Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus

Journal of Virological Methods

Volumn 234, Issue , 2016, Pages 34-42

  Zhang, Jianqiang ^a   Tsai, Yun Long ^b   Lee, Pei Yu Alison ^b   Chen, Qi ^a   Zhang, Yan ^c   Chiang, Cheng Jen ^b   Shen, Yu Han ^b   Li, Fu Chun ^b   Chang, Hsiao Fen Grace ^b   Gauger, Phillip C ^a   Harmon, Karen M ^a   Wang, Hwa Tang Thomas ^b  

^a IOWA STATE UNIVERSITY   (United States)

^b GeneReach USA   (United States)

^c Animal Disease Diagnostic Laboratory   (United States)

Author keywords

Duplex real time RT PCR; IiPCR; PDCoV; PEDV; Porcine deltacoronavirus; Porcine epidemic diarrhea virus

Indexed keywords

ARTICLE; BRACHYSPIRA HYODYSENTERIAE; CLOSTRIDIUM PERFRINGENS; CORONAVIRIDAE; CORONAVIRUS INFECTION; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DILUTION; ENCEPHALITIS VIRUS; EPIDEMIC; ESCHERICHIA COLI; FECES ANALYSIS; GENE SEQUENCE; INTERMETHOD COMPARISON; MICROORGANISM DETECTION; MYCOBACTERIUM INTRACELLULARE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTOCLOSTRIDIUM DIFFICILE; POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION SYSTEM; PORCINE DELTACORONAVIRUS; PORCINE EPIDEMIC DIARRHEA; PORCINE EPIDEMIC DIARRHEA VIRUS; PORCINE RESPIRATORY CORONAVIRUS; PORCINE ROTAVIRUS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION LOOP MEDIATED ISOTHERMAL AMPLIFICATION; RNA EXTRACTION; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SENSITIVITY AND SPECIFICITY; SINGLEPLEX REVERSE TRANSCRIPTION INSULATED ISOTHERMAL POLYMERASE CHAIN REACTION; TRANSMISSIBLE GASTROENTERITIS VIRUS; VIRUS DETECTION; VIRUS STRAIN; ANIMAL; CORONAVIRUS INFECTIONS; EVALUATION STUDY; FECES; GENETICS; ISOLATION AND PURIFICATION; PIG; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SWINE DISEASES; TEMPERATURE; VETERINARY; VIROLOGY;

ANIMALS; CORONAVIRIDAE; CORONAVIRUS INFECTIONS; FECES; POLYMERASE CHAIN REACTION; PORCINE EPIDEMIC DIARRHEA VIRUS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SWINE; SWINE DISEASES; TEMPERATURE;

EID: 84962786148     PISSN: 01660934     EISSN: 18790984     Source Type: Journal    
DOI: 10.1016/j.jviromet.2016.03.016     Document Type: Article

References (47)

1. Alonso C., Goede D.P., Morrison R.B., Davies P.R., Rovira A., Marthaler D.G., Torremorell M. Evidence of infectivity of airborne porcine epidemic diarrhea virus and detection of airborne viral RNA at long distances from infected herds. Vet. Res. 2014, 45:73.
2. Balasuriya U.B., Lee P.Y., Tiwari A., Skillman A., Nam B., Chambers T.M., Tsai Y.L., Ma L.J., Yang P.C., Chang H.F., Wang H.T. Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-pCR (iiRT-pCR) assay using the POCKIT Nucleic Acid Analyzer. J. Virol. Methods 2014, 207:66-72.
3. Caraguel C.G., Stryhn H., Gagne N., Dohoo I.R., Hammell K.L. Selection of a cutoff value for real-time polymerase chain reaction results to fit a diagnostic purpose: analytical and epidemiologic approaches. J. Vet. Diagn. Invest. 2011, 23:2-15.
4. Chen Q., Li G., Stasko J., Thomas J.T., Stensland W.R., Pillatzki A.E., Gauger P.C., Schwartz K.J., Madson D., Yoon K.J., Stevenson G.W., Burrough E.R., Harmon K.M., Main R.G., Zhang J. Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States. J. Clin. Microbiol. 2014, 52:234-243.
5. Chen Q., Gauger P., Stafne M., Thomas J., Arruda P., Burrough E., Madson D., Brodie J., Magstadt D., Derscheid R., Welch M., Zhang J. Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets. Virology 2015, 482:51-59.
6. Chen Q., Gauger P.C., Stafne M.R., Thomas J.T., Madson D.M., Huang H., Zheng Y., Li G., Zhang J. Pathogenesis comparison between the United States porcine epidemic diarrhea virus prototype and S-INDEL-variant strains in conventional neonatal piglets. J. Gen. Virol. 2016, [Epub ahead of print]. 10.1099/jgv.0.000419.
7. Chen Q., Thomas J.T., Giménez-Lirola L.G., Hardham J.M., Gao Q., Gerber P.F., Opriessnig T., Zheng Y., Li G., Gauger P.C., Madson D.M., Magstadt D., Zhang J. Evaluation of serological cross-reactivity and cross-neutralization between the United States porcine epidemic diarrhea virus prototype and S-INDEL-variant strains. BMC Vet. Res. 2016, 12(1):70. 10.1186/s12917-016-0697-5.
8. Grasland B., Bigault L., Bernard C., Quenault H., Toulouse O., Fablet C., Rose N., Touzain F., Blanchard Y. Complete genome sequence of a porcine epidemic diarrhea s gene indel strain isolated in france in december 2014. Genome Announc. 2015, 3(3). e00535-15.
9. Huang Y.W., Dickerman A.W., Pineyro P., Li L., Fang L., Kiehne R., Opriessnig T., Meng X.J. Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States. MBio 2013, 4(5). e00737-13.
10. Jung K., Wang Q., Scheuer K.A., Lu Z., Zhang Y., Saif L.J. Pathology of US porcine epidemic diarrhea virus strain PC21A in gnotobiotic pigs. Emerg. Infect. Dis. 2014, 20:662-665.
11. Jung K., Hu H., Eyerly B., Lu Z., Chepngeno J., Saif L.J. Pathogenicity of 2 porcine deltacoronavirus strains in gnotobiotic pigs. Emerg. Infect. Dis. 2015, 21:650-654.
12. Kim S.H., Kim I.J., Pyo H.M., Tark D.S., Song J.Y., Hyun B.H. Multiplex real-time RT-PCR for the simultaneous detection and quantification of transmissible gastroenteritis virus and porcine epidemic diarrhea virus. J. Virol. Methods 2007, 146:172-177.
13. Lee S., Lee C. Complete genome characterization of korean porcine deltacoronavirus strain KOR/KNU14-04/2014. Genome Announc. 2014, 2.
14. Li W., Li H., Liu Y., Pan Y., Deng F., Song Y., Tang X., He Q. New variants of porcine epidemic diarrhea virus, China, 2011. Emerg. Infect. Dis. 2012, 18:1350-1353.
15. Li G., Chen Q., Harmon K.M., Yoon K.J., Schwartz K.J., Hoogland M.J., Gauger P.C., Main R.G., Zhang J. Full-length genome sequence of porcine deltacoronavirus strain USA/IA/2014/8734. Genome Announc. 2014, 2.
16. Lowe J., Gauger P., Harmon K., Zhang J., Connor J., Yeske P., Loula T., Levis I., Dufresne L., Main R. Role of transportation in spread of porcine epidemic diarrhea virus infection, United States. Emerg. Infect. Dis. 2014, 20:872-874.
17. Lung O., Pasick J., Fisher M., Buchanan C., Erickson A., Ambagala A. Insulated isothermal reverse transcriptase PCR (iiRT-PCR) for rapid and sensitive detection of classical swine fever virus. Transbound. Emerg. Dis. 2015, 10.1111/tbed.12318.
18. Ma Y., Zhang Y., Liang X., Lou F., Oglesbee M., Krakowka S., Li J. Origin, evolution, and virulence of porcine deltacoronaviruses in the United States. MBio 2015, 6:e00064.
19. Madson D.M., Magstadt D.R., Arruda P.H., Hoang H., Sun D., Bower L.P., Bhandari M., Burrough E.R., Gauger P.C., Pillatzki A.E., Stevenson G.W., Wilberts B.L., Brodie J., Harmon K.M., Wang C., Main R.G., Zhang J., Yoon K.J. Pathogenesis of porcine epidemic diarrhea virus isolate (US/Iowa/18984/2013) in 3-week-old weaned pigs. Vet. Microbiol. 2014, 174:60-68.
20. Marthaler D., Raymond L., Jiang Y., Collins J., Rossow K., Rovira A. Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus. Emerg. Infect. Dis. 2014, 20:1347-1350.
21. Mesquita J.R., Hakze-van der Honing R., Almeida A., Lourenco M., van der Poel W.H., Nascimento M.S. AT outbreak of porcine epidemic diarrhea virus in Portugal, 2015. Transbound. Emerg. Dis. 2015, 62:586-588.
22. Opriessnig T., Xiao C.T., Gerber P.F., Zhang J., Halbur P.G. Porcine epidemic diarrhea virus RNA present in commercial spray-dried porcine plasma is not infectious to naive pigs. PLoS One 2014, 9:e104766.
23. Paarlberg P.L. Updated estimated economic welfare impacts of porcine epidemic diarrhea virus (PEDV) 2014, http://ageconsearch.umn.edu/bitstream/174517/2/14-4.%20Updated%20Estimated%20Economic%20Welfare%20Impacts%20of%20PEDV.pdf.
24. Pasick J., Berhane Y., Ojkic D., Maxie G., Embury-Hyatt C., Swekla K., Handel K., Fairles J., Alexandersen S. Investigation into the role of potentially contaminated feed as a source of the first-detected outbreaks of porcine epidemic diarrhea in Canada. Transbound. Emerg. Dis. 2014, 61:397-410.
25. Puranaveja S., Poolperm P., Lertwatcharasarakul P., Kesdaengsakonwut S., Boonsoongnern A., Urairong K., Kitikoon P., Choojai P., Kedkovid R., Teankum K., Thanawongnuwech R. Chinese-like strain of porcine epidemic diarrhea virus, Thailand. Emerg. Infect. Dis. 2009, 15:1112-1115.
26. Sinha A., Gauger P., Zhang J., Yoon K.J., Harmon K. PCR-based retrospective evaluation of diagnostic samples for emergence of porcine deltacoronavirus in US swine. Vet. Microbiol. 2015, 179:296-298.
27. Song D., Park B. Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines. Virus Genes 2012, 44:167-175.
28. Song D., Zhou X., Peng Q., Chen Y., Zhang F., Huang T., Zhang T., Li A., Huang D., Wu Q., He H., Tang Y. Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis. Transbound. Emerg. Dis. 2015, 62:575-580.
29. Stadler J., Zoels S., Fux R., Hanke D., Pohlmann A., Blome S., Weissenbock H., Weissenbacher-Lang C., Ritzmann M., Ladinig A. Emergence of porcine epidemic diarrhea virus in southern Germany. BMC Vet. Res. 2015, 11:142.
30. Stevenson G.W., Hoang H., Schwartz K.J., Burrough E.R., Sun D., Madson D., Cooper V.L., Pillatzki A., Gauger P., Schmitt B.J., Koster L.G., Killian M.L., Yoon K.J. Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences. J. Vet. Diagn. Invest. 2013, 25:649-654.
31. Sun R.Q., Cai R.J., Chen Y.Q., Liang P.S., Chen D.K., Song C.X. Outbreak of porcine epidemic diarrhea in suckling piglets, China. Emerg. Infect. Dis. 2012, 18:161-163.
32. Theuns S., Conceicao-Neto N., Christiaens I., Zeller M., Desmarets L.M., Roukaerts I.D., Acar D.D., Heylen E., Matthijnssens J., Nauwynck H.J. Complete genome sequence of a porcine epidemic diarrhea virus from a novel outbreak in belgium, january 2015. Genome Announc. 2015, 3.
33. Thomas J.T., Chen Q., Gauger P.C., Gimenez-Lirola L.G., Sinha A., Harmon K.M., Madson D.M., Burrough E.R., Magstadt D.R., Salzbrenner H.M., Welch M.W., Yoon K.J., Zimmerman J.J., Zhang J. Effect of porcine epidemic diarrhea virus infectious doses on infection outcomes in naive conventional neonatal and weaned pigs. PLoS One 2015, 10:e0139266.
34. Tsai Y.L., Lin Y.C., Chou P.H., Teng P.H., Lee P.Y. Detection of white spot syndrome virus by polymerase chain reaction performed under insulated isothermal conditions. J. Virol. Methods 2012, 181:134-137.
35. Tsai Y.L., Wang H.T., Chang H.F., Tsai C.F., Lin C.K., Teng P.H., Su C., Jeng C.C., Lee P.Y. Development of TaqMan probe-based insulated isothermal PCR (iiPCR) for sensitive and specific on-site pathogen detection. PLoS One 2012, 7:e45278.
36. Tsai Y.L., Wang H.C., Lo C.F., Tang-Nelson K., Lightner D., Ou B.R., Hour A.L., Tsai C.F., Yen C.C., Chang H.F., Teng P.H., Lee P.Y. Validation of a commercial insulated isothermal PCR-based POCKIT test for rapid and easy detection of white spot syndrome virus infection in Litopenaeus vannamei. PLoS One 2014, 9:e90545.
37. Vlasova A.N., Marthaler D., Wang Q., Culhane M.R., Rossow K.D., Rovira A., Collins J., Saif L.J. Distinct characteristics and complex evolution of PEDV strains, north america, May 2013-February 2014. Emerg. Infect. Dis. 2014, 20:1620-1628.
38. Vui D.T., Thanh T.L., Tung N., Srijangwad A., Tripipat T., Chuanasa T., Nilubol D. Complete genome characterization of porcine epidemic diarrhea virus in Vietnam. Arch. Virol 2015, 160:1931-1938.
39. Wang L., Byrum B., Zhang Y. 2014. Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA. Emerg. Infect. Dis. 2014, 20:1227-1230.
40. Wang L., Byrum B., Zhang Y. New variant of porcine epidemic diarrhea virus, United States, 2014. Emerg. Infect. Dis. 2014, 20:917-919.
41. Wang L., Zhang Y., Byrum B. Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States. J. Virol. Methods 2014, 207:154-157.
42. Wilkes R.P., Tsai Y.L., Lee P.Y., Lee F.C., Chang H.F., Wang H.T. Rapid and sensitive detection of canine distemper virus by one-tube reverse transcription-insulated isothermal polymerase chain reaction. BMC Vet. Res. 2014, 10:213.
43. Wilkes R.P., Tsai Y.L., Lee P.Y., Lee F.C., Chang H.F., Wang H.T. Rapid and sensitive detection of canine distemper virus by one-tube reverse transcription-insulated isothermal polymerase chain reaction. BMC Vet. Res. 2014, 10:213.
44. Wilkes R.P., Kania S.A., Tsai Y.L., Lee P.Y., Chang H.H., Ma L.J., Chang H.F., Wang H.T. Rapid and sensitive detection of Feline immunodeficiency virus using an insulated isothermal PCR-based assay with a point-of-need PCR detection platform. J. Vet. Diagn. Invest. 2015, 27:510-515.
45. Wilkes R.P., Lee P.Y., Tsai Y.L., Tsai C.F., Chang H.H., Chang H.F., Wang H.T. An insulated isothermal PCR method on a field-deployable device for rapid and sensitive detection of canine parvovirus type 2 at points of need. J. Virol. Methods 2015, 220:35-38.
46. Woo P.C., Huang Y., Lau S.K., Yuen K.Y. Coronavirus genomics and bioinformatics analysis. Viruses 2010, 2:1804-1820.
47. Woo P.C., Lau S.K., Lam C.S., Lau C.C., Tsang A.K., Lau J.H., Bai R., Teng J.L., Tsang C.C., Wang M., Zheng B.J., Chan K.H., Yuen K.Y. Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J. Virol. 2012, 86:3995-4008.