h tt p : / / w w w . b j m i c r o b i o l . c o m . b r /
Veterinary
Microbiology
High
frequency
of
hepatitis
E
virus
infection
in
swine
from
South
Brazil
and
close
similarity
to
human
HEV
isolates
Ana
Maria
Passos-Castilho
∗,
Celso
Francisco
Hernandes
Granato
UniversidadeFederaldeSãoPaulo,DepartamentodeMedicina,DivisãodeDoenc¸asInfecciosas,SãoPaulo,SP,Brazil
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t
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c
l
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f
o
Articlehistory:Received29April2016 Accepted19October2016 Availableonline3January2017 AssociateEditor:JoãoAraujoJr.
Keywords: Brazil Genotype3 HepatitisEvirus Pigs Zoonosis
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HepatitisEvirusisresponsibleforacuteandchronicliverinfectionsworldwide.Swine hep-atitisEvirushasbeenisolatedinBrazil,andaprobablezoonotictransmissionhasbeen described,althoughdataarestillscarce.Theaimofthisstudywastoinvestigatethe fre-quencyofhepatitisEvirusinfectioninpigsfromasmall-scalefarmintheruralareaof ParanáState,SouthBrazil.Fecalsampleswerecollectedfrom170pigsandscreenedfor hepatitisEvirusRNAusingaduplexreal-timeRT-PCRtargetingahighlyconserved70nt longsequencewithinoverlappingpartsofORF2andORF3aswellasa113ntsequenceof ORF2.Positivesampleswithhighviralloadsweresubjectedtodirectsequencingand phy-logeneticanalysis.hepatitisEvirusRNAwasdetectedin34(20.0%)ofthe170pigsfollowing positiveresultsinatleastonesetofscreeningreal-timeRT-PCRprimersandprobes.The swinehepatitisEvirusstrainsclusteredwiththegenotypehepatitisEvirus-3breference sequencesinthephylogeneticanalysisandshowedclosesimilaritytohumanhepatitisE virusisolatespreviouslyreportedinBrazil.
©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.Thisis anopenaccessarticleundertheCCBY-NC-NDlicense(http://creativecommons.org/
licenses/by-nc-nd/4.0/).
Introduction
Inendemic areas,hepatitisEvirus (HEV) causes large epi-demicsand sporadic casesin humans,including genotype HEV-1inAsiaandAfrica,genotypeHEV-2inMexicoandAfrica, andgenotypeHEV-4inAsia.Innon-endemicareas,isolated casesofgenotypeHEV-3occurinEurope,Japanandthe Amer-icas.GenotypesHEV-3andHEV-4aredescribedaszoonotic,as theyinfectnumerousmammalianspecies,including domes-ticpigs,andcanbetransmittedthroughtheingestionofraw orundercookedmeatfrominfectedanimals.1
∗ Correspondingauthor.
E-mail:anampassos@gmail.com(A.M.Passos-Castilho).
HEVshowsnotableheterogeneitywithseveralgroupsand genotypes.Arecentconsensushasclassifiedthisvirusinone familyofHepeviridae,dividedin2generanamely Orthohep-evirusandPiscihepevirus.Orthohepevirusisfurtherdivided into 4speciesfromAtoD.OrthohepevirusAisthespecies infectinghumansandswineandotheranimals,suchasboar, deer,mongoose,rabbitandcamel.Theseincludetwo geno-types isolated from humans alone (HEV-1 and HEV-2), two genotypes reported in both humans and different animal speciesand associatedwiththe zoonoticcases(HEV-3 and HEV-4),twoisolatesfromwildboarinJapan(genotypeHEV-5 andHEV-6)andasingleisolatefromdromedarycamelinDubai
http://dx.doi.org/10.1016/j.bjm.2016.10.022
1517-8382/©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.ThisisanopenaccessarticleundertheCC BY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/4.0/).
(genotypeHEV-7).RabbitHEVandcloselyrelatedhuman iso-late havebeen placedas adistant member inHEV-3. The moose virus appearsto cluster closely to genotype HEV-3, whileHEVisolatesfrom minktoferret virus (HEVC2)and HEVisolatesfromfoxtoratvirus(HEVC1).Theseviruseshave notbeenplacedinanyspecificgenotypeandneedcomplete genomic sequences fora definite taxonomic classification. OrthohepevirusBincludesall3avianHEVstrains, Orthohep-evirusConespeciesfromratandanotheronefromferretand OrthohepevirusDincludesbatHEV.Piscihepevirusincludes2 troutHEVstrainswithinasinglespecies.2,3
InBrazil,swineHEVwasfirstisolatedfrompigfecal sam-plesfromtheSãoPauloState,SoutheasternBrazil.4Moreover,
genotypeHEV-3wasfoundinpigsandeffluentsfromapig slaughterhouseinRiodeJaneiroState,SoutheasternBrazil,5,6
and inpigs from the Eastern BrazilianAmazon7 and from
Southern Brazil.8,9 Nonetheless, hepatitis E has only been
studiedasapotentialzoonoticdiseaseinLatinAmerica in thelasttenyears,anddataonthissubjectarestillscarce.
Data on human HEVin Brazil are limited as well. This countryhasbeenclassifiedasmoderatelyendemicforHEV, with seroprevalence from 1% to 4% in blood donors or thegeneralpopulation,13%inindividualsfrom an agricul-tural settlement in the Amazon Basin, and 15% in renal transplant recipients.10–13 Amore recent study observed a
seroprevalence of anti-HEV IgG antibodies of 10% among blooddonorsinthemetropolitanareaofItajaiValley, South-ernBrazil,aregionofpredominantGermanancestrywhere culturalhabits resultinahigh pork consumption.14
Geno-type HEV-3 infection has been described in the country, both amongimmunocompetent and immunocompromised individuals.15–17
Brazilisthefourthbiggestporkexporterintheworld,with animportantincreaseinrecentyears.TheStateofParanáhas oneofthelargestswine productionsinthecountry,and in 2014,thisregionwassolelyresponsiblefor20%ofthenational pigslaughter.Inadditiontoexport,porkconsumptionhasalso increasedinBrazil.18SpecificallyinParanáState,the
predomi-nantEuropeanancestry19,20leadstohigherporkconsumption
than inotherparts ofthecountry.21,22 Theimpactofsuch
habitsandthepotentialtransmissionofswineHEVtohumans inthisregionremainunknown.
Inthepresentstudy,weinvestigatedthefrequencyofHEV infectioninpigsfromasmall-scalefarmintheruralareaof ParanáState,SouthBrazil.
Materials
and
methods
Fecalsamples
ThestudyprotocolwasapprovedbytheInstitutional Commit-teeforEthicsintheUseofResearchAnimals(CEUA-UNIFESP 2014/1004300914).
InSeptember2014,fecalsampleswerecollectedfrom170 pigsfromasmall-scalefarminthemunicipalityofItapejara d’Oeste,inaruralareaofParanáState,SouthernBrazil.This farmisoneofthemanysmallfarmsintheregion,witha cur-rentpopulationofapproximately70sows,5boarsand580pigs thataresoldtoslaughterhouseswhenraisedtoamedianage
of22weeks.Thesamplesizeof170animalswascalculated toallowdeterminingaHEVRNAprevalenceofapproximately 15%9witha95%confidenceinterval(CI).Additionally,
samp-lingwasperformedattheagesof4,7,10,13and16weeks, according to the age distribution ofall the pigs raisedfor slaughter.
RNAextraction,nestedRT-PCRandquantitativeRT-PCR HEV RNA was extracted from the fecal samples using the QIAampviralRNAminikit(QIAGEN,Hilden,Germany).Briefly, fecal samples were first suspended in a 50% solution in ultrapure nuclease-free distilled water, then centrifuged at 20,000×gfor15min,andthesupernatantwasusedtoextract viralRNAaccordingtothemanufacturer’sinstructions. Quan-titative RT-PCR was performed according to a previously describedmodifiedone-stepduplexreal-timeprotocol,23with
aprimerandprobesettargetingahighlyconserved70ntlong sequence withinoverlapping parts of ORF2 and ORF324 as
wellasasetspecificfora113ntsequenceofORF2.25A
pre-viouslycharacterizedplasmidclonefromaBrazilianhuman HEVstrain(KF152884)17wasconstructedwiththeTOPO®TA
Cloning®Kit(Invitrogen,Carlsbad,CA,USA)andthedescribed primers. PlasmidDNA waspurifiedusingtheQIAprep Spin MiniprepKit(Qiagen,Hilden,Germany) andthenlinearized andquantifiedwiththeNanodropND-1000instrument (Wil-mington, DE, USA), followed by transcription to RNA with T7RNApolymerase(Promega,Madison,WI,USA).Standard curvesweregeneratedusing10−1–1010copiesofplasmidRNA.
HEVviralloadswere determinedbasedonstandard curves and were reported as the log10 number of copies of HEV RNApermLoffecalsuspension.Thedetection limitofthe real-timeRT-PCRwasthreecopiesofviralRNAperreaction (2.40log10copiespermLoffecalsuspension),whilethe
quan-tificationlimitwassetat10copiesofviralRNAperreaction (3.00log10 copiespermLoffecalsuspension).Allscreening
reactionswereruninduplicatewithpropercontrols,whereas positive results were confirmed in separate confirmatory reactions.
ThequalitativenestedRT-PCRone-stepreactionwas con-ducted with primers to amplify partial regions of ORF1 and ORF2 of 287nt and 348 nt,respectively, after second-roundPCR.26,27 Allprecautionsandproceduressuggestedto
avoidthepossibilityofcross-contaminationwereemployed. Amplified products were visualized in a 1.5% agarose gel stained with SYBR® Safe (Life Technologies, Austin, TX, USA).
Sequencingandphylogeneticanalysis
Final fragments obtained from the nested RT-PCRanalysis (ORF1287ntandORF2348nt)werepurifiedusingthe ExoSAP-ITPCRClean-upKit(GEHealthcare,ChalfontSt.Giles,UK),and sequencedusingtheBigDye®Terminatorv3.1Cycle Sequenc-ingKitandtheautomatedABI3100DNASequencer(Applied Biosystems,FosterCity,CA,USA),accordingtothe manufac-turer’sinstructions.SequencesfromhumanandswineHEV werecollectedfrompublicdatabases,andphylogenetictrees were constructed using the neighbor-joining method with
Table1–MoleculardetectionofHEV-RNAinpigsfromtheruralareaofParanáState,SouthBrazil,usingreal-timeand
conventionalRT-PCR.
Pigno. Age(weeks) Real-timeRT-PCR ConventionalRT-PCR ORF2/3(70nt) ORF2(113nt) ORF1(287nt) ORF2(348nt)
31 7 + − − − 42 7 + − − − 49 7 − 3.20log10 − + 51 7 − + − − 59 7 − + − − 63 7 + − − − 69 10 − + − − 71 10 + − − − 74 10 + − − − 77 10 + − − − 78 10 + − − − 79 10 − 6.48log10 + + 80 10 − + − − 82 10 5.98log10 5.54log10 + − 84 10 + − − − 85 10 − + − − 86 10 + − − − 91 10 + − − − 96 10 + − − − 100 13 − + − − 108 13 − + − − 115 13 − + − − 118 13 + + − − 119 13 + + − − 123 13 + + − − 126 13 + − − − 130 13 − + − − 132 13 + + − − 133 13 + − − − 134 13 − + − − 136 13 − + − − 138 13 + − − − 146 13 + + − − 147 13 + 3.37log10 − + n/N(%) 21/170(12.4%) 20/170(11.8%) 2/170(1.2%) 3/170(1.8%) Forpositivesamples,viralloadisexpressedasthelog10numberofcopiesofHEV-RNApermLoffecalsuspensionifhigherthanthequantification limitofthereal-timeRT-PCR(>3.00log10copies).Positivesampleswithviralloadbetween2.40and3.00log10copiesareexpressedasthesymbol
+.
theKimura2-parametermodelofnucleotidesubstitutionin MEGAv.5.0(TheBiodesignInstitute,USA).Statisticswas per-formedbybootstrapanalysiswith1000pseudoreplicates.The sequencesreportedinthisstudyareavailableintheGenBank
databaseundertheaccessionnumbersKP966825–KP966829.
Statisticalanalysis
All data were analyzed using SPSS version 11.0 (SPSS
Inc., Chicago, IL, USA). Descriptive statistics consisted of
the characterization of the studied population and the
Table2–HEV-RNAdetectionfrequencyinpigsfromtheruralareaofParanáState,SouthBrazil,byagegroup.
Agegroup(weeks) HEV-RNApositive HEV-RNAnegative p
n(%) n(%) 4 0(0.0) 30(100.0) 0.001a 7 6(9.1) 30(90.9) 10 13(40.6) 19(59.4) 13 15(20.8) 34(79.2) 16 0(0.0) 23(100.0) Total 34(20.0) 136(80.0) 170(100)
Fig.1–Phylogenetictreereconstructedbytheneighbor-joiningmethodwithcommon242-ntORF1sequencesfrom29 isolates,including8porcineisolatesfromBrazil,1humanisolatefromBrazil,andthe2swineisolatesdescribedinthis
study,Brazil79.1swandBrazil82sw(highlightedinred).TheGenBankaccessionnumberinparentheses,thenameofthe
countryoforigin,thespeciesfromwhichitwasisolated,andthegenotype/subtypeoftheisolateidentifyeachviralstrain. Bootstrapvaluesof>50areindicatedforthemajornodesasapercentageofthedataobtainedfrom1000replicates(bar,0.02 substitutionspersite).Majorbranchesindicategenotypes.AvianHEVistheoutgroup.
frequency of HEV-RNA detection with the respective per-centages and 95% CI. The bivariate analysis to compare categorical values consisted of Pearson’s Chi-square test. Non-conditionallogisticregressionwasusedtoidentify asso-ciations between dependent and independentvariables by
the means of odds ratio (OR). For this analysis, the ages of 4 and 7 weeks were grouped to avoid empty cells, as well as the ages of 13 and 16 weeks. The statistical significance levelwas p<0.05.All reported valuesare two-tailed.
Fig.2–Phylogenetictreereconstructedbytheneighbor-joiningmethodwithcommon304-ntORF2sequencesfrom49 isolates,including13porcineisolatesfromBrazil,4humanisolatesfromBrazil,andthe3swineisolatesdescribedinthis
study,Brazil79sw,Brazil49swandBrazil147sw(highlightedinred).TheGenBankaccessionnumberinparentheses,the
nameofthecountryoforigin,thespeciesfromwhichitwasisolated,andthegenotype/subtypeoftheisolateidentifyeach viralstrain.Bootstrapvaluesof>50areindicatedforthemajornodesasapercentageofthedataobtainedfrom1000 replicates(bar,0.02substitutionspersite).Majorbranchesindicategenotypes.AvianHEVistheoutgroup.
Results
HEV-RNAdetectionandsequencing
HEV-RNAwasdetectedin34(20.0%)of170pigsfollowinga positiveresultinatleastonesetofscreeningreal-time RT-PCRprimersandprobes.Seven(20.6%)ofthesesampleswere positivewithbothsetsofprimersandprobes.The70ntORF2/3 setamplified21(12.4%)of170samples,whilethe113ntORF2 setamplified20samples(11.8%).Amongthe34positive sam-ples,only4(11.8%)presentedviralloadshigherthan3.00log10
copiespermLoffecalsuspension(Table1).
Table2showsthedetectionofHEV-RNAbyagegroup.Inthe
agegroupfrom4to7weeks,only9.1%ofpigshaddetectable HEV-RNA,whereas40.6%haddetectableHEV-RNAat10weeks ofage.Theseresultsshowanapproximate7-foldhigherrisk ofundergoingaHEVinfectionattheageof10weeksthanat theagesof4or7weeks(OR=6.84,95%CI2.29–20.48).
Duetothe lowviralloadofthemajorityofthepositive samplesand the difference between the detectionlimit of thescreeningreal-timeRT-PCRandtheconventionalnested RT-PCR,only4(11.8%;4/34)samplescouldbeamplifiedwith conventionalnestedRT-PCRandsubjectedtodirect sequenc-ing.Amongthesesamples,twowereamplifiedwiththesetof primersresultinginafinalproductof287nt,andthreewere amplifiedwiththe384ntset.Sample079wasamplifiedusing bothsetsofprimersontheconventionalnestedRT-PCR.
Phylogeneticanalysis
Thetwosamplesfromthe287ntORF1partialregionshared 99%homologywitheachotherandclusteredwiththe geno-typeHEV-3breferencesequencesinthephylogeneticanalysis (Fig.1).Thethreesamplesfromthe384ntORF2partialregion alsogroupedwiththegenotypeHEV-3breferencesequences inthephylogeneticanalysis.Nucleotideidentityamongthese threesamplesrangedfrom98%to99%(Fig.2).
Discussion
ThepresentdatashowahigherfrequencyofHEVinfection (20.0%) inpigs than previously reported inBrazil. A study performedduring2009inthesameregionwith170fecal sam-plesfrom14pigfarmsfoundHEV-RNAin15.3%ofsamples.9
Anotherstudy thatinvestigatedserum,bileand fecal sam-plesfrom151pigsfromtheeasternBrazilianAmazon,North Brazil,detectedHEV-RNAin9.9%oftheanimals.7Thehigher
infectionrateobservedinourstudycouldbearesultofthe sanitaryconditionsofthesmall-scalepigfarmsintherural areaofParanáState,wherethecontactofpigsofdifferentages mayoccur.However,itcouldalsobeduetothedifferencein methodology,sincepreviousstudiesemployedconventional RT-PCRtechniquesasopposedtothemoresensitivereal-time RT-PCRused inthe present study.Additionally, the duplex RT-PCRtechniqueemployedinthisstudydemonstratedthe importanceofusingmorethanonesetofprimersandprobes forhigherdetectionduringHEVscreening,asonly20.6%of
thepositivesampleshaddetectableHEV-RNAwithbothsets ofprimersandprobes.
PreviousstudiesreportedthatHEVinfection inpigswas morefrequentfrom12to16weeksofageandthatatslaughter age(20–24 weeks),theanimalshadalreadydeveloped anti-HEVantibodies.28 Inthe presentstudy,HEV-RNAwasmore
frequentinpigsaged10weeks(40.6%),althoughthefrequency inpigsaged13 wasstillhigh(20.8%).Nonetheless,noneof the samplesfromthe pigsaged4or16 weekstested posi-tive.Theseobservationsconferwithastudyperformedamong swineherdsinRiodeJaneiro,SoutheastBrazil,showingthat newbornpigsbecamesusceptibletoHEVbetweenweeks7and 9,anageinwhichtheserumlevelsofthematernalantibodies declined.5Theseresultsarealsoinagreementwithastudy
performedinCentralBrazilinswineaged20–30weeks,with 81%ofanti-HEVIgGpositivity.29
Theingestionofraworundercookedporkhasbeen asso-ciatedwithHEVinfection,30,31 andaprobablezoonoticHEV
transmissionhasbeenreportedinBrazil.15Additionally,there
is a known riskof HEVtransmission to people who come in contactwithfeces from infected pigs,which have been reported asanimportantsourceofinfectionfor slaughter-houseworkersandbutchersandhavebeenassociatedwith infection in non-endemic regions.32,33 HEV has also been
describedinsewagesamplesfromaslaughterhousein South-easternBrazil.6
The ORF1 HEV isolates foundin this study shared 88% homologywithahumanHEVsequencefromBrazil15and86% to96%homologywithswineHEVsequencesfromBrazil.5,8,9
TheORF2HEVisolatesshared86–93%homologywithhuman HEVsequencespreviouslycharacterizedbyourresearchgroup inrenaltransplantrecipientsinBrazil16and83–97%homology
withswineHEVsequencesfromBrazil.5,9Amongallcompared
HEV sequences, the highest homology (98–99%) was with human sequences recently isolated in Southeastern Brazil fromapediatriclivertransplantrecipientwithchronicHEV infection.17
Although morestudies are neededto elucidatethe real impactofswineHEVinfectionandzoonotictransmissionin Brazil,takentogether,theseresultsreinforcethehypothesis that domesticpigsmay beanimportantsourceforhuman hepatitisEvirusinfectioninthissetting.
Conclusions
Inconclusion,thisstudyconfirmsthecirculationofthe hep-atitisEvirusandshowsahighfrequencyofHEVinfectionin pigsofdifferentagesraisedforslaughterintheruralareaof ParanáState,SouthBrazil.Theclosesimilaritybetweenthe humanHEVstrainsandthosefoundhereinindicatesthat ade-quatesafetyactionsshouldbetakentopreventHEVinfection whenhandlingpigsand/orconsumingpork.
Conflicts
of
interest
Acknowledgements
This study was supported by the Fundac¸ão de Amparo à PesquisadoEstadodeSãoPaulo(GrantNos.2012/22925-3and 2013.03701-0).WewishtothankMr.Voitena,hisfamily,and VeterinaryDoctor Jessica Voitenaforall theircollaboration andtechnicalassistance.
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