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RESEARCHARTICLE Co-circulation of all the four dengue virus serotypes and detection of a novel clade of DENV-4 (genotype I) virus in Pune, India during 2016 season ShubhamShrivastava1,DivyaTiraki1,ArundhatiDiwan2,SanjayK.Lalwani3, MeeraModak4,AkhileshChandraMishra1,VidyaA.Arankalle1* 1 DepartmentofCommunicableDiseases,InteractiveResearchSchoolforHealthAffairs,Bharati VidyapeethDeemedUniversity,Pune,Maharashtra,India,2 DepartmentofMedicine,BharatiVidyapeeth a1111111111 DeemedUniversityMedicalCollege,Pune,Maharashtra,India,3 DepartmentofPediatrics,Bharati a1111111111 VidyapeethDeemedUniversityMedicalCollege,Pune,Maharashtra,India,4 DepartmentofMicrobiology, a1111111111 BharatiVidyapeethDeemedUniversityMedicalCollege,Pune,Maharashtra,India a1111111111 a1111111111 *[email protected] Abstract OPENACCESS Dengueisthemostcommonmosquito-borneviralinfectionintropicalandsub-tropicalcoun- Citation:ShrivastavaS,TirakiD,DiwanA,Lalwani tries.Inrecentyears,Indiahasreportedincreasedincidencesofconcurrentinfectionwith SK,ModakM,MishraAC,etal.(2018)Co- multipleserotypesofdengueviruses(DENV).Inthepresentstudy,wehavecharacterized circulationofallthefourdenguevirusserotypes DENVcirculatingduringasingleseasonof2016inPune,India.Atotalof64serumsamples anddetectionofanovelcladeofDENV-4 (genotypeI)virusinPune,Indiaduring2016 fromNS1ELISApositivedenguepatientswereusedforPCRamplificationofCprMregion season.PLoSONE13(2):e0192672.https://doi. oftheviralgenomeandsequencing.Phylogeneticanalysisdocumentedcirculationofallthe org/10.1371/journal.pone.0192672 fourDENVserotypeswithpredominanceofDENV-2(40.6%).DENVgenotypingclassified Editor:AftabA.Ansari,EmoryUniversitySchoolof DENV-1toGenotypeV,DENV-2toGenotypeIV,DENV-3toGenotypeIIIandDENV-4to Medicine,UNITEDSTATES GenotypeI.Furtheranalysisrevealedemergenceofanovelclade(D)ofgenotypeIof Received:November18,2017 DENV-4.SubsequentisolationofthreeDENV-4virusesincellculturefollowedbycomplete Accepted:January22,2018 genomesequenceanalysisconfirmedthisobservation.Additionally,anewgenotypewithin serotype-4with>6.7%sequencevariationfromothergenotypeswasidentified.Thisfirst Published:February22,2018 reportofsignificantco-circulationofallthefourserotypesinasingleoutbreakinPunerecon- Copyright:©2018Shrivastavaetal.Thisisan firmsneedformolecularmonitoringofDENV. openaccessarticledistributedunderthetermsof theCreativeCommonsAttributionLicense,which permitsunrestricteduse,distribution,and reproductioninanymedium,providedtheoriginal authorandsourcearecredited. Introduction DataAvailabilityStatement:Allrelevantdataare withinthepaperanditsSupportingInformation Anestimated40%oftheglobalpopulation(~3.9billion)isatriskofdenguevirus(DENV) files. infection[1,2].About2.5%ofpeopleaffectedwithseveredenguedieeachyear[3].Thedis- Funding:ThisworkissupportedbyIndianCouncil easeisendemicinmorethan125countriesandthespreadtonewerareasismainlyattributed ofMedicalResearch(ICMR)grantnumber:ECD/ toreturningtravelersfromendemiccountries[4,5].TherearefourserotypesofDENV NTF/8/2016-17receivedbyACM.Thefunderhad (DENV-1to-4)andallofthemcancausedenguefever(DF),aself-limitingfebrileillness.A noroleinstudydesign,datacollectionand variableproportionofpatientsprogresstolifethreateningdenguehemorrhagicfever(DHF) analysis,decisiontopublish,orpreparationofthe manuscript. characterizedbythrombocytopeniaandhemorrhage,anddengueshocksyndrome(DSS)due PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 1/19 Co-circulationofdenguevirusesinPune,India Competinginterests:Theauthorshavedeclared toexcessiveplasmaleakage[6,7].DENVhasbeenincirculationintheIndiansubcontinent thatnocompetinginterestsexist. since1950s[8].ThefirstvirologicallyprovenepidemicofDFoccurredinKolkatain1963– 1964andatpresentthevirushasspreadto35statesandunionterritoriesinthecountry (NVBDCP,http://nvbdcp.gov.in/den-cd.html)[9]. Onaccountofsequencevariability,dengueserotypesarefurtherclassifiedintodistinct genotypesthatdiffer>6%withinasingleserotype[10–12].Emergenceofnewserotypeorline- age\cladeshiftsincirculatingDENVgenotypesledtoenhancedseverityduringdengueout- breaks[13–17].AlineageshiftinDENV-3wasreportedtocauseseverediseaseinSriLanka [13,18].EmergenceofgenotypeIIIofDENV-3in2005resultedindengueoutbreakinNorth- ernIndia[19].Recently,emergenceofAsianorgenotypeIofDENV-1alsocausedlargeout- breakofdenguewith12,000casesinTamilNadu,SouthIndia[20]. AllthefourserotypesofDENVhavecirculatedinIndiaatdifferenttimes,butgenerallyone serotypedominatesagivenoutbreak.Dengueoutbreakin1996inDelhiwascausedbygeno- typeIVofDENV-2replacinggenotypeVisolatesof1957and1967[21]andvirusremainedin circulationtill2002.Secondoutbreakin2003inDelhiwasduetoemergenceofDENV-3 whichremainedasdominantserotypetill2006[19].Overaperiodfrom2007–2009,DENV-1 becamethepredominantserotypeinDelhibyreplacingDENV-2andDENV-3[22].Earlier dengueoutbreakswereattributedtosuddenemergenceofserotypeorgenotypethatco-circu- latealongwithexistinggenotypeforsometimebeforegettingreplacedbyothersinsubsequent years.Inrecentyears,co-circulationofmultipleserotypeshasbeenreportedfromdifferent partsofIndia[23].Highpercentageofco-infectionwithmorethanoneserotypewasalso observedwithincreaseddiseaseseverity[24–26].In2017,co-circulationofallfourDENV serotypesinsingleoutbreakwasreportedfromOdisha[27]andHyderabad[28]. Punecity,westernIndiawithapopulationof112million(census2011)isendemicforden- gue[29].Inviewofthepossibilityofintroductionofdenguevaccineinnearfuture,itisessen- tialtounderstandthetypeandproportionofcirculatingDENVstrains.Thepresentstudy reportsmolecularcharacterizationofdenguevirusescirculatinginPuneduringthe2016-den- gueseason. Methods Samplecollection Patientspresentingwithdenguelikesymptomsfor<4daystotheMedicineandPediatric OPDsoftheBharatihospital,atertiarycarehospitalfromPunewereincludedinthestudy.To avoidsecondprick,consentfortheuseofbloodsamplefordenguemolecularstudieswas obtainedfromallthesuspectedpatients.Thisincludedwritteninformedconsentfromthe parents(subjectsbelow7yearsofage),writteninformedassentandconsent(subjectsand theirparentsrespectively,agegroup7–17years)andwritteninformedconsent(subjectsabove 17yearsofage).NS1positive(DengueEarlyELISA,Panbio,Windsor,Qld,Australia),leftover serumsamples(n=120)werecollectedfromthediagnosticlaboratoryofthehospital.The studywasapprovedbyInstitutionalEthicsCommittee,BharatiVidyapeethDeemedUniver- sity,PunewithapprovalnumberIEC/2017/04. Virusisolation Onedaypriortoinfection,1x104Verocellswereseededineachwellof96-wellplateand incubatedat37˚Cin5%CO incubator.100μlof10-foldseriallydilutedpatient’sserumin 2 quadruplatewellsin96-wellplatewasusedtoinfectVerocellsgrowninMinimumEssential Medium(MEM,Gibco,ThermoScientific)containing2%fetalbovineserum,1%penicillin PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 2/19 Co-circulationofdenguevirusesinPune,India andstreptomycin.7dayspostinfection,culturesupernatantwasharvestedfromNS1positive wellsandaliquotswerestoredat-80˚C. ViralRNAextraction TotalRNAwasextractedfrom140μlofhumanserumorcellcultureisolatesusingaQIAmp viralRNAkit(QIAGEN,INC,Valencia,CA),aspermanufacturer’sprotocol.RNAwaseluted in50μlofAVEbufferprovidedwiththekit.Foraconventionalgel-basedPCR,aminimumof onenegativecontroleveryfoursampleswithnopresenceoftargetRNAwasincludedasapart oftheextractionprocedure. cDNAsynthesis DenguespecificviralRNAwasreversetranscribedandamplifiedforCprMregionoftheviral genomeasreportedbyChienetal(2006)[30].Forthis,single-strandedcDNAwassynthesized fromtotalRNAusingthehighcapacitycDNAreversetranscriptionkit(Invitrogen).Briefly, 10μloftheextractedRNAwasaddedtothe2XRTmastermixconsistingof2μlof10XRT buffer,0.8μlof100mMdNTPmix,2μlofreverseprimerD2(TTGCACCAACAGTCAATGTC TTCAGGTTC-616)and1μlofMultiScribereversetranscriptase.Thereactionwasthensub- jectedtoreversetranscriptionat25˚Cfor1min,37˚Cfor120min,85˚Cfor5min.Thepre- paredcDNAwasimmediatelyusedorstoredat-20˚Cuntiluse. PCRandsequencing CprMregionwasPCRamplifiedusingAmpliTaqpolymerasekit(Invitrogen).5μlofthesyn- thesizedcDNAwasthenaddedtothePCRmixcontaining10μlofPCRbuffer,10μlofMgCl , 2 5μlofprimersmD1(134-TCAATATGCTGAAACGCGAGAGAAACCG)andD2each,0.5μl dNTPs,1μlofpolymerase.Thereactionmixturewasthensubjectedto35cyclesofdenatur- ationat94˚Cfor1min,annealingat55˚Cfor1min,andextensionat72˚Cfor1min.Theprod- uctswerethenvisualizedfor511bpbyethidiumbromideagarosegelstaining[30].Amplified productswerethenextractedfromthegelsusingQiaquickGelextractionkit(QIAGEN,INC, Valencia,Calif)andbothstrandsweresequencedbyusingaBigDyeTerminatorCycle Sequencingkit(AppliedBiosystems).TheCprMsequenceswereconfirmedbyBLAST(www. ncbi.nlm.nih.gov/BLAST).Theforwardandreversesequenceswerealignedandmanually editedusingCodonCodealignerv.7.0.1softwaretoobtaintheconsensussequence.Newpar- tialCprMsequencesweresubmittedtoGenBankatwww.ncbi.nlm.nih.gov/genbank(acces- sionnumberMG053110-MG053173). Completegenomesequencing FullgenomesequencingofviralgenomeswasdoneusingIonProtonsystem(Lifetechnolo- gies,USA).Briefly,productswerepurified,sizeselected,amplifiedandquantified.Clonal amplificationwascarriedoutbyemulsionPCRandtheIonsphereparticlesweredepositedon toIonPIchip.Allprotonquality-approved,trimmedandfiltered(againsthumangenome) datawereexportedasBAMfilesforbioinformaticsanalysis.Unmappedreadswerequalityfil- teredwithmeanqualityscore>=20,minimumlength20andtrimmedusingPrinSeq-Lite program.ResultinghighqualityreadswereassembledusingMIRAv4.0.2assemblerandcon- tigswereannotatedusingBLASTagainstNCBIdatabase.Completegenomesequenceswere submittedtoGenBankatwww.ncbi.nlm.nih.gov(accessionnumberMG272272-MG272274). PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 3/19 Co-circulationofdenguevirusesinPune,India Phylogeneticanalysis ThesequencesobtainedinthepresentstudyandothersequencesretrievedfromGenBank werealignedusingMAFFTonlinealignmenttool[31].Phylogenetictreeswereconstructed usingMaximumLikelihoodmethodbasedonTamuraNeimodelinMEGA6.06software [32].Geneticdistanceswerecalculatedusingthep-distancemodelofnucleotideandamino acidsubstitution.Therobustnessoftheresultingtreewasassessedwith1000bootstrap replicates. Results Patientcharacteristics During2016-dengueseason,serumsamplesfrom109NS1positivepatientsweresubjectedto RT-PCRand53(48.6%)scoredpositiveforDENV-RNA.Further,11cellculture-grown DENVisolatesobtainedfromadditionalNS1positivepatientsweresubjectedtoRT-PCR.Of the64patients,ageofthepatientsrangedfrom5monthsto65yearswithmedianageof28.6 years.Male(n=35)tofemale(n=29)ratiowas1:0.8.BasedonWHO2009guidelines, 63patientswerecategorizedasdengueillnessofwhich59withoutwarningsignsand4with warningsigns.Onepatientwasclassifiedasseveredengue.DetailsareprovidedinTable1. DENVserotypedistribution Fig1depictsCprMgenephylogeny-basedserotypingof64DENVsequencesobtainedduring thisstudy.Clearly,allthefourserotypeswerecirculatinginPuneduringthe2016season.Of Table1. DemographicsandclinicalparametersofpatientsinfectedwithDENVwithdifferentserotypes. Sr.No. SampleNo. Sampletype NS1Detection Age Gender ClinicalManifestation GenBankAccessionNo. DengueSerotype1andgenotypeV 1 S44 Serum pos 36 M DwoWS MG053110 2 S58 Serum pos 32 F DwoWS MG053111 3 S59 Serum pos 18 M DwoWS MG053112 4 S105 Veroisolates pos 27 F DwoWS MG053113 5 S5 Serum pos 10 F DwoWS MG053114 6 S19 Serum pos 24 M DwoWS MG053115 7 S16 Serum pos 10 M DwoWS MG053116 8 S10 Serum pos 4 M DwoWS MG053117 9 S51 Serum pos 47 M DwoWS MG053118 DengueSerotype2andgenotypeIV(Cosmopolitan) 10 141 Serum pos 30 M DwoWS MG053119 11 812 Serum pos 26 F DwoWS MG053120 12 815 Serum pos 22 M DwoWS MG053121 13 892 Serum pos 60 F DwoWS MG053122 14 1008 Serum neg 21 F DwoWS MG053123 15 1053 Serum pos 20 M DwoWS MG053124 16 1571 Veroisolates pos 25 F DwoWS MG053125 17 S107 Veroisolates pos 16 M DwoWS MG053126 18 S47 Serum pos 25 M DwoWS MG053127 19 S57 Serum pos 24 M DwoWS MG053128 20 S77 Serum pos 5month M DWS MG053129 21 S85 Serum pos 11 F DWS MG053130 22 S94 Serum pos 27 M DwoWS MG053131 23 S87 Serum pos 35 M DwoWS MG053132 (Continued) PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 4/19 Co-circulationofdenguevirusesinPune,India Table1. (Continued) Sr.No. SampleNo. Sampletype NS1Detection Age Gender ClinicalManifestation GenBankAccessionNo. 24 S25 Serum pos 25 F DwoWS MG053133 25 S26 Serum pos 26 M DwoWS MG053134 26 S52 Serum pos 34 F DwoWS MG053135 27 S53 Serum pos 50 M DwoWS MG053136 28 S66 Veroisolates pos 41 M DwoWS MG053137 29 S67 Veroisolates pos 38 F DwoWS MG053138 30 S97 Veroisolates pos 22 M DwoWS MG053139 31 S100 Veroisolates pos 18 M DwoWS MG053140 32 S4 Serum pos 16 F DwoWS MG053141 33 S15 Serum pos 12 F DwoWS MG053142 34 S9 Serum pos 34 F DwoWS MG053143 35 S78 Serum neg 21 F DwoWS MG053144 DengueSerotype3andgenotypeIII 36 1389 Serum pos 19 F DwoWS MG053145 37 984 Serum pos 18 F DwoWS MG053146 38 S108 Serum pos 24 M DwoWS MG053147 39 S73 Serum pos 41 F DwoWS MG053148 40 S45 Veroisolates pos 26 F DwoWS MG053149 41 S33 Serum pos 25 F DwoWS MG053150 42 S111 Veroisolates pos 30 F DwoWS MG053151 43 S56 Serum neg 42 M DwoWS MG053152 44 S54 Serum pos 39 M DwoWS MG053153 45 S50 Veroisolates pos 13 M DwoWS MG053154 46 S74 Serum pos 20 M DwoWS MG053155 47 S112 Veroisolates pos 20 M DwoWS MG053156 48 S1 Serum pos 26 F DwoWS MG053157 49 S76 Veroisolates pos 8 M DwoWS MG053158 50 S81 Serum pos 10 M DwoWS MG053159 51 S82 Serum pos 41 M DWS MG053160 52 S65 Serum pos 18 F DwoWS MG053161 DengueSerotype4andgenotypeI 53 S28 Serum pos 55 M DwoWS MG053162 54 S30 Serum pos 42 M DwoWS MG053163 55 S46 Serum pos 37 M DWS MG053164 56 S80 Serum pos 21 M DwoWS MG053165 57 S2 Serum pos 16 F DwoWS MG053166 58 36 Serum pos 6 F SD MG053167 59 294 Serum pos 65 F DwoWS MG053168 60 1018 Serum pos 2 M DwoWS MG053169 61 1021 Serum pos 20 F DwoWS MG053170 62 1028 Serum pos 17 M DwoWS MG053171 63 S49 Serum pos 47 F DwoWS MG053172 64 S41 Serum pos 23 F DwoWS MG053173 DwoWS:Dengueillnesswithoutwarningsigns DWS:Dengueillnesswithwarningsigns SD:Severedengue https://doi.org/10.1371/journal.pone.0192672.t001 these,DENV-1wasdetectedin9(14.1%,Pune-2016-DENV1),DENV-2in26(40.6%,Pune- 2016-DENV2),DENV-3in17(26.6%,Pune-2016-DENV3)andDENV-4in12(18.7%,Pune- 2016-DENV4)samples.Thus,DENV-2wasfoundtobethepredominantserotypeanda PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 5/19 Co-circulationofdenguevirusesinPune,India Fig1.PhylogeneticanalysesofCprMgenesequencesfrom64DENVpositivecasesforserotypedetermination. EachstrainisidentifiedbyGenbankaccessionnumberfollowedbycountryandyearofisolation.Numbersatthe nodesaresupportvaluesforthemajorbranches(bootstrap;1000replicates).Thesequencesobtainedinthisstudyare markedinfilledcoloredcircles.Scalebarindicatesnumberofbasesubstitutionspersite. https://doi.org/10.1371/journal.pone.0192672.g001 PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 6/19 Co-circulationofdenguevirusesinPune,India Fig2.GenotypinganalysesofCprMgenesequencesofDENV-1serotypeisolates(n=9)fromPune.Eachstrainis indicatedbyGenbankaccessionnumberfollowedbycountryandyearofisolation.Numbersatthenodesaresupport valuesforthemajorbranches(bootstrap;1000replicates).Thesequencesobtainedinthisstudyaremarkedinfilled coloredcircles.Scalebarindicatesnumberofbasesubstitutionspersite. https://doi.org/10.1371/journal.pone.0192672.g002 substantialproportionofpatientswereinfectedwithotherserotypesaswell.Asfarasserotypic distributionamongdifferentclinicalformsisconsidered,theonlyseveredenguepatientwas infectedwithserotype4,patientswithdengueillnesswithoutwarningsignswereinfectedwith eitherof4serotypesandthosewithwarningsignswereinfectedwithserotypes2,3or4. DENVgenotypedistribution TodeterminethegenotypedistributionofDENVwithineachserotype,CprMgenesequences obtainedduringthisstudyandsequencesfromdifferentgeographicallocationsacrossthe globewereretrievedfromNCBIdatabaseandusedforphylogeneticanalyses(Figs2–5). PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 7/19 Co-circulationofdenguevirusesinPune,India PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 8/19 Co-circulationofdenguevirusesinPune,India Fig3.GenotypinganalysesofCprMgenesequencesofDENV-2serotypeisolates(n=26)fromPune.Eachstrain isindicatedbyGenbankaccessionnumberfollowedbycountryandyearofisolation.Numbersatthenodesare supportvaluesforthemajorbranches(bootstrap;1000replicates).Thesequencesobtainedinthisstudyaremarkedin filledcoloredcircles.Scalebarindicatesnumberofbasesubstitutionspersite. https://doi.org/10.1371/journal.pone.0192672.g003 ForDENV-1strains,phylogenetictreerevealedclusteringofDENV-1sequencesintosix genotypes.ThePune-2016-DENV1isolates(n=9)groupedintoAmerican/African(AM/AF) orgenotypeVtogetherwithotherIndianisolatesfrom1962to2011(Fig2).Asreportedearlier (Ceciliaetal,2017),oneisolatefromKerala,2013(KJ755855)belongedtoAsianorgenotypeI. ThePune-2016-DENV1sequencesweresimilarwith99.8±0.3%nucleotideidentities.The currentsequencesclusteredwithisolatesfromIndia(2008–2016),Singapore(2011–15),China (2014)andBrunei(2005). AsevidentfromFig3,DENV-2sequenceswereclassifiedintosixgenotypes.Pune-2016 sequences(n=26)groupedtogetherinCosmopolitanorgenotypeIVandexhibited99.3± 0.3%nucleotidesimilarity.Thisgenotypeisdividedintotwogeographicallydistinctlineages, lineageA(isolatesfromSoutheastAsia,ChinaandOceania)andlineageB(isolatesmostly fromIndiansubcontinent).Pune-2016sequencesbelongedtolineageBandclusteredwith strainsfromIndia(2008–12),Pakistan(2008–13),China(1999),Singapore(2013)andSri Lanka(2003). PhylogeneticanalysisclassifiedPune-2016-DENV3(n=17)CprMsequencesingenotype III(Fig4)withnucleotidesequencesimilarityof99.3±0.3%.GenotypeIIIstrainsexhibitwide geographicdistributionfromAsia,Caribbean,AmericasandEurope.Pune-2016sequences werecloselyrelatedtotheotherisolatesfromIndia(2004–2016),China(2009,2013),Singa- pore(2009),Pakistan(2008–09)andasingleisolatefromSenegal(2009)with99.4±0.3% nucleotidesimilarities.AmongtheotherIndiaisolates,1984-isolate(KF955477)groupedinto GenotypeIIwhileasingleisolatefromnorthernIndia(KC787098,2009)wasassignedto genotypeIVandwasfoundtobecloselyrelatedtoDENV-3prototypestrainofPhilippines, 1956(M93130). DENV-4,therareserotypeinIndiawaspreviouslyreportedin2003fromDelhi,and2007 fromHyderabadand2010fromKerala[33–35].InMaharashtrastate,lastreportofDENV-4 caseswasin1975fromAmalnerdistrictandlaterdetectedinPunein2009afteragapof30 years[36].PhylogeneticanalysisrevealedthatDENV-4sequenceshavebeengroupedinto5 genotypeswithaninter-genotypicsequencedivergenceof>6%[10–12,37,38].Ourdatadoc- umentedthat(1)thePune-2016viruses(n=12)formedadistinctclusterwithingenotypeI and(2)11sequencesearlierclassifiedelsewhere[39,40]asgenotypeIIconstitutedaseparate cluster(Fig5)thatincludedisolatesmostlyfromEastandSoutheastAsiancountriessuchas Japan,China,Taiwan,Indonesia,SingaporeandPhilippines. WefurthercomparedpercentnucleotidedivergenceinCprMregionamongdifferentclus- terswithingenotypeIanddifferentclustersconstitutinggenotypeswithinserotypeIV (Table2).ThenovelclusterincludingcurrentPunestrainswas3.0±0.6%to5.6±0.8%diver- gentwhencomparedtotheotherclusters/cladeswithingenotypeIandtentativelydesignated ascladeD.DENV-4virusesisolatedin2007(EU652498-EU652499)and2010(JN882277) fromtwosouthernIndianstatestogetherwithPune-2016sequencesbelongedtocladeD.The distinctclusterofsequencesearlierclassifiedasgenotypeIIwas6.8%-10.2%differentfrom theknowngenotypesI–V(Table2).Theseresultssuggestedthatthisclustermayrepresenta novelgenotypeVI. Forconfirmationoftheseobservations,fullgenomesequenceanalysiswasdone.We obtainedcompletegenomesequencesofthreeDENV-4strains,isolatedinVerocells(acces- sionnumberMG272272-MG272274).ThecompletegenomelengthsofPune-2016isolatesare PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 9/19 Co-circulationofdenguevirusesinPune,India PLOSONE|https://doi.org/10.1371/journal.pone.0192672 February22,2018 10/19

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Shubham Shrivastava1, Divya Tiraki1, Arundhati Diwan2, Sanjay K. Schwartz E, Weld LH, Wilder-Smith A, von Sonnenburg F, Keystone JS, Kain
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