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1.
J Immunol Methods ; 515: 113442, 2023 04.
Article in English | MEDLINE | ID: covidwho-2269007

ABSTRACT

The RNA synthesis of porcine epidemic diarrhea virus (PEDV) is a sophisticated process performed by a multilingual viral replication complex, together with cellular factors. A key enzyme of this replication complex is RNA-dependent RNA polymerase (RdRp). However, there is limited knowledge about PEDV RdRp. In our present study, a polyclonal antibody against RdRp was prepared by using a prokaryotic expression vector pET-28a-RdRp to study the function of PEDV RdRp and provide a tool to investigate PEDV pathogenesis. In addition, the enzyme activity and half-life of PEDV RdRp were investigated. The result showed that the polyclonal antibody against PEDV RdRp was successfully prepared and was able to be used to detect PEDV RdRp by immunofluorescence and western blotting. Additionally, enzyme activity of PEDV RdRp reached nearly 2 pmol/µg/h and the half-life of PEDV RdRp was 5.47 h.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Swine , RNA-Dependent RNA Polymerase/genetics , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , Swine Diseases/diagnosis
2.
Appl Microbiol Biotechnol ; 107(7-8): 2413-2422, 2023 Apr.
Article in English | MEDLINE | ID: covidwho-2253701

ABSTRACT

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging swine enteric alphacoronavirus that can cause acute diarrhea, vomiting, dehydration, and death of newborn piglets. In this study, we developed a double-antibody sandwich quantitative enzyme-linked immunosorbent assay (DAS-qELISA) for detection of SADS-CoV by using an anti-SADS-CoV N protein rabbit polyclonal antibody (PAb) and a specific monoclonal antibody (MAb) 6E8 against the SADS-CoV N protein. The PAb was used as the capture antibodies and HRP-labeled 6E8 as the detector antibody. The detection limit of the developed DAS-qELISA assay was 1 ng/mL of purified antigen and 101.08TCID50/mL of SADS-CoV, respectively. Specificity assays showed that the developed DAS-qELISA has no cross-reactivity with other swine enteric coronaviruses, such as porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV). Three-day-old piglets were challenged with SADS-CoV and collected anal swab samples which were screened for the presence of SADS-CoV by using DAS-qELISA and reverse transcriptase PCR (RT-PCR). The coincidence rate of the DAS-qELISA and RT-PCR was 93.93%, and the kappa value was 0.85, indicating that DAS-qELISA is a reliable method for applying antigen detection of clinical samples. KEY POINTS: • The first double-antibody sandwich quantitative enzyme-linked immunosorbent assay for detection SADS-CoV infection. • The custom ELISA is useful for controlling the SADS-CoV spread.


Subject(s)
Alphacoronavirus , Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Swine , Rabbits , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , Coronavirus Infections/epidemiology , Enzyme-Linked Immunosorbent Assay , Swine Diseases/diagnosis
3.
Biosensors (Basel) ; 12(12)2022 Dec 08.
Article in English | MEDLINE | ID: covidwho-2154896

ABSTRACT

Porcine epidemic diarrhea virus (PEDV), a coronavirus that causes highly infectious intestinal diarrhea in piglets, has led to severe economic losses worldwide. Rapid diagnosis and timely supervision are significant in the prophylaxis of PEDV. Herein, we proposed a gold-nanorod (GNR) probe-assisted counting method using dark field microscopy (DFM). The antibody-functionalized silicon chips were prepared to capture PEDV to form sandwich structures with GNR probes for imaging under DFM. Results show that our DFM-based assay for PEDV has a sensitivity of 23.80 copies/µL for simulated real samples, which is very close to that of qPCR in this study. This method of GNR probes combined with DFM for quantitative detection of PEDV not only has strong specificity, good repeatability, and a low detection limit, but it also can be implemented for rapid on-site detection of the pathogens.


Subject(s)
Coronavirus Infections , Coronavirus , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Swine , Gold , Swine Diseases/diagnosis , Coronavirus Infections/diagnosis
4.
BMC Vet Res ; 18(1): 369, 2022 Oct 11.
Article in English | MEDLINE | ID: covidwho-2064800

ABSTRACT

BACKGROUND: Swine acute diarrhea syndrome coronavirus (SADS-CoV) causes acute vomiting and diarrhea in piglets, leading to significant financial losses for the pig industry. Recombinase polymerase amplification (RPA) is a rapid nucleic acid amplification technology used under constant temperature conditions. The study established a real-time reverse transcription (RT)-RPA assay for early diagnosis of SADS-CoV.  RESULTS: The detection limit of the real-time RT-RPA was 74 copies/µL of SADS-CoV genomic standard recombinant plasmid in 95% of cases. The assay was performed in less than 30 min and no cross-reactions were observed with eight other common viruses that affect swine, including classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), pseudo rabies virus (PRV), swine influenza virus (SIV), seneca valley virus (SVA), transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV). The coefficient of variation (C.V.) values of the two standards dilutions and three positive clinical sample ranged from 2.95% to 4.71%. A total of 72 clinical fecal samples from swine with diarrheal symptoms were analyzed with the developed RT-RPA and quantitative RT-PCR. There was 98.61% agreement between the RT-RPA and the quantitative real-time PCR results. CONCLUSIONS: These results indicated that the developed RT-RPA assay had good specificity, sensitivity, stability and repeatability. The study successfully established a broadly reactive RT-RPA assay for SADS-CoV detection.


Subject(s)
Alphacoronavirus , Coronavirus Infections , Nucleic Acids , Swine Diseases , Alphacoronavirus/genetics , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , Diarrhea/diagnosis , Diarrhea/veterinary , Real-Time Polymerase Chain Reaction/veterinary , Recombinases , Sensitivity and Specificity , Swine , Swine Diseases/diagnosis
5.
Transbound Emerg Dis ; 69(4): 2173-2181, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1992901

ABSTRACT

Livestock industry supports the livelihood of around 1.3 billion people in the world, with swine industry contributing with 30% of total livestock production worldwide. To maintain and guarantee this production, a pivotal point according to the OIE is addressing potential biohazards. To control them, permanent sero-surveillance is crucial to achieve more focused veterinary public health intervention and prevention strategies, to break the chains of transmission, and to enable fast responses against outbreaks. Within this context, multiplex assays are powerful tools with the potential to simplify surveillance programs, since they reduce time, labour, and variability within analysis. In the present work, we developed a multiplex bead-based assay for the detection of specific antibodies to six relevant pathogens affecting swine: ASFV, CSFV, PRRSV, SIV, TB and HEV. The most immunogenic target antigen of each pathogen was selected as the target protein to coat different microsphere regions in order to develop this multiplex assay. A total of 1544 serum samples from experimental infections as well as field samples were included in the analysis. The 6-plex assay exhibited credible diagnostic parameters with sensitivities ranging from 87.0% to 97.5% and specificities ranging from 87.9% to 100.0%, demonstrating it to be a potential high throughput tool for surveillance of infectious diseases in swine.


Subject(s)
African Swine Fever Virus , African Swine Fever , Porcine respiratory and reproductive syndrome virus , Swine Diseases , African Swine Fever/diagnosis , Animals , Humans , Sensitivity and Specificity , Swine , Swine Diseases/diagnosis
6.
Viruses ; 14(7)2022 07 14.
Article in English | MEDLINE | ID: covidwho-1939018

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.


Subject(s)
Coronavirus Infections , Coronavirus , Porcine epidemic diarrhea virus , Swine Diseases , Alphacoronavirus , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , Feces , Porcine epidemic diarrhea virus/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Swine , Swine Diseases/diagnosis
7.
Angew Chem Int Ed Engl ; 61(31): e202204252, 2022 08 01.
Article in English | MEDLINE | ID: covidwho-1843851

ABSTRACT

Pen-side testing of farm animals for infectious diseases is critical for preventing transmission in herds and providing timely intervention. However, most existing pathogen tests have to be conducted in centralized labs with sample-to-result times of 2-4 days. Herein we introduce a test that uses a dual-electrode electrochemical chip (DEE-Chip) and a barcode-releasing electroactive aptamer for rapid on-farm detection of porcine epidemic diarrhea viruses (PEDv). The sensor exploits inter-electrode spacing reduction and active field mediated transport to accelerate barcode movement from electroactive aptamers to the detection electrode, thus expediting assay operation. The test yielded a clinically relevant limit-of-detection of 6 nM (0.37 µg mL-1 ) in saliva-spiked PEDv samples. Clinical evaluation of this biosensor with 12 porcine saliva samples demonstrated a diagnostic sensitivity of 83 % and specificity of 100 % with a concordance value of 92 % at an analysis time of one hour.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/veterinary , DNA Barcoding, Taxonomic , Diarrhea/diagnosis , Diarrhea/veterinary , Porcine epidemic diarrhea virus/genetics , Saliva , Sensitivity and Specificity , Swine , Swine Diseases/diagnosis
8.
Pol J Vet Sci ; 24(1): 43-49, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1368400

ABSTRACT

In this study, we developed a SYBR Green I real-time PCR method for the rapid and sensitive detection of novel porcine parvovirus 7 (PPV7). Specific primers were designed based on the highly conserved region within the Capsid gene of PPV7. The established method was 1,000 times more sensitive than the conventional PCR method and had a detection limit of 35.6 copies. This method was specific and had no cross-reactions with PCV2, PCV3, PRV, PEDV, PPV1, and PPV6. Experiments testing the intra and interassay precision demonstrated a high reproducibility. Testing the newly established method with 200 clinical samples revealed a detection rate up to 17.5% higher than that of the conventional PCR assay. The established method could provide technical support for clinical diagnosis and epidemiological investigation of PPV7.


Subject(s)
Benzothiazoles , Diamines , Parvoviridae Infections/veterinary , Parvovirus, Porcine/isolation & purification , Quinolines , Real-Time Polymerase Chain Reaction/methods , Swine Diseases/virology , Animals , Parvoviridae Infections/diagnosis , Parvoviridae Infections/virology , Reproducibility of Results , Sensitivity and Specificity , Swine , Swine Diseases/diagnosis
9.
PLoS One ; 16(7): e0254815, 2021.
Article in English | MEDLINE | ID: covidwho-1318322

ABSTRACT

African swine fever (ASF) is a serious contagious disease that causes fatal haemorrhagic fever in domestic and wild pigs, with high morbidity. It has caused devastating damage to the swine industry worldwide, necessitating the focus of attention on detection of the ASF pathogen, the African swine fever virus (ASFV). In order to overcome the disadvantages of conventional diagnostic methods (e.g. time-consuming, demanding and unintuitive), quick detection tools with higher sensitivity need to be explored. In this study, based on the conserved p72 gene sequence of ASFV, we combined the Cas12a-based assay with recombinase polymerase amplification (RPA) and a fluorophore-quencher (FQ)-labeled reporter assay for rapid and visible detection. Five crRNAs designed for Cas12a-based assay showed specificity with remarkable fluorescence intensity under visual inspection. Within 20 minutes, with an initial concentration of two copies of DNA, the assay can produce significant differences between experimental and negative groups, indicating the high sensitivity and rapidity of the method. Overall, the developed RPA-Cas12a-fluorescence assay provides a fast and visible tool for point-of-care ASFV detection with high sensitivity and specificity, which can be rapidly performed on-site under isothermal conditions, promising better control and prevention of ASF.


Subject(s)
African Swine Fever Virus/isolation & purification , African Swine Fever/diagnosis , Bacterial Proteins/genetics , CRISPR-Associated Proteins/genetics , Endodeoxyribonucleases/genetics , Swine Diseases/diagnosis , African Swine Fever/genetics , African Swine Fever/virology , African Swine Fever Virus/genetics , Animals , Bacterial Proteins/chemistry , CRISPR-Associated Proteins/chemistry , CRISPR-Cas Systems , DNA-Directed DNA Polymerase/chemistry , Endodeoxyribonucleases/chemistry , Molecular Diagnostic Techniques , Point-of-Care Systems , Recombinases/chemistry , Swine , Swine Diseases/genetics , Swine Diseases/pathology , Swine Diseases/virology
10.
J Vet Diagn Invest ; 33(3): 457-468, 2021 May.
Article in English | MEDLINE | ID: covidwho-1264088

ABSTRACT

Every day, thousands of samples from diverse populations of animals are submitted to veterinary diagnostic laboratories (VDLs) for testing. Each VDL has its own laboratory information management system (LIMS), with processes and procedures to capture submission information, perform laboratory tests, define the boundaries of test results (i.e., positive or negative), and report results, in addition to internal business and accounting applications. Enormous quantities of data are accumulated and stored within VDL LIMSs. There is a need for platforms that allow VDLs to exchange and share portions of laboratory data using standardized, reliable, and sustainable information technology processes. Here we report concepts and applications for standardization and aggregation of data from swine submissions to multiple VDLs to detect and monitor porcine enteric coronaviruses by RT-PCR. Oral fluids, feces, and fecal swabs were the specimens submitted most frequently for enteric coronavirus testing. Statistical algorithms were used successfully to scan and monitor the overall and state-specific percentage of positive submissions. Major findings revealed a consistently recurrent seasonal pattern, with the highest percentage of positive submissions detected during December-February for porcine epidemic diarrhea virus, porcine deltacoronavirus, and transmissible gastroenteritis virus (TGEV). After 2014, very few submissions tested positive for TGEV. Monitoring VDL data proactively has the potential to signal and alert stakeholders early of significant changes from expected detection. We demonstrate the importance of, and applications for, data organized and aggregated by using LOINC and SNOMED CTs, as well as the use of customized messaging to allow inter-VDL exchange of information.


Subject(s)
Coronaviridae Infections/veterinary , Coronaviridae/isolation & purification , Laboratories/standards , Swine Diseases/virology , Animals , COVID-19 Testing/veterinary , Coronaviridae Infections/diagnosis , Coronaviridae Infections/virology , Disease Outbreaks , Feces/virology , Reference Standards , Seasons , Swine , Swine Diseases/diagnosis
11.
mSphere ; 5(3)2020 05 06.
Article in English | MEDLINE | ID: covidwho-1153652

ABSTRACT

Members of family Coronaviridae cause a variety of diseases in birds and mammals. Porcine hemagglutinating encephalomyelitis virus (PHEV), a lesser-researched coronavirus, can infect naive pigs of any age, but clinical disease is observed in pigs ≤4 weeks of age. No commercial PHEV vaccines are available, and neonatal protection from PHEV-associated disease is presumably dependent on lactogenic immunity. Although subclinical PHEV infections are thought to be common, PHEV ecology in commercial swine herds is unknown. To begin to address this gap in knowledge, a serum IgG antibody enzyme-linked immunosorbent assay (ELISA) based on the S1 protein was developed and evaluated on known-status samples and then used to estimate PHEV seroprevalence in U.S. sow herds. Assessment of the diagnostic performance of the PHEV S1 ELISA using serum samples (n = 924) collected from 7-week-old pigs (n = 84; 12 pigs per group) inoculated with PHEV, porcine epidemic diarrhea virus, transmissible gastroenteritis virus, porcine respiratory coronavirus, or porcine deltacoronavirus showed that a sample-to-positive cutoff value of ≥0.6 was both sensitive and specific, i.e., all PHEV-inoculated pigs were seropositive from days postinoculation 10 to 42, and no cross-reactivity was observed in samples from other groups. The PHEV S1 ELISA was then used to estimate PHEV seroprevalence in U.S. sow herds (19 states) using 2,756 serum samples from breeding females (>28 weeks old) on commercial farms (n = 104) with no history of PHEV-associated disease. The overall seroprevalence was 53.35% (confidence interval [CI], ±1.86%) and herd seroprevalence was 96.15% (CI, ±3.70%).IMPORTANCE There is a paucity of information concerning the ecology of porcine hemagglutinating encephalomyelitis virus (PHEV) in commercial swine herds. This study provided evidence that PHEV infection is endemic and highly prevalent in U.S. swine herds. These results raised questions for future studies regarding the impact of endemic PHEV on swine health and the mechanisms by which this virus circulates in endemically infected populations. Regardless, the availability of the validated PHEV S1 enzyme-linked immunosorbent assay (ELISA) provides the means for swine producers to detect and monitor PHEV infections, confirm prior exposure to the virus, and to evaluate the immune status of breeding herds.


Subject(s)
Antibodies, Viral/blood , Betacoronavirus 1/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Swine Diseases/epidemiology , Animals , Antibodies, Viral/immunology , Betacoronavirus 1/immunology , Coronavirus Infections/diagnosis , Cross Reactions/immunology , Enzyme-Linked Immunosorbent Assay/methods , Immunoglobulin G/blood , Immunoglobulin G/immunology , Porcine Respiratory Coronavirus/immunology , Porcine epidemic diarrhea virus/immunology , Seroepidemiologic Studies , Swine , Swine Diseases/diagnosis , Transmissible gastroenteritis virus/immunology , United States/epidemiology
12.
J Infect Chemother ; 26(5): 523-526, 2020 May.
Article in English | MEDLINE | ID: covidwho-828066

ABSTRACT

Transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) are the main pathogens causing viral diarrhea in pig, mixed infections of these two viruses are very common in intensive pig rearing. However, there is a lack of a method to simultaneously detect and distinguish PEDV and TGEV in preclinical levels. In this study, we aimed to establish a dual ultrasensitive nanoparticle DNA probe-based PCR assay (dual UNDP-PCR) based on functionalized magnetic bead enrichment and specific nano-technology amplification for simultaneous detection and distinguish diagnosis of PEDV and TGEV. The detection limit of dual UNDP-PCR for single or multiple infections of PEDV and TGEV is 25 copies/g, which is 400 times more sensitive than the currently known duplex RT-PCR, showing better specificity and sensitivity without cross-reaction with other viruses. For pre-clinical fecal samples, the dual UNDP-PCR showed a markedly higher positive detection rate (52.08%) than conventional duplex RT-PCR (13.21%), can rapidly and accurately identify targeted pathogens whenever simple virus infection or co-infection. In summary, this study provides a technique for detecting and distinguishing PEDV and TGEV in preclinical levels, which is high sensitivity, specificity, repeatability, low cost and broad application prospect.


Subject(s)
DNA Probes/chemistry , Gastroenteritis, Transmissible, of Swine/diagnosis , Nanoparticles/chemistry , Porcine epidemic diarrhea virus/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/veterinary , Transmissible gastroenteritis virus/isolation & purification , Animals , DNA Probes/genetics , Diarrhea/veterinary , Diarrhea/virology , Feces/virology , Gastroenteritis, Transmissible, of Swine/virology , Limit of Detection , Magnets , Porcine epidemic diarrhea virus/genetics , RNA, Viral/genetics , RNA, Viral/isolation & purification , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity , Swine , Swine Diseases/diagnosis , Swine Diseases/virology , Transmissible gastroenteritis virus/genetics
13.
J Virol Methods ; 279: 113855, 2020 05.
Article in English | MEDLINE | ID: covidwho-827847

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) causes very high mortality in newborn piglets. The mucosal immune system in the gut must eliminate potential pathogens while maintaining a mutually beneficial relationship with the commensal microbiota. Antibodies derived from the secretory immunoglobulin A (SIgA) class, act as the first line of antigen-specific immunity in the gut by recognizing both pathogens and commensals. Therefore, the measurement of SIgA levels is an important index in evaluating PEDV infections and immune status. A simple and rapid method for the detection of PEDV-specific SIgA using an immunochromatographic test strip has been developed; incorporating a colloidal gold-labeled anti-SIgA secretory component (SC) mAb probe for the detection of anti-PEDV-specific SIgA in swine. On the strip, a gold-labeled anti-SIgA SC mAb was applied to a conjugate pad; purified PEDV particles and goat anti-mouse antibodies were blotted onto a nitrocellulose membrane to form the test and control lines, respectively. Results showed that the immunochromatographic test strip had high sensitivity and specificity. When compared with enzyme-linked immunosorbent assay, kappa value suggesting that the strip could be used to detect PEDV specific SIgA in colostrum samples. Furthermore, the strip assay is rapid and easy to perform with no requirement for professional-level skills or equipment. We found that the immunochromatographic test strip was a rapid, sensitive, and reliable method for the identification of PEDV specific SIgA, indicating its suitability for epidemiological surveillance as well as vaccine immunity when studying PEDV.


Subject(s)
Antibodies, Viral/analysis , Colostrum/immunology , Immunoassay/methods , Immunoglobulin A, Secretory/isolation & purification , Porcine epidemic diarrhea virus/immunology , Animals , Female , Gold Colloid , Reagent Strips , Sensitivity and Specificity , Specific Pathogen-Free Organisms , Swine , Swine Diseases/diagnosis , Swine Diseases/immunology , Swine Diseases/virology
14.
J Vet Diagn Invest ; 32(4): 572-576, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-823306

ABSTRACT

Porcine epidemic diarrhea, a disease caused by porcine epidemic diarrhea virus (PEDV), results in large economic losses to the global swine industry. To manage this disease effectively, it is essential to detect PEDV early and accurately. We developed a sensitive and accurate droplet digital PCR (ddPCR) assay to detect PEDV. The optimal primer-to-probe concentration and melting temperature were identified as 300:200 nM and 59.2°C, respectively. The specificity of the ddPCR assay was confirmed by negative test results for common swine pathogens. The detection limit for the ddPCR was 0.26 copies/µL, which is a 5.7-fold increase in sensitivity compared to that of real-time PCR (rtPCR). Both ddPCR and rtPCR assays exhibited good linearity, although ddPCR provided higher sensitivity for clinical detection compared to that of rtPCR. Our ddPCR methodology provides a promising tool for evaluating the PEDV viral load when used for clinical testing, particularly for detecting samples with low-copy viral loads.


Subject(s)
Coronavirus Infections/veterinary , Polymerase Chain Reaction/veterinary , Porcine epidemic diarrhea virus/isolation & purification , Swine Diseases/diagnosis , Viral Load/veterinary , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Polymerase Chain Reaction/methods , Sensitivity and Specificity , Sus scrofa , Swine , Swine Diseases/virology
15.
Virulence ; 11(1): 707-718, 2020 01 01.
Article in English | MEDLINE | ID: covidwho-517705

ABSTRACT

With the outbreak of the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, coronaviruses have become a global research hotspot in the field of virology. Coronaviruses mainly cause respiratory and digestive tract diseases, several coronaviruses are responsible for porcine diarrhea, such as porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and emerging swine acute diarrhea syndrome coronavirus (SADS-CoV). Those viruses have caused huge economic losses and are considered as potential public health threats. Porcine torovirus (PToV) and coronaviruses, sharing similar genomic structure and replication strategy, belong to the same order Nidovirales. Here, we developed a multiplex TaqMan-probe-based real-time PCR for the simultaneous detection of PEDV, PDCoV, PToV, and SADS-CoV for the first time. Specific primers and TaqMan fluorescent probes were designed targeting the ORF1a region of PDEV, PToV, and SADS-CoV and the ORF1b region of PDCoV. The method showed high sensitivity and specificity, with a detection limit of 1 × 102 copies/µL for each pathogen. A total of 101 clinical swine samples with signs of diarrhea were analyzed using this method, and the result showed good consistency with conventional reverse transcription PCR (RT-PCR). This method improves the efficiency for surveillance of these emerging and reemerging swine enteric viruses and can help reduce economic losses to the pig industry, which also benefits animal and public health.


Subject(s)
Communicable Diseases, Emerging/veterinary , Coronaviridae Infections/veterinary , Coronaviridae/isolation & purification , Polymerase Chain Reaction , Swine Diseases/diagnosis , Animals , Coinfection/diagnosis , Coinfection/veterinary , Communicable Diseases, Emerging/diagnosis , Coronaviridae/genetics , Coronaviridae Infections/diagnosis , Diarrhea/diagnosis , Diarrhea/veterinary , Open Reading Frames/genetics , Polymerase Chain Reaction/standards , RNA, Viral/genetics , Reproducibility of Results , Sensitivity and Specificity , Swine
16.
J Virol Methods ; 283: 113906, 2020 09.
Article in English | MEDLINE | ID: covidwho-437357

ABSTRACT

Since 2014, porcine epidemic diarrhea virus (PEDV) has reemerged in Europe. RT-PCR methods have been described for the detection of PEDV, but none have been validated according to a norm. In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. The method was validated from sample preparation (feces or jejunum) through to nucleic acid extraction and RT-qPCR detection. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. The analytical and diagnostic specificities and sensitivities of this RT-qPCR were 100% in this study. A LoD of 50 genome copies/5 µl of extract from fecal matrices spiked with virus or RNA transcript and 100 genome copies/5 µl of extract from jejunum matrices spiked with virus were obtained. The Lower LQ (LLQ) was 100 genome copies/5 µl and the Upper LQ (ULQ) 108 copies/5 µl. This method is the first, validated according a norm for PEDV and may serve as a global reference method to harmonize detection and quantification of PEDV viral RNA in both field and experimental settings.


Subject(s)
Microbiological Techniques/methods , Porcine epidemic diarrhea virus/isolation & purification , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction/methods , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Diarrhea/virology , Europe , Feces/virology , Limit of Detection , Porcine epidemic diarrhea virus/genetics , RNA, Viral/genetics , Sensitivity and Specificity , Sequence Alignment , Swine , Swine Diseases/diagnosis , Swine Diseases/virology
17.
Virus Res ; 285: 198024, 2020 08.
Article in English | MEDLINE | ID: covidwho-276152

ABSTRACT

Discovered in 2017, swine enteric alphacoronavirus (SeACoV), also known as swine acute diarrhea syndrome coronavirus (SADS-CoV) or porcine enteric alphacoronavirus (PEAV), is the fifth porcine CoV identified in diarrheal piglets. The presumed name "SADS-CoV" may not be appropriate since current studies have not provided strong evidence for high pathogenicity of the virus. SeACoV was the most recently recognized CoV of potential bat origin prior to the novel human severe acute respiratory syndrome CoV 2 (SARS-CoV-2), associated with the pandemic CoV disease 2019 (COVID-19). Although SeACoV is recognized as a regional epizootic virus currently, it possesses the most extensive cell species tropism in vitro among known CoVs. This review summarizes the emergence of SeACoV and updates the research progress made from 2017 to early 2020, mainly focusing on the etiology, epidemiology, evolutionary perspective, potential for interspecies transmission, pathogenesis and diagnosis.


Subject(s)
Alphacoronavirus , Coronavirus Infections/veterinary , Swine Diseases/virology , Alphacoronavirus/genetics , Alphacoronavirus/pathogenicity , Alphacoronavirus/ultrastructure , Animals , Cell Line , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Genome, Viral , Humans , Molecular Epidemiology , Species Specificity , Swine , Swine Diseases/diagnosis , Swine Diseases/epidemiology , Swine Diseases/transmission , Viral Tropism
18.
J Clin Virol ; 128: 104391, 2020 07.
Article in English | MEDLINE | ID: covidwho-252517

ABSTRACT

BACKGROUND: During the past two decades, three novel coronaviruses (CoVs) have emerged to cause international human epidemics with severe morbidity. CoVs have also emerged to cause severe epidemics in animals. A better understanding of the natural hosts and genetic diversity of CoVs are needed to help mitigate these threats. OBJECTIVE: To design and evaluate a molecular diagnostic tool for detection and identification of all currently recognized and potentially future emergent CoVs from the Orthocoronavirinae subfamily. STUDY DESIGN AND RESULTS: We designed a semi-nested, reverse transcription RT-PCR assay based upon 38 published genome sequences of human and animal CoVs. We evaluated this assay with 14 human and animal CoVs and 11 other non-CoV respiratory viruses. Through sequencing the assay's target amplicon, the assay correctly identified each of the CoVs; no cross-reactivity with 11 common respiratory viruses was observed. The limits of detection ranged from 4 to 4 × 102 copies/reaction, depending on the CoV species tested. To assess the assay's clinical performance, we tested a large panel of previously studied specimens: 192 human respiratory specimens from pneumonia patients, 5 clinical specimens from COVID-19 patients, 81 poultry oral secretion specimens, 109 pig slurry specimens, and 31 aerosol samples from a live bird market. The amplicons of all RT-PCR-positive samples were confirmed by Sanger sequencing. Our assay performed well with all tested specimens across all sample types. CONCLUSIONS: This assay can be used for detection and identification of all previously recognized CoVs, including SARS-CoV-2, and potentially any emergent CoVs in the Orthocoronavirinae subfamily.


Subject(s)
Bird Diseases/diagnosis , Coronavirus Infections/diagnosis , Coronavirus/isolation & purification , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Reverse Transcriptase Polymerase Chain Reaction/methods , Swine Diseases/diagnosis , Animals , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Bird Diseases/virology , Birds , COVID-19 , Coronavirus/genetics , Coronavirus Infections/virology , Genetic Variation , Humans , Pandemics , Pneumonia, Viral/virology , Severe acute respiratory syndrome-related coronavirus/genetics , Severe acute respiratory syndrome-related coronavirus/isolation & purification , SARS-CoV-2 , Swine , Swine Diseases/virology
20.
Arch Virol ; 165(4): 845-851, 2020 Apr.
Article in English | MEDLINE | ID: covidwho-877

ABSTRACT

Porcine deltacoronavirus (PDCoV) is a novel coronavirus that can cause vomiting and watery diarrhea in pigs and death in piglets. Since PDCoV was first detected in 2009 in Hong Kong, the prevalence of PDCoV has increased in recent years, resulting in serious economic losses to the swine industry. The coronavirus spike (S) protein is an antigen that has been demonstrated to contain epitopes that induce neutralizing antibodies. The presence of serum and milk IgA antibodies against pathogens that replicate primarily on mucosal surfaces is important for mucosal immunity. Here, an indirect anti-PDCoV IgA antibody enzyme-linked immunosorbent assay (PDCoV S1 IgA ELISA) using the purified S1 portion of S protein as the coating antigen was developed to detect PDCoV IgA antibodies in serum and sow's milk. A receiver operating characteristic (ROC) curve analysis showed high specificity and sensitivity of the PDCoV-S1-IgA-ELISA based on samples confirmed by IFA. Anti-PDCoV IgA antibodies in 152 serum samples and 65 milk samples collected from six farms that had experienced diarrhea outbreaks within previous last two years were detected by this assay, and 62.5% of the serum samples and 100% of the milk samples were positive for PDCoV. The indirect ELISA method established in this study will provide a convenient tool for measurement of serum and milk IgA levels against PDCoV in pig herds, rapid detection of PDCoV infection in pigs, and evaluation of the immunogenicity of vaccines.


Subject(s)
Antibodies, Viral/blood , Coronavirus Infections/veterinary , Coronavirus/immunology , Immunoglobulin A/blood , Swine Diseases/blood , Animals , Coronavirus/genetics , Coronavirus/isolation & purification , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Enzyme-Linked Immunosorbent Assay/methods , Swine , Swine Diseases/diagnosis
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