Complete Genome Sequences of a Korean Virulent Porcine Epidemic Diarrhea Virus and Its Attenuated Counterpart

Abstract

cA virulent porcine epidemic diarrhea virus (PEDV) strain, DR13, was obtained from suckling pigs suspected of having porcine epidemic diarrhea in 1999 in Korea, and its attenuated counterpart was derived from virulent strain DR13 by serial propagation in Vero cells. This report describes the first complete genome sequences of virulent PEDV and its attenuated counterpart, which will provide important insights into the molecular basis of the attenuation of PEDV. P orcine epidemic diarrhea virus (PEDV), first reported in 1978 (6), is an enveloped, single-stranded RNA virus belonging to the family Coronaviridae. PEDV causes an acute and highly contagious enteric disease characterized by severe diarrhea, dehydration, and a high mortality rate in swine. A virulent strain, DR13, was obtained from suckling pigs suspected of having porcine epidemic diarrhea in 1999, and an attenuated counterpart was derived from virulent strain DR13 by serial propagation in Vero cells (7). To date, the complete genome sequences of a virulent and attenuated PEDV strain pair have not been reported. Therefore, to provide important insights into the molecular basis of PEDV attenuation, it is necessary to analyze the complete genome sequences of virulent DR13 and its attenuated counterpart.Both ends of the genomes of the virulent and attenuated PEDV strain pair were confirmed by a system for the rapid amplification of cDNA ends (Invitrogen Corp.). The other parts were generated by analyzing ϳ28 overlapping cDNA fragments to complete the entire genomes and were determined by primer-walking sequencing. The genome of virulent DR13 is 28,029 nucleotides (nt) long after exclusion of the poly(A) tail, whereas that of attenuated DR13 contains 27,931 nt [excluding the poly(A) tail], which is 95 to 102 nt shorter than those of other sequenced virulent PEDVs (1, 4). The organization of the genomes of the virulent and attenuated PEDV strain pair is similar to that of other reported PEDV genomes (1, 4), with the characteristic gene order 5=-replicase (1a/ 1b)-S-ORF3-E-M-N-3=, and both their 5= (292 nt) and 3= (334 and 333 nt for virulent and attenuated DR13, respectively) ends contain untranslated regions (UTRs). Downstream of the 5= UTR, the PEDV genome contains two large open reading frames (ORF1a and ORF1ab) encoding two large nonstructural precursor polyproteins (replicases pp1a and pp1ab), the latter of which is expressed by programmed translational frameshifting (3). The precursor polyproteins are proteolytically ϳ15 replicase proteins (5). While the sizes of ORF1a and ORF1ab of virulent DR13 are 12,354 nt (nt 293 to 12,646) and 20,346 nt (nt 293 to 12,601 and 12601 to 20,637), those of attenuated DR13 are 12,330 nt (nt 293 to 12622) and 20,322 nt (nt 293 to 12,577 and 12,577 to 20,613). Moreover, and surprisingly, attenuated DR13 has 4,149-, 276-, and 210-nt ORFs in its S, ORF3 and E genes, which are 3, 399, and 21 nt shorter than those of its virulent counterpart.The virulent and attenuated DR13 strains have hexameric XUA(A/G)AC motifs at sites i...

Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014

“…A comparison of the complete genome sequences of strain DR13, a virulent PEDV strain from Korea, and its attenuated counterpart showed specific changes in ORFs 1ab and 3 and in S and E genes of the attenuated strain; as a result of these changes, the ORFs and genes in the attenuated strain are shorter than those in the virulent strain ( 20 ). However, in contrast to the findings for the virulent–attenuated DR13 strain pair and the strong evidence of the role of ORF 3 alterations in the pathogenesis of or cell culture adaptation of feline infectious peritonitis virus ( 31 ), we did not observe any of the following: characteristic changes in the ORF 3–E gene region, other than S INDELs; a potentially recombinant ORF 1b region; or any reports of decreased severity of PEDV in the field.…”

Genetic variation analysis of reemerging porcine epidemic diarrhea virus prevailing in central China from 2010 to 2011

“…The complete genome sequence of PEDV is approximately 28 kb, including a 5′ untranslated region (UTR), a 3′ UTR and at least seven open reading frames (ORFs): ORF1a, ORF1b, and ORF2-6 [2]. The 5′ two-thirds of the genome are occupied by ORF1a and ORF1b, which encode nonstructural proteins.…”

Complete Genome Sequence of a Virulent Porcine Epidemic Diarrhea Virus Strain

“…The complete genome of ZJCZ4 exhibited 98.1%, 97.3%, 96.9%, and 97.3% nucleotide homologies with those of CH/FJND-3/ 2011, CH/S, CV777, and attenuated DR13, respectively (2,5). Among the genes, the S gene of ZJCZ4 encoding the amino acid sequence shows 93.2% to 97.0% homology, which is a lower level of homology than those found in other strains.…”