2014 Complete Genome Characterization of Korean Porcine Deltacoronavirus Strain KOR_KNU14-04_2014

2 Pages·2014·0.14 MB·English

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Complete Genome Characterization of Korean Porcine Deltacoronavirus
Strain KOR/KNU14-04/2014
SunheeLee,ChangheeLee
AnimalVirologyLaboratory,SchoolofLifeSciences,BK21PlusKNUCreativeBioResearchGroup,KyungpookNationalUniversity,Daegu,RepublicofKorea
InApril2014,porcinedeltacoronavirus(PDCoV)wasfirstidentifiedinfecesfromdiarrheicpigletsinSouthKoreaandfoundto
becloselyrelatedtootherPDCoVstrains.ThecompletegenomeoftheKoreanPDCoVstrain,KOR/KNU14-04/2014,wasse-
quencedandanalyzedtocharacterizePDCoVcirculatinginSouthKorea.
Received5October2014 Accepted17October2014 Published26November2014
CitationLeeS,LeeC.2014.CompletegenomecharacterizationofKoreanporcinedeltacoronavirusstrainKOR/KNU14-04/2014.GenomeAnnounc.2(6):e01191-14.doi:
10.1128/genomeA.01191-14.
Copyright©2014LeeandLee.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttribution3.0Unportedlicense.
AddresscorrespondencetoChangheeLee,[email protected].
Coronavirusesareenveloped,single-stranded,positive-sense 24,002to25,030),the603-ntNS7gene(nt24,096to24,698),and
RNAvirusesbelongingtothefamilyCoronaviridaeofthe the392-nt3=UTR.
orderNidovirales,whicharefurtherdividedinto4genera,Al- The full-length PEDV genome of KNU14-04 has nucleotide
phacoronavirus,Betacoronavirus,Gammacoronavirus,andDel- identitiesof98.8to99.0%and99.6to99.8%to2Chinesestrains
tacoronavirus(1,2).VirusesoftheAlphacoronavirusandBeta- (GenBank accession numbers JQ065042 and JQ065043) and 8
coronavirus genera have been detected in swine (3). The fifth United States strains (accession numbers KJ462462, KJ481931,
porcinecoronaviruswasidentifiedin2012inaninvestigation KJ567050, KJ569769, KJ601777, KJ601778, KJ601779, and
to discover new deltacoronaviruses in mammals and birds KJ601780), respectively. Comparing the complete genome of
from China (2). In February 2014, the presence of porcine KNU14-04totheChinesestrainHKU15-155,a3-ntinsertion
deltacoronavirus (PDCoV) was first announced in Ohio, was observed in each of the S genes and the 3= UTR of strain
UnitedStates,andsincethen,thisnovelcoronavirushasbeen KNU14-04, which is also present in strain United States/IA/
reportedin17U.S.states(4–7). 2014/8734(4).
SincethediscoveryofPDCoVinChina,wehaveconducteda Toourknowledge,thisisthefirsttimethatthecompletege-
surveillancestudytoidentifythepresenceofPDCoVandtesteda nome sequence of PDCoV from South Korea has been deter-
totalof108fecaland5intestinalhomogenatesamplesfrompigs mined. Our sequence data will provide further insight into the
with diarrheal disease. These samples were initially negative for understandingoftheepidemiologyandevolutionofPDCoVin
transmissiblegastroenteritisvirus(TGEV),porcineepidemicdi- SouthKoreaandfacilitateinvestigationsonthegeneticdiversity
arrheavirus(PEDV),androtavirus,orpositiveforatleastoneof ofPDCoVworldwide.
threeviruses.Twofecalsamplesreceivedfromdifferentpigfarms Nucleotidesequenceaccessionnumber.TheseKOR/KNU14-
in April and June of 2014, each of which had been positive for 04/2014PDCoVsequencedatahavebeendepositedinGenBank
rotavirusandnegativeforallthreeviralpathogens,respectively, undertheaccessionno.KM820765.
testedpositiveforPDCoVbyreversetranscription(RT)-PCRfol-
lowedbysequencingconfirmationofPCRamplicons.Tofurther ACKNOWLEDGMENTS
investigatethegeneticrelationshipoftheKoreanandpreviously WegratefullythankGun-SeokParkandJae-HoShinfromKyungpook
reportedChineseandU.S.strains,thecompletegenomeofarep- National University for their technical assistance with the NGS
resentativePDCoVstrain,KNU14-04,wassequencedusingrapid analysis.
amplification of cDNA ends (RACE) and next-generation se- ThisresearchwassupportedbytheBasicScienceResearchProgram
quencing(NGS)asdescribedpreviously(8–10).TheKNU14-04 throughtheNationalResearchFoundationofKorea(NRF)fundedbythe
MinistryofScience,ICT&FuturePlanning(2013R1A2A2A01004355).
NGSreadswereassembledusingthefull-lengthPDCoVreference
genomesfromGenBank(4,5).
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