Danish Agriculture and Food Council, Vinkelvej 13, DK-8620, Kjellerup, Denmark
| | - M Boye
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Gronnegaardsvej 15, DK-1870, Frederiksberg, Denmark
| | - S Rasmussen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - F Granberg
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - T K Fischer
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - S E Midgley
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - L D Rasmussen
- Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark.,National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave, DK-4771, Denmark
| | - Ø Angen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark.,Statens Serum Institut (SSI), Artillerivej 5, Copenhagen S, DK-2300, Denmark
| | - J P Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Gronnegaardsvej 15, DK-1870, Frederiksberg, Denmark
| | - S E Jorsal
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
| | - L E Larsen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet, Lyngby, DK-2800, Denmark
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18
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Diseases of the Alimentary Tract. Vet Med (Auckl) 2017. [PMCID: PMC7167529 DOI: 10.1016/b978-0-7020-5246-0.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Wang L. Real-Time Reverse Transcription Polymerase Chain Reaction for Rapid Detection of Transmissible Gastroenteritis Virus. SPRINGER PROTOCOLS HANDBOOKS 2016. [PMCID: PMC7121909 DOI: 10.1007/978-1-4939-3414-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Transmissible gastroenteritis (TGE) is a highly contagious disease of pigs caused by the TGE virus (TGEV). Rapid detection of the virus in the affected pigs’ feces is critical for controlling the disease outbreaks. The real-time RT-PCR assay described in this chapter can quickly detect the presence of TGEV in fecal samples with high sensitivity and specificity.
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Affiliation(s)
- Leyi Wang
- Animal Disease Diagnostic Lab, Ohio Department of Agriculture, Reynoldsburg, Ohio USA
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20
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Huang Y, Xing N, Wang Z, Zhang X, Zhao X, Du Q, Chang L, Tong D. Ultrasensitive Detection of RNA and DNA Viruses Simultaneously Using Duplex UNDP-PCR Assay. PLoS One 2015; 10:e0141545. [PMID: 26544710 PMCID: PMC4636378 DOI: 10.1371/journal.pone.0141545] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/10/2015] [Indexed: 12/03/2022] Open
Abstract
Mixed infection of multiple viruses is common in modern intensive pig rearing. However, there are no methods available to detect DNA and RNA viruses in the same reaction system in preclinical level. In this study, we aimed to develop a duplex ultrasensitive nanoparticle DNA probe-based PCR assay (duplex UNDP-PCR) that was able to simultaneously detect DNA and RNA viruses in the same reaction system. PCV2 and TGEV are selected as representatives of the two different types of viruses. PCV2 DNA and TGEV RNA were simultaneously released from the serum sample by boiling with lysis buffer, then magnetic beads and gold nanoparticles coated with single and/or duplex specific probes for TGEV and PCV2 were added to form a sandwich-like complex with nucleic acids released from viruses. After magnetic separation, DNA barcodes specific for PCV2 and TGEV were eluted using DTT and characterized by specific PCR assay for specific DNA barcodes subsequently. The duplex UNDP-PCR showed similar sensitivity as that of single UNDP-PCR and was able to detect 20 copies each of PCV2 and TGEV in the serum, showing approximately 250-fold more sensitivity than conventional duplex PCR/RT-PCR assays. No cross-reaction was observed with other viruses. The positive detection rate of single MMPs- and duplex MMPs-based duplex UNDP-PCR was identical, with 29.6% for PCV2, 9.3% for TGEV and 3.7% for PCV2 and TGEV mixed infection. This duplex UNDP-PCR assay could detect TGEV (RNA virus) and PCV2 (DNA virus) from large-scale serum samples simultaneously without the need for DNA/RNA extraction, purification and reverse transcription of RNA, and showed a significantly increased positive detection rate for PCV2 (29%) and TGEV (11.7%) preclinical infection than conventional duplex PCR/RT-PCR. Therefore, the established duplex UNDP-PCR is a rapid and economical detection method, exhibiting high sensitivity, specificity and reproducibility.
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Affiliation(s)
- Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Na Xing
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Zengguo Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Xiujuan Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Xiaomin Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Qian Du
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Lingling Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
- * E-mail:
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Ojkic D, Hazlett M, Fairles J, Marom A, Slavic D, Maxie G, Alexandersen S, Pasick J, Alsop J, Burlatschenko S. The first case of porcine epidemic diarrhea in Canada. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2015; 56:149-152. [PMID: 25694663 PMCID: PMC4298265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In January, 2014, increased mortality was reported in piglets with acute diarrhea on an Ontario farm. Villus atrophy in affected piglets was confined to the small intestine. Samples of colon content were PCR-positive for porcine epidemic diarrhea virus (PEDV). Other laboratory tests did not detect significant pathogens, confirming this was the first case of PED in Canada.
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Affiliation(s)
- Davor Ojkic
- Address all correspondence to Dr. Davor Ojkic; e-mail:
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22
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Huang Y, Harding JCS. Pathological Features and Proposed Diagnostic Criteria of Porcine Periweaning Failure-to-Thrive Syndrome. Vet Pathol 2014; 52:489-96. [DOI: 10.1177/0300985814542810] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Porcine periweaning failure-to-thrive syndrome (PFTS) is a clinical syndrome characterized by anorexia and progressive debilitation of newly weaned pigs. The objectives of the current case-control study were to describe the histopathologic features of PFTS in North America and test for selected pathogens in case and control pigs on 8 farms allegedly fulfilling the clinical definition of PFTS. Based on observations during farm visits, 5 farms fully met the case definition (PFTS farms), whereas 3 farms only partially fulfilled the definition (NON-PFTS farms). Necropsy and histopathologic examination were performed on case (n = 8 or 9) and control (n = 4) pigs from each farm. Superficial gastritis, which was mainly localized in the fundus and characterized by attenuation of superficial foveolar cells, was significantly more frequent in case pigs from PFTS farms compared with all the other pigs (odds ratio [OR], 16.7). The same was found for thymic atrophy (OR, 30.1) and small intestinal (SI) villous atrophy in the duodenum (OR, 28.7), jejunum (OR, 67.4), and ileum (OR, 56.3). All pigs with PFTS had at least 2 of these 3 lesions: gastritis, thymic atrophy, and SI villous atrophy. PFTS was not associated with any relevant porcine pathogen tested. We propose the diagnosis of PFTS be based on the fulfillment of the clinical case definition, the presence of the above lesions, and exclusion of other common swine diseases and pathogens. However, PFTS can be ruled out if debilitated pigs do not have at least 2 of the above 3 lesions.
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Affiliation(s)
- Y. Huang
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Prairie Diagnostic Services, Inc, Saskatoon, Saskatchewan, Canada
| | - J. C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Yuan W, Zheng Y, Sun M, Zhang X, Qi Y, Sun J. Development of a TaqMan-based real-time reverse transcription polymerase chain reaction assay for the detection of encephalomyocarditis virus. J Virol Methods 2014; 207:60-5. [PMID: 24996131 DOI: 10.1016/j.jviromet.2014.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 06/01/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022]
Abstract
Encephalomyocarditis virus (EMCV) is one of the major zoonosis pathogens and can cause acute myocarditis in young pigs or reproductive failure in sows. In this study, a TaqMan-based real-time reverse transcription polymerase chain reaction (RT-PCR) assay targeting 3D gene of EMCV was developed and their sensitivities and specificities were investigated. The results indicated that the standard curve had a wide dynamic range (10(1)-10(6) copies/μL) with a linear correlation (R(2)) of 0.996 between the cycle threshold (Ct) value and template concentration. The real-time RT-PCR assay is highly sensitive and able to detect 1.4×10(2) copies/μL of EMCV RNA, as no cross-reaction was observed with other viruses. These data suggested that the real-time RT-PCR assay developed in this study will be suitable for future surveillance and specific diagnosis of EMCV-infection.
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Affiliation(s)
- Wanzhe Yuan
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China
| | - Yingshuai Zheng
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China
| | - Mingtan Sun
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China
| | - Xiuyuan Zhang
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China
| | - Yan Qi
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China
| | - Jiguo Sun
- College of Animal Medicine, Agricultural University of Hebei, Baoding 071001, Hebei, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071001, Hebei, China; North China Research Center of Animal Epidemic Pathogen Biology, China, Agriculture Ministry, Baoding 071001, Hebei, China.
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Huang Y, Harding JCS. Attempted experimental reproduction of porcine periweaning-failure-to-thrive syndrome using tissue homogenates. PLoS One 2014; 9:e90065. [PMID: 24594806 PMCID: PMC3940845 DOI: 10.1371/journal.pone.0090065] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/29/2014] [Indexed: 11/29/2022] Open
Abstract
Porcine periweaning failure-to-thrive syndrome (PFTS) is characterized by anorexia and progressive debilitation of newly weaned pigs, of which some also demonstrate repetitive oral behaviour. Although no relevant porcine pathogens have been shown to be causally associated, inoculation of susceptible pigs using tissue homogenates is needed to rule out infectious etiologies. Eight snatched-farrowed porcine-colostrum-deprived (SF-pCD) pigs were inoculated with tissue homogenates made from PFTS-affected pigs orally, or combined orally, intraperitoneally (i.p.) and intramuscularly (i.m.) at day (D) 14 of age (INOC). On D21, i.p. and i.m. inoculation were repeated. Four sham-inoculated pigs served as control (CTRL). Three INOC pigs developed mixed bacterial septicemia between the first and second inoculation. All other pigs survived until termination on D49. Average daily gain (ADG) and the frequencies of diarrhea did not differ between INOC and CTRL pigs D14 and D29. Additionally, the progressive debilitation characteristic of PFTS was not observed in any pig, and repetitive oral behaviour was observed in both groups. In conclusion, PFTS was not experimentally reproduced by the current experimental approach providing evidence that PFTS may not have an infectious etiology.
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Affiliation(s)
- Yanyun Huang
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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A novel watery diarrhoea caused by the co-infection of neonatal piglets with Clostridium perfringens type A and Escherichia coli (K88, 987P). Vet J 2013; 197:812-6. [DOI: 10.1016/j.tvjl.2013.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 03/09/2013] [Accepted: 05/06/2013] [Indexed: 11/17/2022]
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Pathak E, El-Borai FE, Campos-Herrera R, Johnson EG, Stuart RJ, Graham JH, Duncan LW. Use of real-time PCR to discriminate parasitic and saprophagous behaviour by nematophagous fungi. Fungal Biol 2012; 116:563-73. [DOI: 10.1016/j.funbio.2012.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 01/06/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
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Sun D, Shi H, Chen J, Shi D, Zhu Q, Zhang H, Liu S, Wang Y, Qiu H, Feng L. Generation of a mouse scFv library specific for porcine aminopeptidase N using the T7 phage display system. J Virol Methods 2012; 182:99-103. [PMID: 22481024 PMCID: PMC7119651 DOI: 10.1016/j.jviromet.2012.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 03/20/2012] [Indexed: 11/25/2022]
Abstract
Porcine aminopeptidase N (pAPN) is a common cellular receptor for swine transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV). To investigate single-chain fragment variable (scFv) repertoire against pAPN, the genes encoding the immunoglobulin light chain variable region (VL) and heavy chain variable region (VH) were amplified by reverse transcript polymerase chain reaction (RT-PCR) using a series of degenerate primers from the spleen of BABL/c mice immunized with native pAPN. The VL and VH amplicons were combined randomly by a 12 amino acid flexible linker by splicing by overlap extension PCR (SOE-PCR), which produced the scFv gene repertoire. After ligation of the scFv gene repertoire into the T7Select10-3b vector, a mouse scFv phage library specific for pAPN was produced through in vitro packaging. The primary scFv library against pAPN contained 2.0×10(7) recombinant phage clones, and the titer of the amplified library was 3.6×10(9)pfu/mL. BstNI restriction analysis and DNA sequencing revealed that 28 phage clones from the primary pAPN scFv library showed excellent diversity. The effectiveness of the scFv library against pAPN was verified further by phage ELISA using the recombinant protein of the pAPN C subunit as coating antigen. The construction and evaluation of a murine scFv library against the common receptor pAPN of porcine coronaviruses TGEV and PEDV using the T7 phage display system are described.
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Affiliation(s)
- Dongbo Sun
- Division of Swine Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Nangang District, Harbin 150001, China.
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28
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Zhu E, Sambath S. Express Transmissible Gastroenteritis Virus Spike Gene B and C Antigen Sites in Multiple Expression Systems. ADVANCES IN INTELLIGENT AND SOFT COMPUTING 2012. [PMCID: PMC7123857 DOI: 10.1007/978-3-642-27537-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to illuminate the antigenicity of porcine transmissible gastroenteritis virus (TGEV) spike protein B and C antigen sites, the truncated spike gene including B and C antigen sites of Chinese isolate TH-98 was expressed respectively in E.coli, baculovirus and pichia pastoris expression systems. Dot enzyme-linked immunosorbent assays (Dot-ELISA) based on these three recombinant proteins were developed preliminarily. Ten sera obtained correspondingly from ten piglets two months old which showed up clinical symptom were used for examination. The study indicates that the assays are rapid, reliable and sensitive and it has the potential for use as serological methods for TGEV diagnosis.
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Affiliation(s)
- Egui Zhu
- South China Normal University, Guangzhou, 510631 China, People's Republic
| | - Sabo Sambath
- South China Normal University, Guangzhou, 510631 China, People's Republic
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29
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Sun Y, Liang M, Qu J, Jin C, Zhang Q, Li J, Jiang X, Wang Q, Lu J, Gu W, Zhang S, Li C, Wang X, Zhan F, Yao W, Bi Z, Wang S, Li D. Early diagnosis of novel SFTS bunyavirus infection by quantitative real-time RT-PCR assay. J Clin Virol 2011; 53:48-53. [PMID: 22024488 DOI: 10.1016/j.jcv.2011.09.031] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/19/2011] [Accepted: 09/29/2011] [Indexed: 01/05/2023]
Abstract
BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease recently identified to be caused by a novel bunyavirus (SFTSV). The clinical diagnosis is urgently needed to differentiate the disease from other infections. OBJECTIVE To develop a sensitive quantitative real-time RT-PCR assay for rapid detection of SFTSV viral RNA and evaluate potential use for clinical diagnosis of SFTS. STUDY DESIGN Primers and probes were designed to target the L, M, and S segments of SFTSV, and standard curves were established based on serial dilutions of in vitro transcribed viral RNA or viral RNA extracts. The serum samples collected from 70 laboratory confirmed SFTS patients, 114 non-SFTS patients, and 400 healthy donors were analyzed. RESULTS Based on three optimized primer-probe sets to detect L, M, S genes of SFTSV, the quantitative real-time RT-PCR assay could discriminate SFTSV infection from other vector-borne viral diseases in human with potential detection limit of 10 viral RNA copies/μl or 10 TCID(50)/ml virus load. Strong linear correlations (r(2)>0.99) between the C(t) values and viral RNA standards over a liner range were obtained. The assay specificity was determined by sequence alignment and experimentally tested on various related viruses. Evaluation of the study method with clinical serum samples showed 98.6% clinical diagnostic sensitivity and over 99% specificity. CONCLUSION The quantitative real-time RT-PCR assay established in this study can be used as a reliable method for early diagnosis of SFTSV infection.
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Affiliation(s)
- Yulan Sun
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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One-step RT-qPCR with an internal control system for the detection of turkey rotaviruses in faecal samples. J Virol Methods 2011; 177:112-7. [PMID: 21816176 DOI: 10.1016/j.jviromet.2011.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 07/15/2011] [Accepted: 07/19/2011] [Indexed: 01/02/2023]
Abstract
Turkey rotaviruses are one of the major pathogens responsible for the poult enteritis syndrome (PES). In this study a one step real-time reverse transcription polymerase chain reaction (RT-qPCR) assay targeting the rotaviral non-structural protein 4 (NSP4) was developed. The NSP4 is a highly conserved gene inside the turkey rotavirus genome and contains an internal control system to monitor any potential RT-qPCR inhibitors. The detection limit of the optimized NSP4-RT-qPCR assay ranged from 8.15 to 8.15 × 10(5) copy numbers. In total 149 faecal samples were collected from eight different flocks of commercial turkey farms. Faecal samples from hens and toms were collected separately at 2-week intervals from the 2nd week of age through the 16th and 20th week of age (age of slaughter for female and male, respectively) and tested. One farm reared only hens. The samples were tested previously using conventional RT-PCR targeting the same gene. When the conventional RT-PCR was compared with the developed NSP4-RT-qPCR, the results revealed that 11% of the samples of the conventional RT-PCR were false negative. The results indicate that this NSP4-RT-qPCR is highly sensitive for the detection of turkey rotaviruses in faeces. In addition, it could be suitable for the development of high-throughput screening.
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31
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Li P, Ren X. Reverse transcription loop-mediated isothermal amplification for rapid detection of transmissible gastroenteritis virus. Curr Microbiol 2010; 62:1074-80. [PMID: 21127872 PMCID: PMC7080135 DOI: 10.1007/s00284-010-9825-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 11/15/2010] [Indexed: 11/28/2022]
Abstract
Transmissible gastroenteritis virus (TGEV) is the causative agent of porcine transmissible gastroenteritis, and sensitive detection methods are required for preventing the disease. In this article, reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was developed to detect TGEV. Three pairs of primers targeting the nucleocapsid (N) gene of TGEV were synthesized and used in the RT-LAMP. The optimization, sensitivity, and specificity of the RT-LAMP were evaluated. Our results showed that the RT-LAMP amplified the N gene with high specificity, efficiency, and rapidity at isothermal condition. The optimal reaction condition was achieved at 60°C for 30 min. The RT-LAMP assay was more sensitive than gel-based RT-PCR and PCR. It had a higher sensitivity than enzyme-linked immunosorbent assay (ELISA) using the equal virus templates. In addition, the established RT-LAMP differentiated TGEV from porcine epidemic diarrhea virus, porcine rotavirus, porcine pseudorabies virus, porcine reproductive and respiratory syndrome virus, and avian infectious bronchitis virus. The approach is suitable for detecting TGEV for field diagnostics or in less-equipped laboratories due to its convenience and simplicity.
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Affiliation(s)
- Pengchong Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, 59 Mucai Street, Xiangfang, 150030, Harbin, China
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