Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014 - Volume 20, Number 10—October 2014 - Emerging Infectious Disease journal - CDC
Volume 20, Number 10—October 2014
Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014
Porcine epidemic diarrhea virus (PEDV) (family Coronaviridae family, genus alphacoronavirus) has an enveloped, single-stranded, positive-sense RNA genome of ≈28 kb (1). The 5′ two thirds of the genome contains 2 large open reading frames (ORFs), 1a and 1b, that encode 2 nonstructural polyproteins, pp1a and pp1b, that direct genome replication and transcription. The remaining PEDV genome contains ORFs specifying structural and nonstructural proteins in the following order: spike (S), ORF 3, envelope (E), membrane (M) and nucleoprotein (N) (2,3).
Porcine epidemic diarrhea (PED) was first documented in the United Kingdom in 1971 as a swine disease resembling transmissible gastroenteritis (4). In 1978, the etiologic agent of PED was identified in Belgium as a new coronavirus and was designated as PEDV, prototype strain CV777 (1). Within 2 decades, PEDV was reported in several other European countries; Hungary, Italy, Germany, France, Switzerland, and the Czech Republic (5). Currently, the virus causes only isolated outbreaks in Europe. In Asia, PEDV was first identified in 1982 and is now considered endemic, causing substantial economic losses to pork producers in China, South Korea, Thailand, and Vietnam (5). However, it was not until 2010 that massive PED outbreaks were reported in China; the outbreaks have been characterized by 80%–100% illness among infected swine herds and a 50%–90% mortality rate among infected suckling piglets (6–8).
North America was free of PEDV until its sudden and intense emergence in the United States in April 2013 (9). Since then, PEDV has spread rapidly across the United States, causing high rates of death among piglets and substantial economic losses (10–12). As of July 24, 2014, PEDV had been reported in 31 US states (13). In Canada, PEDV was first detected in January 2014 on a pig farm in Ontario Province; since then, the virus has been reported on farms in Manitoba, Prince Edward Island, and Quebec Provinces (14), continuing its spread throughout North America. There are no official reports of PEDV in Mexico; however, in 2013, the University of Minnesota (UM) Veterinary Diagnostic Laboratory (St. Paul, MN, USA) tested swine samples from Mexico and found them positive for PEDV.
The complete genomic sequence of the PEDV prototype strain, CV777, was determined in 2001 (15). A decade later, complete genomes were sequenced for several PEDV strains from China and South Korea (6,8,15–22). Comparisons of full-length genomes showed that different PEDV strains are more closely related to bat alphacoronaviruses than to other known alphacoronaviruses (23), suggesting that interspecies transmission of coronavirus may have occurred decades ago between bats and pigs or through an intermediate host.
Phylogenetic analysis has shown that some PEDV strains that have reported decreased virulence in the field contain distinct insertions and deletions in the S gene (S INDELS). Soon after the emergence of PEDV in the United States, the complete genomes were determined for several strains from Colorado, Minnesota, and Iowa, USA (10,24,25); these PEDV strains shared ≥99.5% nt identity with strain AH2012 from China, suggesting a common ancestor for that strain and US strains (25,26). An additional 43 complete-genome PEDV sequences are now available: 16 from the United States, including a recent PEDV variant from Ohio (OH851) that contains specific S INDELs and was reported with reduced disease severity (27); 23 from China; and 4 from South Korea. In addition, new, complete-genome PEDV sequences are being generated and released almost monthly.
A major impediment to understanding the origin, evolution, and diversity of PEDV in the United States is the lack of complete-genome PEDV sequences worldwide. To determine the phylogenetic relationship between the new US strains and the globally emerging and historic PEDV strains, we sequenced and analyzed the complete genomes of 74 strains from North America.
Dr Vlasova is a research scientist at The Ohio State University. Her primary research interest is the use of a gnotobiotic pig model to focus on viral epidemiology, vaccine development, gut microbiome and probiotic effects on immunity, and innate immune responses to enteric viral infections. Dr Marthaler is a scientist at the University of Minnesota. His primary research interests are the epidemiology and phylogenetic analysis of porcine enteric viruses.
We thank the staff of the UM Veterinary Diagnostic Laboratory for technical assistance.
Funding was provided by the Rapid Agricultural Response Fund, established by the Minnesota legislature and administered by the UM Agricultural Experiment Station; the UM Veterinary Diagnostic Laboratory; and the National Pork Board (grant no. 13-238).
- Pensaert MB, de Bouck P. A new coronavirus-like particle associated with diarrhea in swine. Arch Virol. 1978;58:243–7.
- Duarte M, Laude H. Sequence of the spike protein of the porcine epidemic diarrhoea virus. J Gen Virol. 1994;75:1195–200.
- Bridgen A, Tobler K, Ackermann M. Identification of coronaviral conserved sequences and application to viral genome amplification. Adv Exp Med Biol. 1993;342:81–2.
- Wood EN. An apparently new syndrome of porcine epidemic diarrhoea. Vet Rec. 1977;100:243–4.
- Song D, Park B. Porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines. Virus Genes.2012;44:167–75.
- Luo Y, Zhang J, Deng X, Ye Y, Liao M, Fan H. Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in South China. J Virol. 2012;86:9551.
- Gao Y, Kou Q, Ge X, Zhou L, Guo X, Yang H. Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China. Arch Virol. 2013;158:711–5.
- Fan H, Zhang J, Ye Y, Tong T, Xie K, Liao M. Complete genome sequence of a novel porcine epidemic diarrhea virus in south China. J Virol.2012;86:10248–9.
- Stevenson GW, Hoang H, Schwartz KJ, Burrough ER, Sun D, Madson D, Emergence of Porcine Epidemic Diarrhea Virus in the United States: clinical signs, lesions, and viral genomic sequences. J Vet Diagn Invest. 2013;25:649–54.
- Chen Q, Li G, Stasko J, Thomas JT, Stensland WR, Pillatzki AE, Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States. J Clin Microbiol. 2014;52:234–43.
- Cima G. Viral disease affects US pigs: porcine epidemic diarrhea found in at least 11 states. J Am Vet Med Assoc. 2013;243:30–1 .
- Mole B. Deadly pig virus slips through US borders. Nature. 2013;499:388.
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services. Swine enteric coronavirus disease testing summary report. 2014 July 24 [cited 2014 Jul 24].http://www.aphis.usda.gov/animal_health/animal_dis_spec/swine/downloads/swine_report_7_24_14.pdf
- Canadian Swine Health Board. Porcine epidemic diarrhea (PED) Alert. 2014 [cited 2014 May 27]. http://www.swinehealth.ca/PED-Alert.php
- Kocherhans R, Bridgen A, Ackermann M, Tobler K. Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence. Virus Genes. 2001;23:137–44.
- Chen J, Liu X, Shi D, Shi H, Zhang X, Feng L. Complete genome sequence of a porcine epidemic diarrhea virus variant. J Virol. 2012;86:3408.
- Chen J, Wang C, Shi H, Qiu HJ, Liu S, Shi D, Complete genome sequence of a Chinese virulent porcine epidemic diarrhea virus strain. J Virol.2011;85:11538–9.
- Li B, Liu H, He K, Guo R, Ni Y, Du L, Complete genome sequence of a recombinant porcine epidemic diarrhea virus strain from eastern China. Genome Announc. 2013;1:e00105-13.
- Tian Y, Su D, Zhang H, Chen RA, He D. Complete genome sequence of a very virulent porcine epidemic diarrhea virus strain, CH/GDGZ/2012, isolated in southern China. Genome Announc. 2013;1:e00645-13.
- Park SJ, Kim HK, Song DS, An DJ, Park BK. Complete genome sequences of a Korean virulent porcine epidemic diarrhea virus and its attenuated counterpart. J Virol. 2012;86:5964.
- Wang XM, Niu BB, Yan H, Gao DS, Huo JY, Chen L, Complete genome sequence of a variant porcine epidemic diarrhea virus strain isolated in central China. Genome Announc. 2013;1:e00243-12.
- Wei ZY, Lu WH, Li ZL, Mo JY, Zeng XD, Zeng ZL, Complete genome sequence of novel porcine epidemic diarrhea virus strain GD-1 in China. J Virol.2012;86:13824–5.
- Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, Prevalence and genetic diversity of coronaviruses in bats from China. J Virol.2006;80:7481–90.
- Hoang H, Killian ML, Madson DM, Arruda PH, Sun D, Schwartz KJ, Full-length genome sequence of a plaque-cloned virulent porcine epidemic diarrhea virus isolate (USA/Iowa/18984/2013) from a midwestern US swine herd. Genome Announc. 2013;1:e01049-13.
- Marthaler D, Jiang Y, Otterson T, Goyal S, Rossow K, Collins J. Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States. Genome Announc. 2013;1:e00555-13.
- Huang YW, Dickerman AW, Pineyro P, Li L, Fang L, Kiehne R, Origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the United States. MBio. 2013;4:e00737–13.
- Wang L, Byrum B, Zhang Y. New variant of porcine epidemic diarrhea virus, United States, 2014. Emerg Infect Dis. 2014;20:917–9.
- Marthaler D, Rossow K, Culhane M, Collins J, Goyal S, Ciarlet M, Identification, phylogenetic analysis and classification of porcine group C rotavirus VP7 sequences from the United States and Canada. Virology. 2013;446:189–98.
- Marthaler D, Rossow K, Gramer M, Collins J, Goyal S, Tsunemitsu H, Detection of substantial porcine group B rotavirus genetic diversity in the United States, resulting in a modified classification proposal for G genotypes. Virology. 2012;433:85–96.
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol.2013;30:2725–9.
- Bálint A, Farsang A, Zadori Z, Hornyak A, Dencso L, Almazan F, Molecular characterization of feline infectious peritonitis virus strain DF-2 and studies of the role of ORF3abc in viral cell tropism. J Virol. 2012;86:6258–67.
Suggested citation for this article: Vlasova AN, Marthaler D, Wang Q, Culhane MR, Rossow KD, Rovira A, et al. Distinct characteristics and complex evolution of PEDV strains, North America, May 2013–February 2014. Emerg Infect Dis. 2014 Oct [date cited].http://dx.doi.org/10.3201/eid2010.140491
1These first authors contributed equally to this article.