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Full Zika Sequences From Bahia Patients Co-infected With Chikungunya


niman

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LOCUS       KU940228               10676 bp    RNA     linear   VRL 23-MAR-2016
DEFINITION  Zika virus isolate Bahia07, partial genome.
ACCESSION   KU940228
VERSION     KU940228.1  GI:1007624023
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10676)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Metagenomic Next-Generation Sequencing for Detection of Zika and
            Chikungunya Virus Co-Infections in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10676)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, Box #0134, San
            Francisco, CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURPI+ v. v1.0; Geneious v. v8.0
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10676
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia07"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="01-Jul-2015"
     5'UTR           1..105
     CDS             106..10377
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="AMQ76465.1"
                     /db_xref="GI:1007624024"
                     /translation="MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI
                     RMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKK
                     RRGADTSVGIVGLLLTTAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQI
                     MDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVT
                     LPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKV
                     IYLVMILLIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIE
                     LVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWG
                     NGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET
                     DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWF
                     HDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAE
                     MDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAG
                     TDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVG
                     EKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFG
                     AAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGC
                     SVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSR
                     MENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGK
                     SYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLE
                     CDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGI
                     EESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTR
                     GPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTA
                     GSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLA
                     ILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQT
                     AISALEGDLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGL
                     ATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSE
                     VLTAVGLICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKD
                     AEVTGNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWY
                     VYVKTGKRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMW
                     HVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARN
                     IQTLPGIFKTKGGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAIT
                     QGRREEETPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAP
                     TRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLY
                     IMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEV
                     PERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKT
                     KHQEWDFVVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQR
                     RGRIGRNPNKPGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADK
                     VAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIM
                     EDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAALGVMEALGTL
                     PGHMTERFQEAIDNLAVLMRAETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFV
                     LMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSP
                     QDNQMAIIIMVAVGLLGLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPA
                     SAWAIYAALTTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPL
                     LMIGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIV
                     VTDIDTMTIDPQVEKKMGQVLLIAVAVSSAILSRTAWGWGEAGALITAATSTLWEGSP
                     NKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQ
                     MSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPHGK
                     VIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFH
                     MAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMM
                     ETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRP
                     VKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHG
                     SYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPD
                     PQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAV
                     EAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGA
                     RFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWD
                     TRISRFDLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQ
                     DQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRPEKVTNWLQSNGWDR
                     LKRMAVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHH
                     FNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR
                     DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKT
                     PVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLST
                     QVRYLGEEGSTPGVL"
     mat_peptide     106..480
                     /product="capsid"
     mat_peptide     481..750
                     /product="pro"
     mat_peptide     751..975
                     /product="membane protein"
     mat_peptide     976..2490
                     /product="envelope protein"
     mat_peptide     2491..3576
                     /product="NS1"
     mat_peptide     3577..4230
                     /product="NS2A"
     mat_peptide     4231..4662
                     /product="NS2B"
     mat_peptide     4663..6471
                     /product="NS3"
     mat_peptide     6472..6912
                     /product="NS4A"
     mat_peptide     6913..8418
                     /product="NS4B"
     mat_peptide     8419..10374
                     /product="NS5"
     3'UTR           10378..10676
ORIGIN      
        1 gttgttgatc tgtgtgaatc agactgcgac agttcgagtt tgaagcgaaa gctagcaaca
       61 gtatcaacag gttttatttg gatttggaaa cgagagtttc tggtcatgaa aaacccaaaa
      121 aagaaatccg gaggattccg gattgtcaat atgctaaaac gcggagtagc ccgtgtgagc
      181 ccctttgggg gcttgaagag gctgccagcc ggacttctgc tgggtcatgg gcccatcagg
      241 atggtcttgg cgattctagc ctttttgaga ttcacggcaa tcaagccatc actgggtctc
      301 atcaatagat ggggttcagt ggggaaaaaa gaggctatgg aaataataaa gaagttcaag
      361 aaagatctgg ctgccatgct gagaataatc aatgctagga aggagaagaa gagacgaggc
      421 gcagatacta gtgtcggaat tgttggcctc ctgctgacca cagctatggc agcggaggtc
      481 actagacgtg ggagtgcata ctatatgtac ttggacagaa acgatgctgg ggaggccata
      541 tcttttccaa ccacattggg gatgaataag tgttatatac agatcatgga tcttggacac
      601 atgtgtgatg ccaccatgag ctatgaatgc cctatgctgg atgagggggt ggaaccagat
      661 gacgtcgatt gttggtgcaa cacgacgtca acttgggttg tgtacggaac ctgccatcac
      721 aaaaaaggtg aagcacggag atctagaaga gctgtgacgc tcccctccca ttccactagg
      781 aagctgcaaa cgcggtcgca aacctggttg gaatcaagag aatacacaaa gcacttgatt
      841 agagtcgaaa attggatatt caggaaccct ggcttcgcgt tagcagcagc tgccatcgct
      901 tggcttttgg gaagctcaac gagccaaaaa gtcatatact tggtcatgat actgctgatt
      961 gccccggcat acagcatcag gtgcatagga gtcagcaata gggactttgt ggaaggtatg
     1021 tcaggtggga cttgggttga tgttgtcttg gaacatggag gttgtgtcac cgtaatggca
     1081 caggacaaac cgactgtcga catagagctg gttacaacaa cagtcagcaa catggcggag
     1141 gtaagatcct actgctatga ggcatcaata tcagacatgg cttcggacag ccgctgccca
     1201 acacaaggtg aagcctacct tgacaagcaa tcagacactc aatatgtctg caaaagaacg
     1261 ttagtggaca gaggctgggg aaatggatgt ggactttttg gcaaagggag cctggtgaca
     1321 tgcgctaagt ttgcatgctc caagaaaatg accgggaaga gcatccagcc agagaatctg
     1381 gagtaccgga taatgctgtc agttcatggc tcccagcaca gtgggatgat cgttaatgac
     1441 acaggacatg aaactgatga gaatagagcg aaggttgaga taacgcccaa ttcaccaaga
     1501 gccgaagcca ccctgggggg ttttggaagc ctaggacttg attgtgaacc gaggacaggc
     1561 cttgactttt cagatttgta ttacttgact atgaataaca agcactggtt ggttcacaag
     1621 gagtggttcc acgacattcc attaccttgg cacgctgggg cagacaccgg aactccacac
     1681 tggaacaaca aagaagcact ggtagagttc aaggacgcac atgccaaaag gcaaactgtc
     1741 gtggttctag ggagtcaaga aggagcagtt cacacggccc ttgctggagc tctagaggct
     1801 gagatggatg gtgcaaaggg aaggctgtcc tctggccact tgaaatgtcg cctgaaaatg
     1861 gataaactta gattgaaggg cgtgtcatac tccttgtgta ccgcagcgtt cacattcacc
     1921 aagatcccgg ctgaaacact gcacgggaca gtcacagtgg aggtacagta cgcagggact
     1981 gatggacctt gcaaggttcc agctcagatg gcggtggaca tgcaaactct gaccccagtt
     2041 gggaggttga taaccgctaa ccccgtaatc actgaaagca ctgagaactc taagatgatg
     2101 ctggaacttg atccaccatt tggggactcc tacattgtca taggagtcgg ggagaagaag
     2161 atcacccacc actggcacag gagtggcagc accattggaa aagcatttga agccactgtg
     2221 agaggtgcca agagaatggc agtcttggga gacacagcct gggactttgg atcagttgga
     2281 ggcgctctca actcattggg caagggcatc catcaaattt ttggagcagc tttcaaatca
     2341 ttgtttggag gaatgtcctg gttctcacaa attctcattg gaacgttgct gatgtggttg
     2401 ggtctgaaca caaagaatgg atctatttcc cttatgtgct tggccttagg gggagtgttg
     2461 atcttcttat ccacagccgt ctctgctgat gtggggtgct cggtggactt ctcaaagaag
     2521 gagacgagat gcggtacagg ggtgttcgtc tataacgacg ttgaagcctg gagggacagg
     2581 tacaagtacc atcctgactc cccccgtaga ttggcagcag cagtcaagca agcctgggaa
     2641 gatggtatct gcgggatctc ctctgtttca agaatggaaa acatcatgtg gagatcagta
     2701 gaaggggagc tcaacgcaat cctggaagag aatggagttc aactgacggt cgttgtggga
     2761 tctgtaaaaa accccatgtg gagaggtcca cagagattgc ccgtgcctgt gaacgagctg
     2821 ccccacggct ggaaggcttg ggggaaatcg tacttcgtca gagcagcaaa gacaaataac
     2881 agctttgtcg tggatggtga cacactgaag gaatgcccac tcaaacatag agcatggaac
     2941 agctttcttg tggaggatca tgggttcggg gtatttcaca ctagtgtctg gctcaaggtt
     3001 agagaagatt attcattaga gtgtgatcca gccgttattg gaacagctgt taagggaaag
     3061 gaggctgtac acagtgatct aggctactgg attgagagtg agaagaatga cacatggagg
     3121 ctgaagaggg cccatctgat cgagatgaaa acatgtgaat ggccaaagtc ccacacattg
     3181 tggacagatg gaatagaaga gagtgatctg atcataccca agtctttagc tgggccactc
     3241 agccatcaca ataccagaga gggctacagg acccaaatga aagggccatg gcacagtgaa
     3301 gagcttgaaa ttcggtttga ggaatgccca ggcactaagg tccacgtgga ggaaacatgt
     3361 ggaacaagag gaccatctct gagatcaacc actgcaagcg gaagggtgat cgaggaatgg
     3421 tgctgcaggg agtgcacaat gcccccactg tcgttccggg ctaaagatgg ctgttggtat
     3481 ggaatggaga taaggcccag gaaagaacca gaaagcaact tagtaaggtc aatggtgact
     3541 gcaggatcaa ctgatcacat ggatcacttc tcccttggag tgcttgtgat tctgctcatg
     3601 gtgcaggaag ggctgaagaa gagaatgacc acaaagatca tcataagcac atcaatggca
     3661 gtgctggtag ctatgatcct gggaggattt tcaatgagtg acctggctaa gcttgcaatt
     3721 ttgatgggtg ccaccttcgc ggaaatgaac actggaggag atgtagctca tctggcgctg
     3781 atagcggcat tcaaagtcag accagcgttg ctggtatctt tcatcttcag agctaattgg
     3841 acaccccgtg aaagcatgct gctggccttg gcctcgtgtc ttttgcaaac tgcgatctcc
     3901 gccttggaag gcgacctgat ggttctcatc aatggttttg ctttggcctg gttggcaata
     3961 cgagcgatgg ttgttccacg cactgataac atcaccttgg caatcttggc tgctctgaca
     4021 ccactggccc ggggcacact gcttgtggcg tggagagcag gccttgctac ttgcgggggg
     4081 tttatgctcc tctctctgaa gggaaaaggc agtgtgaaga agaacttacc atttgtcatg
     4141 gccctgggac taaccgctgt gaggctggtc gaccccatca acgtggtggg actgctgttg
     4201 ctcacaagga gtgggaagcg gagctggccc cctagcgaag tactcacagc tgttggcctg
     4261 atatgcgcat tggctggagg gttcgccaag gcagatatag agatggctgg gcccatggcc
     4321 gcggtcggtc tgctaattgt cagttacgtg gtctcaggaa agagtgtgga catgtacatt
     4381 gaaagagcag gtgacatcac atgggaaaaa gatgcggaag tcactggaaa cagtccccgg
     4441 ctcgatgtgg cgctagatga gagtggtgat ttctccctgg tggaggatga cggtcccccc
     4501 atgagagaga tcatactcaa ggtggtcctg atgaccatct gtggcatgaa cccaatagcc
     4561 ataccctttg cagctggagc gtggtacgta tacgtgaaga ctggaaaaag gagtggtgct
     4621 ctatgggatg tgcctgctcc caaggaagta aaaaaggggg agaccacaga tggagtgtac
     4681 agagtaatga ctcgtagact gctaggttca acacaagttg gagtgggagt tatgcaagag
     4741 ggggtctttc acactatgtg gcacgtcaca aaaggatccg cgctgagaag cggtgaaggg
     4801 agacttgatc catactgggg agatgtcaag caggatctgg tgtcatactg tggtccatgg
     4861 aagctagatg ccgcctggga cgggcacagc gaggtgcagc tcttggccgt gccccccgga
     4921 gagagagcga ggaacatcca gactctgccc ggaatattta agacaaaggg tggggacatt
     4981 ggagcggttg cgctggatta cccagcagga acttcaggat ctccaatcct agacaagtgt
     5041 gggagagtga taggacttta tggcaatggg gtcgtgatca aaaatgggag ttatgttagt
     5101 gccatcaccc aagggaggag ggaggaagag actcctgttg agtgcttcga gccttcgatg
     5161 ctgaagaaga agcagctaac tgtcttagac ttgcatcctg gagctgggaa aaccaggaga
     5221 gttcttcctg aaatagtccg tgaagccata aaaacaagac tccgtactgt gatcttagct
     5281 ccaaccaggg ttgtcgctgc tgaaatggag gaagccctta gagggcttcc agtgcgttat
     5341 atgacaacag cagtcaatgt cacccactct ggaacagaaa tcgtcgactt aatgtgccat
     5401 gccaccttca cttcacgtct actacagcca atcagagtcc ccaattataa tctgtatatt
     5461 atggatgagg cccacttcac agatccctca agtatagcag caagaggata catttcaaca
     5521 agggttgaga tgggcgaggc ggctgccatc ttcatgaccg ccacgccacc aggaacccgt
     5581 gacgcatttc cggactccaa ctcaccaatt atggacaccg aagtggaagt cccagagaga
     5641 gcctggagct caggctttga ttgggtgacg gatcattctg gaaaaacagt ttggtttgtt
     5701 ccaagcgtga ggaacggcaa tgagatcgca gcttgtctga caaaggctgg aaaacgggtc
     5761 atacagctca gcagaaagac ttttgagaca gagttccaga aaacaaaaca tcaagagtgg
     5821 gactttgtcg tgacaactga catttcagag atgggcgcca actttaaagc tgaccgtgtc
     5881 atagattcca ggagatgcct aaagccggtc atacttgatg gcgagagagt cattctggct
     5941 ggacccatgc ctgtcacaca tgccagcgct gcccagagga gggggcgcat aggcaggaat
     6001 cccaacaaac ctggagatga gtatctgtat ggaggtgggt gcgcagagac tgacgaagac
     6061 catgcacact ggcttgaagc aagaatgctc cttgacaata tttacctcca agatggcctc
     6121 atagcctcgc tctatcgacc tgaggccgac aaagtagcag ccattgaggg agagttcaag
     6181 cttaggacgg agcaaaggaa gacctttgtg gaactcatga aaagaggaga tcttcctgtt
     6241 tggctggcct atcaggttgc atctgccgga ataacctaca cagatagaag atggtgcttt
     6301 gatggcacga ccaacaacac cataatggaa gacagtgtgc cggcagaggt gtggaccaga
     6361 cacggagaga aaagagtgct caaaccgagg tggatggatg ccagagtttg ttcagatcat
     6421 gcggccctga agtcattcaa ggagtttgcc gctgggaaaa gaggagcggc tcttggagtg
     6481 atggaagccc tgggaacact gccaggacac atgacagaga gattccagga agccattgac
     6541 aacctcgctg tgctcatgcg ggcagagact ggaagcaggc cttacaaagc cgcggcggcc
     6601 caaatgccgg agaccctaga gaccattatg cttttggggt tgctaggaac agtctcgctg
     6661 ggaatctttt tcgtcttgat gaggaacaag ggcataggga agatgggctt tggaatggtg
     6721 actcttgggg ccagcgcatg gctcatgtgg ctctcggaaa ttgagccagc cagaattgca
     6781 tgtgtcctca ttgttgtgtt cctattgctg gtggtgctca tacctgagcc agaaaagcaa
     6841 agatctcccc aggacaacca aatggcaatc atcatcatgg tagcagtagg tcttctgggc
     6901 ttgattaccg ccaatgaact cggatggttg gagagaacaa agagtgacct aagccatcta
     6961 atgggaagga gagaggaggg ggcaaccata ggattctcaa tggacattga cctgcggcca
     7021 gcctcagctt gggccatcta tgctgccttg acaactttca ttaccccagc cgtccaacat
     7081 gcagtgacca cttcatacaa caactactcc ttaatggcga tggccacgca agctggagtg
     7141 ttgtttggta tgggcaaagg gatgccattc tacgcatggg actttggagt cccgctgcta
     7201 atgataggtt gctactcaca attaacaccc ctgaccctaa tagtggccat cattttgctc
     7261 gtggcgcact acatgtactt gatcccaggg ctgcaggcag cagctgcgcg tgctgcccag
     7321 aagagaacgg cagctggcat catgaagaac cctgttgtgg atggaatagt ggtgactgac
     7381 attgacacaa tgacaattga cccccaagtg gagaaaaaga tgggacaggt gctactcata
     7441 gcagtagccg tctccagcgc catactgtcg cggaccgcct gggggtgggg ggaggctggg
     7501 gctctgatca cagccgcaac ttccactttg tgggaaggct ctccgaacaa gtactggaac
     7561 tcctctacag ccacttcact gtgtaacatt tttaggggaa gttacttggc tggagcttct
     7621 ctaatctaca cagtaacaag aaacgctggc ttggtcaaga gacgtggggg tggaacagga
     7681 gagaccctgg gagagaaatg gaaggcccgc ttgaaccaga tgtcggccct ggagttctac
     7741 tcctacaaaa agtcaggcat caccgaggtg tgcagagaag aggcccgccg cgccctcaag
     7801 gacggtgtgg caacgggagg ccatgctgtg tcccgaggaa gtgcaaagct gagatggttg
     7861 gtggagcggg gatacctgca gccccatgga aaggtcattg atcttggatg tggcagaggg
     7921 ggctggagtt actacgccgc caccatccgc aaagttcaag aagtgaaagg atacacaaaa
     7981 ggaggccctg gtcatgaaga acccgtgttg gtgcaaagct atgggtggaa catagtccgt
     8041 cttaagagtg gggtggacgt ctttcatatg gcggctgagc cgtgtgacac gttgctgtgt
     8101 gacataggtg agtcatcatc tagtcctgaa gtggaagaag cacggacgct cagagttctc
     8161 tccatggtgg gggattggct tgaaaaaaga ccaggagcct tttgtataaa agtgttgtgc
     8221 ccatacacca gcactatgat ggaaaccctg gagcgactgc agcgtaggta tgggggagga
     8281 ctggtcagag tgccactctc ccgcaactct acacatgaga tgtactgggt ctctggagcg
     8341 aaaagcaaca ccataaaaag tgtgtccacc acgagccagc tcctcttggg gcgcatggac
     8401 gggcctagga ggccagtgaa atatgaggag gatgtgaatc tcggctctgg cacgcgggct
     8461 gtggtaagct gcgctgaagc tcccaacatg aagatcattg gtaaccgcat tgaaaggatc
     8521 cgcagtgagc acgcggaaac gtggttcttt gacgagaacc acccatatag gacatgggct
     8581 taccatggaa gctatgaggc ccccacacaa gggtcagcgt cctctctagt aaacggggtt
     8641 gtcaggctcc tgtcaaaacc ctgggatgtg gtgactggag tcacaggaat agccatgacc
     8701 gacaccacac cgtatggtca gcaaagagtt ttcaaggaaa aagtggacac tagggtgcca
     8761 gacccccaag aaggcactcg tcaggttatg agcatggtct cttcctggtt gtggaaagag
     8821 ctaggcaaac acaaacggcc acgagtctgt accaaagaag agttcatcaa caaggttcgt
     8881 agcaatgcag cactaggggc aatatttgaa gaggaaaaag agtggaagac tgcagtggaa
     8941 gctgtgaacg atccaaggtt ctgggctcta gtggacaagg aaagagagca ccacctgaga
     9001 ggagagtgcc agagttgtgt gtacaacatg atgggaaaaa gagaaaagaa acaaggggaa
     9061 tttggaaagg ccaagggcag ccgcgccatc tggtatatgt ggctaggggc tagatttcta
     9121 gagttcgaag cccttggatt cttgaacgag gatcactgga tggggagaga gaactcagga
     9181 ggtggtgttg aagggctggg attacaaaga ctcggatatg tcctagaaga gatgagtcgc
     9241 ataccaggag gaaggatgta tgcagatgac actgctggct gggacacccg catcagcagg
     9301 tttgatctgg agaatgaagc tctaatcacc aaccaaatgg agaaagggca cagggccttg
     9361 gcattggcca taatcaagta cacataccaa aacaaagtgg taaaggtcct tagaccagct
     9421 gaaaaaggga aaacagttat ggacattatt tcgagacaag accaaagggg gagcggacaa
     9481 gttgtcactt acgctcttaa cacatttacc aacctagtgg tgcaactcat tcggaatatg
     9541 gaggctgagg aagttctcga gatgcaagac ttgtggctgc tgcggaggcc agagaaagtg
     9601 accaactggt tgcagagcaa cggatgggat aggctcaaac gaatggcagt cagtggagat
     9661 gattgcgttg tgaagccaat tgatgatagg tttgcacatg ccctcaggtt cttgaatgat
     9721 atgggaaaag ttaggaagga cacacaagag tggaaaccct caactggatg ggacaactgg
     9781 gaagaagttc cgttttgctc ccaccacttc aacaagctcc atctcaagga cgggaggtcc
     9841 attgtggttc cctgccgcca ccaagatgaa ctgattggcc gggcccgcgt ctctccaggg
     9901 gcgggatgga gcatccggga gactgcttgc ctagcaaaat catatgcgca aatgtggcag
     9961 ctcctttatt tccacagaag ggacctccga ctgatggcca atgccatttg ctcatctgtg
    10021 ccagttgact gggttccaac tgggagaact acctggtcaa tccatggaaa gggagaatgg
    10081 atgaccactg aagacatgct tgtggtgtgg aacagagtgt ggattgagga gaacgaccac
    10141 atggaagaca agaccccagt tacgaaatgg acagacattc cctatttggg aaaaagggaa
    10201 gacttgtggt gtggatctct catagggcac agaccgcgca ccacctgggc tgagaacatt
    10261 aaaaacacag tcaacatggt gcgcaggatc ataggtgatg aagaaaagta catggactac
    10321 ctatccaccc aagttcgcta cttgggtgaa gaagggtcta cacctggagt gctgtaagca
    10381 ccagtcttaa tgttgtcagg cctgctagtc agccacagct tggggaaagc tgtgcagcct
    10441 gtgacccccc caggagaagc tgggaaacca agcctatagt caggccgaga acgccatggc
    10501 acggaagaag ccatgctgcc tgtgagcccc tcagaggaca ctgagtcaaa aaaccccacg
    10561 cgcttggagg cgcaggatgg gaaaagaagg tggcgacctt ccccaccctt caatctgggg
    10621 cctgaactgg agatcagctg tggatctcca gaagagggac tagtggttag aggaga
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1882018820100%0.099%KU509998.1
1881418814100%0.099%KJ776791.1
1880318803100%0.099%KU729218.1
1880318803100%0.099%KU321639.1
1879218792100%0.099%KU707826.1
1879218792100%0.099%KU365779.1
1877618776100%0.099%KU926309.1
1877618776100%0.099%KU365780.1
1877018770100%0.099%KU647676.1
1877018770100%0.099%KU365777.1
1876418764100%0.099%KU501217.1
187611876199%0.099%KU497555.1
1875918759100%0.099%KU729217.2
1875918759100%0.099%KU527068.1
1875918759100%0.099%KU501216.1
1875318753100%0.099%KU820897.1
1875318753100%0.099%KU501215.1
1875318753100%0.099%KU365778.1
1875318753100%0.099%KU312312.1
1874818748100%0.099%KU922960.1
1874218742100%0.099%KU926310.1
1874218742100%0.099%KU922923.1
1874218742100%0.099%KU853013.1
1874018740100%0.099%KU853012.1
1873718737100%0.099%KU870645.1
1872018720100%0.099%KU820898.1
1871518715100%0.099%KU955590.1
1870918709100%0.099%KU740184.2
1870918709100%0.099%KU761564.1
1868718687100%0.099%KU955589.1
1868718687100%0.099%KU820899.2
1855418554100%0.099%KU866423.1
1851518515100%0.099%KU744693.1
1839318393100%0.099%KU681081.3
180181801899%0.098%JN860885.1
1801718017100%0.098%KU955593.1
180071800798%0.099%KF993678.1
1783217832100%0.098%EU545988.1
1764517645100%0.098%KU681082.3
163991639999%0.095%HQ234499.1
1258912589100%0.089%KF383115.1
1258712587100%0.089%KU720415.1
1258212582100%0.089%KF383119.1
125821258299%0.089%HQ234498.1
1256212562100%0.089%KF268948.1
1256012560100%0.089%LC002520.1
1255412554100%0.089%KF268950.1
1254912549100%0.089%KF268949.1
1254312543100%0.089%KU955595.1
1253212532100%0.089%KU955592.1
1252612526100%0.089%KU955594.1
1251512515100%0.089%KF383116.1
1251012510100%0.089%KU955591.1
1250412504100%0.089%DQ859059.1
1248812488100%0.089%AY632535.2
124731247399%0.089%HQ234501.1
1242712427100%0.088%KF383117.1
123771237799%0.088%HQ234500.1
1219812198100%0.088%KF383118.1
121941219497%0.089%KF383121.1
9736973697%0.084%KF383120.1
5099509927%0.099%KU312314.1
5066506627%0.099%KU312313.1
4765476525%0.099%KU646828.1
4754475425%0.099%KU646827.1
3517351718%0.099%KU312315.1
3277327717%0.099%KU740199.1
2748274814%0.099%KJ634273.1
2098209811%0.099%KU686218.1
2049204911%0.099%KU179098.1
178117819%0.099%KM078936.1
177717779%0.099%KM078961.1
177517759%0.099%KM078930.1
177217729%0.099%KM078971.1
177217729%0.099%KM078970.1
177217729%0.099%KM078933.1
177017709%0.099%KM078929.1
162816288%0.099%KJ873160.1
144714477%0.099%KJ873161.1
139713977%0.099%KM851039.1
137313737%0.099%KU556802.1
136313637%0.098%KM851038.1
126212626%0.099%KU232300.1
125812586%0.099%KT200609.1
125312536%0.099%KU232290.1
124912496%0.099%KU232297.1
124312436%0.099%KU232294.1
124012406%0.099%KU232292.1
123612366%0.099%KU232298.1
123612369%0.088%AF013415.1
123212326%0.099%KU232296.1
123212326%0.099%KU232293.1
122912296%0.099%KU232295.1
121812186%0.099%KU232288.1
121412146%0.099%KU232289.1
121012106%0.099%KU232299.1
120512056%0.099%KU232291.1
115811586%0.099%KU758878.1
102610265%0.099%KU867812.1
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LOCUS       KU940227               10551 bp    RNA     linear   VRL 23-MAR-2016
DEFINITION  Zika virus isolate Bahia08, partial genome.
ACCESSION   KU940227
VERSION     KU940227.1  GI:1007624013
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10551)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Metagenomic Next-Generation Sequencing for Detection of Zika and
            Chikungunya Virus Co-Infections in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10551)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, Box #0134, San
            Francisco, CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURPI+ v. v1.0; Geneious v. v8.0
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10551
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia08"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="15-Jul-2015"
     CDS             <1..10252
                     /codon_start=2
                     /product="polyprotein"
                     /protein_id="AMQ76464.1"
                     /db_xref="GI:1007624014"
                     /translation="SGGFRIVNMLKRGVARVSPFGGLKRLXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLRIINARKEKKRRGADTS
                     VGIVGLLLTTAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIXXXXLGHMC
                     DATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVTLPSHSXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAIAWLLGSSTSQKVIYLVMIL
                     LIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVS
                     NMAEVRSYCYEASISDTASDSRCPTQGEAYLDKQSDTQYXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXYRIMLSVHGSQHSGMIVNDTGHETDEXXXXX
                     EITPNSPRAEATLGGFGSLGLDCEPRTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XAGADTGTPHWNNKEALXXXXXXXXXXXXXVVLGSQEGAVHTALAGALEAEMDGAKGR
                     LSSGHLKCRLKMDKLRLKGVSYSLCNAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKV
                     PAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHH
                     WHRSGSTIGKAFEATVRGAKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGCSVDFSKK
                     ETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWR
                     SVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAA
                     KTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIG
                     TAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLII
                     PKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRST
                     TASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTAGSTDHMD
                     HFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLAILMGATF
                     AEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQTAISALEG
                     DLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLMAWRAGLATCGGFM
                     LLSLKGKGSVKKNLPFVMALGLTAVXXXXXXXVVGLLLLTRSGKRSWPPSEVLTAVGL
                     ICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKDAEVTGNS
                     PRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWXXXXXXGK
                     RSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSA
                     LRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGXXXXXXXXXXXX
                     XXXXXGDIGAVALDYPAGTSGSPILDKCGRVXXXXXXXXXXXXXXXXXXXTQGRREEE
                     TPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAE
                     MEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIXXXXXX
                     XXXXXXXXXXXXXXXXXMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSS
                     GFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDF
                     VVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRN
                     PNKPXXXXLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGX
                     XXXXXXXXXXXXXLMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAE
                     VWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAAXXXXXXXXXXXXXXTER
                     FQEAIDNLAVLMRAETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFVLMRNKGI
                     GKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSPQDNQMAI
                     IIMVAVGLLGLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPASAWAIYA
                     ALTTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYS
                     QLTPLTLIVAXXXXXXXXXXXXXGLQAAAARAAQKRTAAGIMKNPVVDGIVVTDIDTM
                     TIDPQVXXXXXXXXXXXXXXXXXXXXXXXXXXGEAGALITAATSTLWEGSPNKYWNSS
                     TATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKXXXXXXXXXXXX
                     XXXXXXXXXVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPHGKVIDLGCG
                     RGGWSYYAATIRKVQEVKGXXXXXXXXXXXXXXXXXXXXXVRLKSGVDVFHMAAEPCD
                     TLLCDXGESSSSPEVEEARTLRVLSMVGDXXXXXXXXXXXXXXXXXXXTMMETLERLQ
                     RRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDV
                     NLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPTQ
                     GSASSLVNGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRXXXXXXXXXX
                     XXSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAVEAVNDPR
                     FWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGARFLEFEA
                     LGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRFD
                     LEXXXXXXXXXXXXXXXXXXXXIKYTYQNKVVKVLRPAEKGKTVMDIISRQDXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
                     XXXXXXXXXXXXXXXXXXXXXXXGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLK
                     DGRSIVXXXXXXXXXXXXXXXSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMAN
                     AICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTD
                     IPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGE
                     EGSTPGVL"
     mat_peptide     2..355
                     /product="capsid"
     mat_peptide     356..625
                     /product="pro"
     mat_peptide     626..850
                     /product="membane protein"
     mat_peptide     851..2365
                     /product="envelope protein"
     mat_peptide     2366..3451
                     /product="NS1"
     mat_peptide     3452..4105
                     /product="NS2A"
     mat_peptide     4106..4537
                     /product="NS2B"
     mat_peptide     4538..6346
                     /product="NS3"
     mat_peptide     6347..6787
                     /product="NS4A"
     mat_peptide     6788..8293
                     /product="NS4B"
     mat_peptide     8294..10249
                     /product="NS5"
     gap             80..252
                     /estimated_length=173
     gap             651..764
                     /estimated_length=114
     gap             1122..1257
                     /estimated_length=136
     gap             2110..2240
                     /estimated_length=131
     gap             9339..9596
                     /estimated_length=258
     3'UTR           10253..10551
ORIGIN      
        1 atccggagga ttccggattg tcaatatgct aaaacgcgga gtagcccgtg tgagcccctt
       61 tgggggcttg aagaggctg                                            
          [gap 173 bp]    Expand Ns
      253              gctgagaa taatcaatgc taggaaggag aagaagagac gaggcgcaga
      301 tactagtgtc ggaattgttg gcctcctgct gaccacagct atggcagcgg aggtcactag
      361 acgtgggagt gcatactata tgtacttgga cagaaacgat gctggggagg ccatatcttt
      421 tccaaccaca ttggggatga ataagtgtta tatacnnnnn nnnnatcttg gacacatgtg
      481 tgatgccacc atgagctatg aatgccctat gctggatgag ggggtggaac cagatgacgt
      541 cgattgttgg tgcaacacga cgtcaacttg ggttgtgtac ggaacctgcc atcacaaaaa
      601 aggtgaagca cggagatcta gaagagctgt gacgctcccc tcccattcca          
          [gap 114 bp]    Expand Ns
      765                                                 ctgcca tcgcttggct
      781 tttgggaagc tcaacgagcc aaaaagtcat atacttggtc atgatactgc tgattgcccc
      841 ggcatacagc atcaggtgca taggagtcag caatagggac tttgtggaag gtatgtcagg
      901 tgggacttgg gttgatgttg tcttggaaca tggaggttgt gtcaccgtaa tggcacagga
      961 caaaccgact gtcgacatag agctggttac aacaacagtc agcaacatgg cggaggtaag
     1021 atcctactgc tatgaggcat caatatcaga cacggcttcg gacagccgct gcccaacaca
     1081 aggtgaagcc taccttgaca agcaatcaga cactcaatat g                   
          [gap 136 bp]    Expand Ns
     1258                                                               gta
     1261 ccggataatg ctgtcagttc atggctccca gcacagtggg atgatcgtta atgacacagg
     1321 acatgaaact gatgagannn nnnnnnnnnn ngagataacg cccaattcac caagagccga
     1381 agccaccctg gggggttttg gaagcctagg acttgattgt gaaccgagga cnnnnnnnnn
     1441 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     1501 nnnnnnnnnn nnnnnnnnnn nnnnnnacgc tggggcagac accggaactc cacactggaa
     1561 caacaaagaa gcactgnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnngtggt
     1621 tctagggagt caagaaggag cagttcacac ggcccttgct ggagctctag aggctgagat
     1681 ggatggtgca aagggaaggc tgtcctctgg ccacttgaaa tgtcgcctga aaatggataa
     1741 acttagattg aagggcgtgt catactcctt gtgtaacgca gcgttcacat tcaccaagat
     1801 cccggctgaa acactgcacg ggacagtcac agtggaggta cagtacgcag ggactgatgg
     1861 accttgcaag gttccagctc agatggcggt ggacatgcaa actctgaccc cagttgggag
     1921 gttgataacc gctaaccccg taatcactga aagcactgag aactctaaga tgatgctgga
     1981 acttgatcca ccatttgggg actcctacat tgtcatagga gtcggggaga agaagatcac
     2041 ccaccactgg cacaggagtg gcagcaccat tggaaaagca tttgaagcca ctgtgagagg
     2101 tgccaagag                                                       
          [gap 131 bp]    Expand Ns
     2241                       cacaaattct cattggaacg ttgctgatgt ggttgggtct
     2281 gaacacaaag aatggatcta tttcccttat gtgcttggcc ttagggggag tgttgatctt
     2341 cttatccaca gccgtctctg ctgatgtggg gtgctcggtg gacttctcaa agaaggagac
     2401 gagatgcggt acaggggtgt tcgtctataa cgacgttgaa gcctggaggg acaggtacaa
     2461 gtaccatcct gactcccccc gtagattggc agcagcagtc aagcaagcct gggaagatgg
     2521 tatctgcggg atctcctctg tttcaagaat ggaaaacatc atgtggagat cagtagaagg
     2581 ggagctcaac gcaatcctgg aagagaatgg agttcaactg acggtcgttg tgggatctgt
     2641 aaaaaacccc atgtggagag gtccacagag attgcccgtg cctgtgaacg agctgcccca
     2701 cggctggaag gcttggggga aatcgtactt cgtcagagca gcaaagacaa ataacagctt
     2761 tgtcgtggat ggtgacacac tgaaggaatg cccactcaaa catagagcat ggaacagctt
     2821 tcttgtggag gatcatgggt tcggggtatt tcacactagt gtctggctca aggttagaga
     2881 agattattca ttagagtgtg atccagccgt tattggaaca gctgttaagg gaaaggaggc
     2941 tgtacacagt gatctaggct actggattga gagtgagaag aatgacacat ggaggctgaa
     3001 gagggcccat ctgatcgaga tgaaaacatg tgaatggcca aagtcccaca cattgtggac
     3061 agatggaata gaagagagtg atctgatcat acccaagtct ttagctgggc cactcagcca
     3121 tcacaatacc agagagggct acaggaccca aatgaaaggg ccatggcaca gtgaagagct
     3181 tgaaattcgg tttgaggaat gcccaggcac taaggtccac gtggaggaaa catgtggaac
     3241 aagaggacca tctctgagat caaccactgc aagcggaagg gtgatcgagg aatggtgctg
     3301 cagggagtgc acaatgcccc cactgtcgtt ccgggctaaa gatggctgtt ggtatggaat
     3361 ggagataagg cccaggaaag aaccagaaag caacttagta aggtcaatgg tgactgcagg
     3421 atcaactgat cacatggatc acttctccct tggagtgctt gtgattctgc tcatggtgca
     3481 ggaagggctg aagaagagaa tgaccacaaa gatcatcata agcacatcaa tggcagtgct
     3541 ggtagctatg atcctgggag gattttcaat gagtgacctg gctaagcttg caattttgat
     3601 gggtgccacc ttcgcggaaa tgaacactgg aggagatgta gctcatctgg cgctgatagc
     3661 ggcattcaaa gtcagaccag cgttgctggt atctttcatc ttcagagcta attggacacc
     3721 ccgtgaaagc atgctgctgg ccttggcctc gtgtcttttg caaactgcga tctccgcctt
     3781 ggaaggcgac ctgatggttc tcatcaatgg ttttgctttg gcctggttgg caatacgagc
     3841 gatggttgtt ccacgcactg ataacatcac cttggcaatc ttggctgctc tgacaccact
     3901 ggcccggggc acactgctta tggcgtggag agcaggcctt gctacttgcg gggggtttat
     3961 gctcctctct ctgaagggaa aaggcagtgt gaagaagaac ttaccatttg tcatggccct
     4021 gggactaacc gctgtgannn nnnnnnnnnn nnnnnacgtg gtgggactgc tgttgctcac
     4081 aaggagtggg aagcggagct ggccccctag cgaagtactc acagctgttg gcctgatatg
     4141 cgcattggct ggagggttcg ccaaggcaga tatagagatg gctgggccca tggccgcggt
     4201 cggtctgcta attgtcagtt acgtggtctc aggaaagagt gtggacatgt acattgaaag
     4261 agcaggtgac atcacatggg aaaaagatgc ggaagtcact ggaaacagtc cccggctcga
     4321 tgtggcgcta gatgagagtg gtgatttctc cctggtggag gatgacggtc cccccatgag
     4381 agagatcata ctcaaggtgg tcctgatgac catctgtggc atgaacccaa tagccatacc
     4441 ctttgcagct ggagcgtggt annnnnnnnn nnnnnntgga aaaaggagtg gtgctctatg
     4501 ggatgtgcct gctcccaagg aagtaaaaaa gggggagacc acagatggag tgtacagagt
     4561 aatgactcgt agactgctag gttcaacaca agttggagtg ggagttatgc aagagggggt
     4621 ctttcacact atgtggcacg tcacaaaagg atccgcgctg agaagcggtg aagggagact
     4681 tgatccatac tggggagatg tcaagcagga tctggtgtca tactgtggtc catggaagct
     4741 agatgccgcc tgggacgggc acagcgaggt gcagctcttg gccgtgcccc ccggagnnnn
     4801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnngggg acattggagc
     4861 ggttgcgctg gattacccag caggaacttc aggatctcca atcctagaca agtgtgggag
     4921 agtgatnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     4981 nacccaaggg aggagggagg aagagactcc tgttgagtgc ttcgagcctt cgatgctgaa
     5041 gaagaagcag ctaactgtct tagacttgca tcctggagct gggaaaacca ggagagttct
     5101 tcctgaaata gtccgtgaag ccataaaaac aagactccgt actgtgatct tagctccaac
     5161 cagggttgtc gctgctgaaa tggaggaagc ccttagaggg cttccagtgc gttatatgac
     5221 aacagcagtc aatgtcaccc actctggaac agaaatcgtc gacttaatgt gccatgccac
     5281 cttcacttca cgtctactac agccaatcag agtccccaat tataatctgt atattatnnn
     5341 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     5401 nnnnatgggc gaggcggctg ccatcttcat gaccgccacg ccaccaggaa cccgtgacgc
     5461 atttccggac tccaactcac caattatgga caccgaagtg gaagtcccag agagagcctg
     5521 gagctcaggc tttgattggg tgacggatca ttctggaaaa acagtttggt ttgttccaag
     5581 cgtgaggaac ggcaatgaga tcgcagcttg tctgacaaag gctggaaaac gggtcataca
     5641 gctcagcaga aagacttttg agacagagtt ccagaaaaca aaacatcaag agtgggactt
     5701 tgtcgtgaca actgacattt cagagatggg cgccaacttt aaagctgacc gtgtcataga
     5761 ttccaggaga tgcctaaagc cggtcatact tgatggcgag agagtcattc tggctggacc
     5821 catgcctgtc acacatgcca gcgctgccca gaggaggggg cgcataggca ggaatcccaa
     5881 caaaccnnnn nnnnnnnnnc tgtatggagg tgggtgcgca gagactgacg aagaccatgc
     5941 acactggctt gaagcaagaa tgctccttga caatatttac ctccaagatg gcctcatagc
     6001 ctcgctctat cgacctgagg ccgacaaagt agcagccatt gagggnnnnn nnnnnnnnnn
     6061 nnnnnnnnnn nnnnnnnnnn nnnnnnaact catgaaaaga ggagatcttc ctgtttggct
     6121 ggcctatcag gttgcatctg ccggaataac ctacacagat agaagatggt gctttgatgg
     6181 cacgaccaac aacaccataa tggaagacag tgtgccggca gaggtgtgga ccagacacgg
     6241 agagaaaaga gtgctcaaac cgaggtggat ggatgccaga gtttgttcag atcatgcggc
     6301 cctgaagtca ttcaaggagt ttgccgctgg gaaaagagga gcggctnnnn nnnnnnnnnn
     6361 nnnnnnnnnn nnnnnnnnnn nnnnnnngac agagagattc caggaagcca ttgacaacct
     6421 cgctgtgctc atgcgggcag agactggaag caggccttac aaagccgcgg cggcccaaat
     6481 gccggagacc ctagagacca ttatgctttt ggggttgcta ggaacagtct cgctgggaat
     6541 ctttttcgtc ttgatgagga acaagggcat agggaagatg ggctttggaa tggtgactct
     6601 tggggccagc gcatggctca tgtggctctc ggaaattgag ccagccagaa ttgcatgtgt
     6661 cctcattgtt gtgttcctat tgctggtggt gctcatacct gagccagaaa agcaaagatc
     6721 tccccaggac aaccaaatgg caatcatcat catggtagca gtaggtcttc tgggcttgat
     6781 taccgccaat gaactcggat ggttggagag aacaaagagt gacctaagcc atctaatggg
     6841 aaggagagag gagggggcaa ccataggatt ctcaatggac attgacctgc ggccagcctc
     6901 agcttgggcc atctatgctg ccttgacaac tttcattacc ccagccgtcc aacatgcagt
     6961 gaccacttca tacaacaact actccttaat ggcgatggcc acgcaagctg gagtgttgtt
     7021 tggtatgggc aaagggatgc cattctacgc atgggacttt ggagtcccgc tgctaatgat
     7081 aggttgctac tcacaattaa cacccctgac cctaatagtg gccannnnnn nnnnnnnnnn
     7141 nnnnnnnnnn nnnnnnnnnn nagggctgca ggcagcagct gcgcgtgctg cccagaagag
     7201 aacggcagct ggcatcatga agaaccctgt tgtggatgga atagtggtga ctgacattga
     7261 cacaatgaca attgaccccc aagtggnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnggggagg ctggggctct
     7381 gatcacagcc gcaacttcca ctttgtggga aggctctccg aacaagtact ggaactcctc
     7441 tacagccact tcactgtgta acatttttag gggaagttac ttggctggag cttctctaat
     7501 ctacacagta acaagaaacg ctggcttggt caagagacgt gggggtggaa caggagagac
     7561 cctgggagag aaatggaagg nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     7621 nnnnnnnnnn nnnnnnnnnn nggtgtgcag agaagaggcc cgccgcgccc tcaaggacgg
     7681 tgtggcaacg ggaggccatg ctgtgtcccg aggaagtgca aagctgagat ggttggtgga
     7741 gcggggatac ctgcagcccc atggaaaggt cattgatctt ggatgtggca gagggggctg
     7801 gagttactac gccgccacca tccgcaaagt tcaagaagtg aaaggannnn nnnnnnnnnn
     7861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnng tccgtcttaa
     7921 gagtggggtg gacgtctttc atatggcggc tgagccgtgt gacacgttgc tgtgtgacat
     7981 nggtgagtca tcatctagtc ctgaagtgga agaagcacgg acgctcagag ttctctccat
     8041 ggtgggggat nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     8101 nnnnngcact atgatggaaa ccctggagcg actgcagcgt aggtatgggg gaggactggt
     8161 cagagtgcca ctctcccgca actctacaca tgagatgtac tgggtctctg gagcgaaaag
     8221 caacaccata aaaagtgtgt ccaccacgag ccagctcctc ttggggcgca tggacgggcc
     8281 taggaggcca gtgaaatatg aggaggatgt gaatctcggc tctggcacgc gggctgtggt
     8341 aagctgcgct gaagctccca acatgaagat cattggtaac cgcattgaaa ggatccgcag
     8401 tgagcacgcg gaaacgtggt tctttgacga gaaccaccca tataggacat gggcttacca
     8461 tggaagctat gaggccccca cacaagggtc agcgtcctct ctagtaaacg gggttgtcag
     8521 gctcctgtca aaaccctggg atgtggtgac tggagtcaca ggaatagcca tgaccgacac
     8581 cacaccgtat ggtcagcaaa gagttttcaa ggaaaaagtg gacactaggg nnnnnnnnnn
     8641 nnnnnnnnnn nnnnnnnnnn nnnngagcat ggtctcttcc tggttgtgga aagagctagg
     8701 caaacacaaa cggccacgag tctgtaccaa agaagagttc atcaacaagg ttcgtagcaa
     8761 tgcagcacta ggggcaatat ttgaagagga aaaagagtgg aagactgcag tggaagctgt
     8821 gaacgatcca aggttctggg ctctagtgga caaggaaaga gagcaccacc tgagaggaga
     8881 gtgccagagt tgtgtgtaca acatgatggg aaaaagagaa aagaaacaag gggaatttgg
     8941 aaaggccaag ggcagccgcg ccatctggta tatgtggcta ggggctagat ttctagagtt
     9001 cgaagccctt ggattcttga acgaggatca ctggatgggg agagagaact caggaggtgg
     9061 tgttgaaggg ctgggattac aaagactcgg atatgtccta gaagagatga gtcgcatacc
     9121 aggaggaagg atgtatgcag atgacactgc tggctgggac acccgcatca gcaggtttga
     9181 tctggagnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
     9241 nnnnnnaatc aagtacacat accaaaacaa agtggtaaag gtccttagac cagctgaaaa
     9301 agggaaaaca gttatggaca ttatttcgag acaagacc                       
          [gap 258 bp]    Expand Ns
     9597                                                              tggg
     9601 aaaagttagg aaggacacac aagagtggaa accctcaact ggatgggaca actgggaaga
     9661 agttccgttt tgctcccacc acttcaacaa gctccatctc aaggacggga ggtccattgt
     9721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnntctc caggggcggg
     9781 atggagcatc cgggagactg cttgcctagc aaaatcatat gcgcaaatgt ggcagctcct
     9841 ttatttccac agaagggacc tccgactgat ggccaatgcc atttgctcat ctgtgccagt
     9901 tgactgggtt ccaactggga gaactacctg gtcaatccat ggaaagggag aatggatgac
     9961 cactgaagac atgcttgtgg tgtggaacag agtgtggatt gaggagaacg accacatgga
    10021 agacaagacc ccagttacga aatggacaga cattccctat ttgggaaaaa gggaagactt
    10081 gtggtgtgga tctctcatag ggcacagacc gcgcaccacc tgggctgaga acattaaaaa
    10141 cacagtcaac atggtgcgca ggatcatagg tgatgaagaa aagtacatgg actacctatc
    10201 cacccaagtt cgctacttgg gtgaagaagg gtctacacct ggagtgctgt aagcaccagt
    10261 cttaatgttg tcaggcctgc tagtcagcca cagcttgggg aaagctgtgc agcctgtgac
    10321 ccccccagga gaagctggga aaccaagcct atagtcaggc cgagaacgcc atggcacgga
    10381 agaagccatg ctgcctgtga gcccctcaga ggacactgag tcaaaaaacc ccacgcgctt
    10441 ggaggcgcag gatgggaaaa gaaggtggcg accttcccca cccttcaatc tggggcctga
    10501 actggagatc agctgtggat ctccagaaga gggactagtg gttagaggag a
//
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
32323232100%0.099%KU729218.1
32273227100%0.099%KU707826.1
32273227100%0.099%KU509998.1
32273227100%0.099%KU365780.1
32273227100%0.099%KU365779.1
32273227100%0.099%KU365777.1
32273227100%0.099%KU321639.1
32233223100%0.099%KU926309.1
32183218100%0.099%KU501217.1
32183218100%0.099%KU501216.1
32183218100%0.099%KU501215.1
32183218100%0.099%KU365778.1
32143214100%0.099%KU955589.1
32143214100%0.099%KU870645.1
32143214100%0.099%KU926310.1
32143214100%0.099%KU820899.2
32143214100%0.099%KU312312.1
32143214100%0.099%KJ776791.1
32093209100%0.099%KU955590.1
32093209100%0.099%KU866423.1
32093209100%0.099%KU853013.1
32093209100%0.099%KU497555.1
32073207100%0.099%KU853012.1
32053205100%0.099%KU922960.1
32053205100%0.099%KU922923.1
32053205100%0.099%KU729217.2
32053205100%0.099%KU647676.1
32003200100%0.099%KU820898.1
32003200100%0.099%KU740184.2
32003200100%0.099%KU820897.1
32003200100%0.099%KU761564.1
31823182100%0.099%KU527068.1
31693169100%0.099%KU744693.1
31373137100%0.099%KU681081.3
31193119100%0.098%KF993678.1
30883088100%0.098%KU955593.1
30883088100%0.098%JN860885.1
30633063100%0.098%EU545988.1
30613061100%0.098%KU681082.3
28452845100%0.095%HQ234499.1
23162316100%0.089%KF268949.1
23162316100%0.089%KF268948.1
23092309100%0.088%KF383118.1
23092309100%0.088%KF268950.1
23072307100%0.088%KU955594.1
23072307100%0.088%KU720415.1
23072307100%0.088%LC002520.1
23072307100%0.088%HQ234498.1
23072307100%0.088%AY632535.2
22982298100%0.088%KF383121.1
22982298100%0.088%KF383119.1
22982298100%0.088%KF383115.1
22592259100%0.088%DQ859059.1
22442244100%0.088%KF383116.1
22412241100%0.088%HQ234501.1
22352235100%0.088%KU955595.1
22352235100%0.088%KU955592.1
22352235100%0.088%KU955591.1
22262226100%0.087%HQ234500.1
22232223100%0.087%KF383117.1
2176217667%0.099%KU646827.1
2170217067%0.099%KU646828.1
19921992100%0.085%KF383120.1
93793728%0.0100%KU312315.1
93793728%0.0100%KU312314.1
93193128%0.099%KU312313.1
57457481%2e-15969%DQ859064.1
51851816%1e-14298%KU740199.1
47747715%4e-13099%KU872850.1
2152156%2e-5199%KJ634273.1
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LOCUS       KU940224               10525 bp    RNA     linear   VRL 23-MAR-2016
DEFINITION  Zika virus isolate Bahia09, partial genome.
ACCESSION   KU940224
VERSION     KU940224.1  GI:1007623989
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10525)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Metagenomic Next-Generation Sequencing for Detection of Zika and
            Chikungunya Virus Co-Infections in Bahia, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10525)
  AUTHORS   Sardi,S.I., Somasekar,S., Bandeira,A.C., Naccache,S.N., Campos,G.S.
            and Chiu,C.Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAR-2016) Laboratory Medicine, University of
            California, San Francisco, 185 Berry Street, Box #0134, San
            Francisco, CA 94107, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: SURPI+ v. v1.0; Geneious v. v8.0
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10525
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="Bahia09"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="01-Aug-2015"
     CDS             <1..10226
                     /codon_start=3
                     /product="polyprotein"
                     /protein_id="AMQ76459.1"
                     /db_xref="GI:1007623990"
                     /translation="LKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
                     PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLT
                     TAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQIMDLGHMCDATMSYECP
                     MLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVTLPSHSTRKLQTRSQTW
                     LESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKVIYLVMILLIAPAYSIR
                     CIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC
                     YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAK
                     FACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRA
                     EATLGGFGSLGLDCEPRTGLDFSDLYYLXMNNKHWLVHKEWFHDIPLPWHAGADTGTP
                     HWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCR
                     LKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQ
                     TLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIG
                     KAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQI
                     LIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGCSVDFSKKETRCGTGVF
                     VYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSRMENIMWRSVEGELNAI
                     LEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVD
                     GDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGTAVKGKEAV
                     HSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGIEESDLIIPKSLAGPLS
                     HHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTRGPSLRSTTASGRVIEE
                     WCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSMVTAGSTDHMDHFSLGVLVI
                     LLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLAILMGATFAEMNTGGDV
                     AHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQTAISALEGDLMVLINGF
                     ALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGLATCGGFMLLSLKGKGS
                     VKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFA
                     KADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDE
                     SGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWYVYVKTGKRSGALWDVP
                     APKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLD
                     PYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKGGDIG
                     AVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRREEETPVECFEPS
                     MLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGLP
                     VRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAAR
                     GYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHS
                     GKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISEM
                     GANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYL
                     YGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRK
                     TFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKR
                     VLKPRWMDARVCSDHAALKSFKEFAAGKRGAALGVMEALGTLPGHMTERFQEAIDNLA
                     VLMRAETGSRPYKAAAAQMPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVT
                     LGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSPQDNQMAIIIMVAVGLL
                     GLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPASAWAIYAALTTFITPA
                     VQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPLLMIGCYSQLTPLTLIV
                     AIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIVVTDIDTMTIDPQVEKK
                     MGQVLLIAVAVSSAILSRTAWGWGEAGALITAATSTLWEGSPNKYWNSSTATSLCNIF
                     RGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQMSALEFYSYKKSGITE
                     VCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPHGKVIDLGCGRGGWSYYAA
                     TIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFHMAAEPCDTLLCDIGES
                     SSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMMETLERLQRRYGGGLVR
                     VPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRPVKYEEDVNLGSGTRAV
                     VSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPTQGSASSLVNG
                     VVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWL
                     WKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAVEAVNDPRFWALVDKER
                     EHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHW
                     MGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRFDLENEALITN
                     QMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQRGSGQVVTYALNTF
                     TNLVVQLIRNMEAEEVLEMQDLWLLRRPEKVTNWLQSNGWDRLKRMAVSGDDCVVKPI
                     DDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLKDGRSIVVPC
                     RHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVPVD
                     WVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKRED
                     LWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL"
     mat_peptide     3..329
                     /product="capsid"
     mat_peptide     330..599
                     /product="pro"
     mat_peptide     600..824
                     /product="membane protein"
     mat_peptide     825..2339
                     /product="envelope protein"
     mat_peptide     2340..3425
                     /product="NS1"
     mat_peptide     3426..4079
                     /product="NS2A"
     mat_peptide     4080..4511
                     /product="NS2B"
     mat_peptide     4512..6320
                     /product="NS3"
     mat_peptide     6321..6761
                     /product="NS4A"
     mat_peptide     6762..8267
                     /product="NS4B"
     mat_peptide     8268..10223
                     /product="NS5"
     3'UTR           10227..10525
ORIGIN      
        1 tgctaaaacg cggagtagcc cgtgtgagcc cctttggggg cttgaagagg ctgccagccg
       61 gacttctgct gggtcatggg cccatcagga tggtcttggc gattctagcc tttttgagat
      121 tcacggcaat caagccatca ctgggtctca tcaatagatg gggttcagtg gggaaaaaag
      181 aggctatgga aataataaag aagttcaaga aagatctggc tgccatgctg agaataatca
      241 atgctaggaa ggagaagaag agacgaggcg cagatactag tgtcggaatt gttggcctcc
      301 tgctgaccac agctatggca gcggaggtca ctagacgtgg gagtgcatac tatatgtact
      361 tggacagaaa cgatgctggg gaggccatat cttttccaac cacattgggg atgaataagt
      421 gttatataca gatcatggat cttggacaca tgtgtgatgc caccatgagc tatgaatgcc
      481 ctatgctgga tgagggggtg gaaccagatg acgtcgattg ttggtgcaac acgacgtcaa
      541 cttgggttgt gtacggaacc tgccatcaca aaaaaggtga agcacggaga tctagaagag
      601 ctgtgacgct cccctcccat tccactagga agctgcaaac gcggtcgcaa acctggttgg
      661 aatcaagaga atacacaaag cacttgatta gagtcgaaaa ttggatattc aggaaccctg
      721 gcttcgcgtt agcagcagct gccatcgctt ggcttttggg aagctcaacg agccaaaaag
      781 tcatatactt ggtcatgata ctgctgattg ccccggcata cagcatcagg tgcataggag
      841 tcagcaatag ggactttgtg gaaggtatgt caggtgggac ttgggttgat gttgtcttgg
      901 aacatggagg ttgtgtcacc gtaatggcac aggacaaacc gactgtcgac atagagctgg
      961 ttacaacaac agtcagcaac atggcggagg taagatccta ctgctatgag gcatcaatat
     1021 cagacatggc ttcggacagc cgctgcccaa cacaaggtga agcctacctt gacaagcaat
     1081 cagacactca atatgtctgc aaaagaacgt tagtggacag aggctgggga aatggatgtg
     1141 gactttttgg caaagggagc ctggtgacat gcgctaagtt tgcatgctcc aagaaaatga
     1201 ccgggaagag catccagcca gagaatctgg agtaccggat aatgctgtca gttcatggct
     1261 cccagcacag tgggatgatc gttaatgaca caggacatga aactgatgag aatagagcga
     1321 aggttgagat aacgcccaat tcaccaagag ccgaagccac cctggggggt tttggaagcc
     1381 taggacttga ttgtgaaccg aggacaggcc ttgacttttc agatttgtat tacttganna
     1441 tgaataacaa gcactggttg gttcacaagg agtggttcca cgacattcca ttaccttggc
     1501 acgctggggc agacaccgga actccacact ggaacaacaa agaagcactg gtagagttca
     1561 aggacgcaca tgccaaaagg caaactgtcg tggttctagg gagtcaagaa ggagcagttc
     1621 acacggccct tgctggagct ctagaggctg agatggatgg tgcaaaggga aggctgtcct
     1681 ctggccactt gaaatgtcgc ctgaaaatgg ataaacttag attgaagggc gtgtcatact
     1741 ccttgtgtac cgcagcgttc acattcacca agatcccggc tgaaacactg cacgggacag
     1801 tcacagtgga ggtacagtac gcagggactg atggaccttg caaggttcca gctcagatgg
     1861 cggtggacat gcaaactctg accccagttg ggaggttgat aaccgctaac cccgtaatca
     1921 ctgaaagcac tgagaactct aagatgatgc tggaacttga tccaccattt ggggactcct
     1981 acattgtcat aggagtcggg gagaagaaga tcacccacca ctggcacagg agtggcagca
     2041 ccattggaaa agcatttgaa gccactgtga gaggtgccaa gagaatggca gtcttgggag
     2101 acacagcctg ggactttgga tcagttggag gcgctctcaa ctcattgggc aagggcatcc
     2161 atcaaatttt tggagcagct ttcaaatcat tgtttggagg aatgtcctgg ttctcacaaa
     2221 ttctcattgg aacgttgctg atgtggttgg gtctgaacac aaagaatgga tctatttccc
     2281 ttatgtgctt ggccttaggg ggagtgttga tcttcttatc cacagccgtc tctgctgatg
     2341 tggggtgctc ggtggacttc tcaaagaagg agacgagatg cggtacaggg gtgttcgtct
     2401 ataacgacgt tgaagcctgg agggacaggt acaagtacca tcctgactcc ccccgtagat
     2461 tggcagcagc agtcaagcaa gcctgggaag atggtatctg cgggatctcc tctgtttcaa
     2521 gaatggaaaa catcatgtgg agatcagtag aaggggagct caacgcaatc ctggaagaga
     2581 atggagttca actgacggtc gttgtgggat ctgtaaaaaa ccccatgtgg agaggtccac
     2641 agagattgcc cgtgcctgtg aacgagctgc cccacggctg gaaggcttgg gggaaatcgt
     2701 acttcgtcag agcagcaaag acaaataaca gctttgtcgt ggatggtgac acactgaagg
     2761 aatgcccact caaacataga gcatggaaca gctttcttgt ggaggatcat gggttcgggg
     2821 tatttcacac tagtgtctgg ctcaaggtta gagaagatta ttcattagag tgtgatccag
     2881 ccgttattgg aacagctgtt aagggaaagg aggctgtaca cagtgatcta ggctactgga
     2941 ttgagagtga gaagaatgac acatggaggc tgaagagggc ccatctgatc gagatgaaaa
     3001 catgtgaatg gccaaagtcc cacacattgt ggacagatgg aatagaagag agtgatctga
     3061 tcatacccaa gtctttagct gggccactca gccatcacaa taccagagag ggctacagga
     3121 cccaaatgaa agggccatgg cacagtgaag agcttgaaat tcggtttgag gaatgcccag
     3181 gcactaaggt ccacgtggag gaaacatgtg gaacaagagg accatctctg agatcaacca
     3241 ctgcaagcgg aagggtgatc gaggaatggt gctgcaggga gtgcacaatg cccccactgt
     3301 cgttccgggc taaagatggc tgttggtatg gaatggagat aaggcccagg aaagaaccag
     3361 aaagcaactt agtaaggtca atggtgactg caggatcaac tgatcacatg gatcacttct
     3421 cccttggagt gcttgtgatt ctgctcatgg tgcaggaagg gctgaagaag agaatgacca
     3481 caaagatcat cataagcaca tcaatggcag tgctggtagc tatgatcctg ggaggatttt
     3541 caatgagtga cctggctaag cttgcaattt tgatgggtgc caccttcgcg gaaatgaaca
     3601 ctggaggaga tgtagctcat ctggcgctga tagcggcatt caaagtcaga ccagcgttgc
     3661 tggtatcttt catcttcaga gctaattgga caccccgtga aagcatgctg ctggccttgg
     3721 cctcgtgtct tttgcaaact gcgatctccg ccttggaagg cgacctgatg gttctcatca
     3781 atggttttgc tttggcctgg ttggcaatac gagcgatggt tgttccacgc actgataaca
     3841 tcaccttggc aatcttggct gctctgacac cactggcccg gggcacactg cttgtggcgt
     3901 ggagagcagg ccttgctact tgcggggggt ttatgctcct ctctctgaag ggaaaaggca
     3961 gtgtgaagaa gaacttacca tttgtcatgg ccctgggact aaccgctgtg aggctggtcg
     4021 accccatcaa cgtggtggga ctgctgttgc tcacaaggag tgggaagcgg agctggcccc
     4081 ccagcgaagt actcacagct gttggcctga tatgcgcatt ggctggaggg ttcgccaagg
     4141 cagatataga gatggctggg cccatggccg cggtcggtct gctaattgtc agttacgtgg
     4201 tctcaggaaa gagtgtggac atgtacattg aaagagcagg tgacatcaca tgggaaaaag
     4261 atgcggaagt cactggaaac agtccccggc tcgatgtggc gctagatgag agtggtgatt
     4321 tctccctggt ggaggatgac ggtcccccca tgagagagat catactcaag gtggtcctga
     4381 tgaccatctg tggcatgaac ccaatagcca taccctttgc agctggagcg tggtacgtat
     4441 acgtgaagac tggaaaaagg agtggtgctc tatgggatgt gcctgctccc aaggaagtaa
     4501 aaaaggggga gaccacagat ggagtgtaca gagtaatgac tcgtagactg ctaggttcaa
     4561 cacaagttgg agtgggagtt atgcaagagg gggtctttca cactatgtgg cacgtcacaa
     4621 aaggatccgc gctgagaagc ggtgaaggga gacttgatcc atactgggga gatgtcaagc
     4681 aggatctggt gtcatactgt ggtccatgga agctagatgc cgcctgggac gggcacagcg
     4741 aggtgcagct cttggccgtg ccccccggag agagagcgag gaacatccag actctgcccg
     4801 gaatatttaa gacaaagggt ggggacattg gagcggttgc gctggattac ccagcaggaa
     4861 cttcaggatc tccaatccta gacaagtgtg ggagagtgat aggactttat ggcaatgggg
     4921 tcgtgatcaa aaatgggagt tatgttagtg ccatcaccca agggaggagg gaggaagaga
     4981 ctcctgttga gtgcttcgag ccttcgatgc tgaagaagaa gcagctaact gtcttagact
     5041 tgcatcctgg agctgggaaa accaggagag ttcttcctga aatagtccgt gaagccataa
     5101 aaacaagact ccgtactgtg atcttagctc caaccagggt tgtcgctgct gaaatggagg
     5161 aagcccttag agggcttcca gtgcgttata tgacaacagc agtcaatgtc acccactctg
     5221 gaacagaaat cgtcgactta atgtgccatg ccaccttcac ttcacgtcta ctacagccaa
     5281 tcagagtccc caattataat ctgtatatta tggatgaggc ccacttcaca gatccctcaa
     5341 gtatagcagc aagaggatac atttcaacaa gggttgagat gggcgaggcg gctgccatct
     5401 tcatgaccgc cacgccacca ggaacccgtg acgcatttcc ggactccaac tcaccaatta
     5461 tggacaccga agtggaagtc ccagagagag cctggagctc aggctttgat tgggtgacgg
     5521 atcattctgg aaaaacagtt tggtttgttc caagcgtgag gaacggcaat gagatcgcag
     5581 cttgtctgac aaaggctgga aaacgggtca tacagctcag cagaaagact tttgagacag
     5641 agttccagaa aacaaaacat caagagtggg actttgtcgt gacaactgac atttcagaga
     5701 tgggcgccaa ctttaaagct gaccgtgtca tagattccag gagatgccta aagccggtca
     5761 tacttgatgg cgagagagtc attctggctg gacccatgcc tgtcacacat gccagcgctg
     5821 cccagaggag ggggcgcata ggcaggaatc ccaacaaacc tggagatgag tatctgtatg
     5881 gaggtgggtg cgcagagact gacgaagacc atgcacactg gcttgaagca agaatgctcc
     5941 ttgacaatat ttacctccaa gatggcctca tagcctcgct ctatcgacct gaggccgaca
     6001 aagtagcagc cattgaggga gagttcaagc ttaggacgga gcaaaggaag acctttgtgg
     6061 aactcatgaa aagaggagat cttcctgttt ggctggccta tcaggttgca tctgccggaa
     6121 taacctacac agatagaaga tggtgctttg atggcacgac caacaacacc ataatggaag
     6181 acagtgtgcc ggcagaggtg tggaccagac acggagagaa aagagtgctc aaaccgaggt
     6241 ggatggatgc cagagtttgt tcagatcatg cggccctgaa gtcattcaag gagtttgccg
     6301 ctgggaaaag aggagcggct cttggagtga tggaagccct gggaacactg ccaggacaca
     6361 tgacagagag attccaggaa gccattgaca acctcgctgt gctcatgcgg gcagagactg
     6421 gaagcaggcc ttacaaagcc gcggcggccc aaatgccgga gaccctagag accattatgc
     6481 ttttggggtt gctaggaaca gtctcgctgg gaatcttttt cgtcttgatg aggaacaagg
     6541 gcatagggaa gatgggcttt ggaatggtga ctcttggggc cagcgcatgg ctcatgtggc
     6601 tctcggaaat tgagccagcc agaattgcat gtgtcctcat tgttgtgttc ctattgctgg
     6661 tggtgctcat acctgagcca gaaaagcaaa gatctcccca ggacaaccaa atggcaatca
     6721 tcatcatggt agcagtaggt cttctgggct tgattaccgc caatgaactc ggatggttgg
     6781 agagaacaaa gagtgaccta agccatctaa tgggaaggag agaggagggg gcaaccatag
     6841 gattctcaat ggacattgac ctgcggccag cctcagcttg ggccatctat gctgccttga
     6901 caactttcat taccccagcc gtccaacatg cagtgaccac ttcatacaac aactactcct
     6961 taatggcgat ggccacgcaa gctggagtgt tgtttggtat gggcaaaggg atgccattct
     7021 acgcatggga ctttggagtc ccgctgctaa tgataggttg ctactcacaa ttaacacccc
     7081 tgaccctaat agtggccatc attttgctcg tggcgcacta catgtacttg atcccagggc
     7141 tgcaggcagc agctgcgcgt gctgcccaga agagaacggc agctggcatc atgaagaacc
     7201 ctgttgtgga tggaatagtg gtgactgaca ttgacacaat gacaattgac ccccaagtgg
     7261 agaaaaagat gggacaggtg ctactcatag cagtagccgt ctccagcgcc atactgtcgc
     7321 ggaccgcctg ggggtggggg gaggctgggg ctctgatcac agccgcaact tccactttgt
     7381 gggaaggctc tccgaacaag tactggaact cctctacagc cacttcactg tgtaacattt
     7441 ttaggggaag ttacttggct ggagcttctc taatctacac agtaacaaga aacgctggct
     7501 tggtcaagag acgtgggggt ggaacaggag agaccctggg agagaaatgg aaggcccgct
     7561 tgaaccagat gtcggccctg gagttctact cctacaaaaa gtcaggcatc accgaggtgt
     7621 gcagagaaga ggcccgccgc gccctcaagg acggtgtggc aacgggaggc catgctgtgt
     7681 cccgaggaag tgcaaagctg agatggttgg tggagcgggg atacctgcag ccccatggaa
     7741 aggtcattga tcttggatgt ggcagagggg gctggagtta ctacgccgcc accatccgca
     7801 aagttcaaga agtgaaagga tacacaaaag gaggccctgg tcatgaagaa cccgtgttgg
     7861 tgcaaagcta tgggtggaac atagtccgtc ttaagagtgg ggtggacgtc tttcatatgg
     7921 cggctgagcc gtgtgacacg ttgctgtgtg acataggtga gtcatcatct agtcctgaag
     7981 tggaagaagc acggacgctc agagttctct ccatggtggg ggattggctt gaaaaaagac
     8041 caggagcctt ttgtataaaa gtgttgtgcc catacaccag cactatgatg gaaaccctgg
     8101 agcgactgca gcgtaggtat gggggaggac tggtcagagt gccactctcc cgcaactcta
     8161 cacatgagat gtactgggtc tctggagcga aaagcaacac cataaaaagt gtgtccacca
     8221 cgagccagct cctcttgggg cgcatggacg ggcctaggag gccagtgaaa tatgaggagg
     8281 atgtgaatct cggctctggc acgcgggctg tggtaagctg cgctgaagct cccaacatga
     8341 agatcattgg taaccgcatt gaaaggatcc gcagtgagca cgcggaaacg tggttctttg
     8401 acgagaacca cccatatagg acatgggctt accatggaag ctatgaggcc cccacacaag
     8461 ggtcagcgtc ctctctagta aacggggttg tcaggctcct gtcaaaaccc tgggatgtgg
     8521 tgactggagt cacaggaata gccatgaccg acaccacacc gtatggtcag caaagagttt
     8581 tcaaggaaaa agtggacact agggtgccag acccccaaga aggcactcgt caggttatga
     8641 gcatggtctc ttcctggttg tggaaagagc taggcaaaca caaacggcca cgagtctgta
     8701 ccaaagaaga gttcatcaac aaggttcgta gcaatgcagc actaggggca atatttgaag
     8761 aggaaaaaga gtggaagact gcagtggaag ctgtgaacga tccaaggttc tgggctctag
     8821 tggacaagga aagagagcac cacctgagag gagagtgcca gagttgtgtg tacaacatga
     8881 tgggaaaaag agaaaagaaa caaggggaat ttggaaaggc caagggcagc cgcgccatct
     8941 ggtatatgtg gctaggggct agatttctag agttcgaagc ccttggattc ttgaacgagg
     9001 atcactggat ggggagagag aactcaggag gtggtgttga agggctggga ttacaaagac
     9061 tcggatatgt cctagaagag atgagtcgca taccaggagg aaggatgtat gcagatgaca
     9121 ctgctggctg ggacacccgc atcagcaggt ttgatctgga gaatgaagct ctaatcacca
     9181 accaaatgga gaaagggcac agggccttgg cattggccat aatcaagtac acataccaaa
     9241 acaaagtggt aaaggtcctt agaccagctg aaaaagggaa aacagttatg gacattattt
     9301 cgagacaaga ccaaaggggg agcggacaag ttgtcactta cgctcttaac acatttacca
     9361 acctagtggt gcaactcatt cggaatatgg aggctgagga agttctcgag atgcaagact
     9421 tgtggctgct gcggaggcca gagaaagtga ccaactggtt gcagagcaac ggatgggata
     9481 ggctcaaacg aatggcagtc agtggagatg attgcgttgt gaagccaatt gatgataggt
     9541 ttgcacatgc cctcaggttc ttgaatgata tgggaaaagt taggaaggac acacaagagt
     9601 ggaaaccctc aactggatgg gacaactggg aagaagttcc gttttgctcc caccacttca
     9661 acaagctcca tctcaaggac gggaggtcca ttgtggttcc ctgccgccac caagatgaac
     9721 tgattggccg ggcccgcgtc tctccagggg cgggatggag catccgggag actgcttgcc
     9781 tagcaaaatc atatgcgcaa atgtggcagc tcctttattt ccacagaagg gacctccgac
     9841 tgatggccaa tgccatttgc tcatctgtgc cagttgactg ggttccaact gggagaacta
     9901 cctggtcaat ccatggaaag ggagaatgga tgaccactga agacatgctt gtggtgtgga
     9961 acagagtgtg gattgaggag aacgaccaca tggaagacaa gaccccagtt acgaaatgga
    10021 cagacattcc ctatttggga aaaagggaag acttgtggtg tggatctctc atagggcaca
    10081 gaccgcgcac cacctgggct gagaacatta aaaacacagt caacatggtg cgcaggatca
    10141 taggtgatga agaaaagtac atggactacc tatccaccca agttcgctac ttgggtgaag
    10201 aagggtctac acctggagtg ctgtaagcac cagtcttaat gttgtcaggc ctgctagtca
    10261 gccacagctt ggggaaagct gtgcagcctg tgaccccccc aggagaagct gggaaaccaa
    10321 gcctatagtc aggccgagaa cgccatggca cggaagaagc catgctgcct gtgagcccct
    10381 cagaggacac tgagtcaaaa aaccccacgc gcttggaggc gcaggatggg aaaagaaggt
    10441 ggcgaccttc cccacccttc aatctggggc ctgaactgga gatcagctgt ggatctccag
    10501 aagagggact agtggttaga ggaga
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Sequences producing significant alignments:

Select:AllNone Selected:0

Sequences producing significant alignments:
Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccession
1843518435100%0.0100%KU940224.1
1842918429100%0.099%KU940228.1
1830918309100%0.099%KU509998.1
1830318303100%0.099%KJ776791.1
1829418294100%0.099%KU729218.1
1829418294100%0.099%KU321639.1
1828518285100%0.099%KU707826.1
1828518285100%0.099%KU365779.1
1827318273100%0.099%KU926309.1
1827318273100%0.099%KU365780.1
1826718267100%0.099%KU647676.1
1826718267100%0.099%KU365777.1
1826418264100%0.099%KU501217.1
182601826099%0.099%KU497555.1
1825818258100%0.099%KU729217.2
1825818258100%0.099%KU527068.1
1825818258100%0.099%KU501216.1
1825418254100%0.099%KU820897.1
1825418254100%0.099%KU501215.1
1825418254100%0.099%KU365778.1
1825418254100%0.099%KU312312.1
1824918249100%0.099%KU922960.1
1824518245100%0.099%KU926310.1
1824518245100%0.099%KU922923.1
1824518245100%0.099%KU853013.1
1824418244100%0.099%KU853012.1
1824018240100%0.099%KU870645.1
1822718227100%0.099%KU820898.1
1822218222100%0.099%KU955590.1
1821818218100%0.099%KU740184.2
1821818218100%0.099%KU761564.1
1820018200100%0.099%KU955589.1
1820018200100%0.099%KU820899.2
1809218092100%0.099%KU866423.1
1806018060100%0.099%KU744693.1
1796117961100%0.099%KU681081.3
176901769099%0.099%KF993678.1
1765917659100%0.098%KU955593.1
176581765899%0.098%JN860885.1
1751917519100%0.098%EU545988.1
1735317353100%0.098%KU681082.3
163341633499%0.095%HQ234499.1
1323613236100%0.089%KU720415.1
132301323099%0.089%HQ234498.1
1322713227100%0.089%KF383119.1
1322513225100%0.089%KF383115.1
1321413214100%0.089%LC002520.1
1321213212100%0.089%KF268949.1
1321213212100%0.089%KF268948.1
1320513205100%0.089%KF268950.1
1320013200100%0.089%KU955595.1
1319813198100%0.089%KU955594.1
1319113191100%0.089%KU955592.1
1318913189100%0.089%DQ859059.1
1317313173100%0.089%KU955591.1
1317113171100%0.089%KF383116.1
1316913169100%0.089%AY632535.2
131461314699%0.089%HQ234501.1
1310013100100%0.088%KF383117.1
130751307599%0.088%HQ234500.1
1290012968100%0.088%KF383118.1
128251282597%0.089%KF383121.1
107961079697%0.084%KF383120.1
50791452387%0.095%KU940227.1
4895489526%0.099%KU312314.1
4868486826%0.099%KU312313.1
4652465225%0.099%KU646828.1
4643464325%0.099%KU646827.1
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To the Editor: Zika virus (ZIKV) is a mosquito-borne flavivirus related to yellow fever virus, dengue virus (DENV), and West Nile virus (WNV). It is a single-stranded positive RNA virus (10,794-nt genome) that is closely related to the Spondweni virus and is transmitted by many Aedes spp. mosquitoes, including Ae. africanus, Ae. luteocephalus, Ae. hensilli, andAe. aegypti. The virus was identified in rhesus monkeys during sylvatic yellow fever surveillance in the Zika Forest in Uganda in 1947 and was reported in humans in 1952 (1).

In 2007, an outbreak of ZIKV was reported in Yap Island, Federated States of Micronesia (2). ZIKV also caused a major epidemic in the French Polynesia in 2013–2014 (3), and New Caledonia reported imported cases from French Polynesia in 2013 and reported an outbreak in 2014 (4).

A new challenge has arisen in Brazil with the emergence of ZIKV and co-circulation with others arboviruses (i.e., DENV and chikungunya virus [CHIKV]). We report ZIKV infection in Brazil associated with a recent ongoing outbreak in Camaçari, Bahia, Brazil, of an illness characterized by maculopapular rash, fever, myalgias/arthralgia, and conjunctivitis.

On March 26, 2015, serum samples were obtained from 24 patients (Table) at Santa Helena Hospital in Camaçari who were given a presumptive diagnosis of an acute viral illness by emergency department physicians. These patients were given treatment for a dengue-like illness, and blood samples were obtained for complete blood counts and serologic testing by using an ELISA specific for IgG and IgM against DENV.

Serum samples were analyzed at the Federal University of Bahia by reverse transcription PCR (RT-PCR) to detect DENV, CHIKV, WNV, Mayaro virus, and ZIKV. In brief, serum samples were subjected to RNA extraction by using the QIAamp Viral RNA Mini Kit (QIAGEN, Hilden, Germany). RNA was reverse transcribed by using the SuperScript II Reverse Transcription Kit (Invitrogen, Carlsbad, CA, USA) and subjected to PCRs specific for DENV (5) CHIKV (6), WNV (7) and Mayaro virus (8). A positive RT-PCR for a partial region of the envelope gene with primers ZIKVENF and ZIKVENVR (positions 1538–1558 and 1902–1883, respectively) (9) was considered indicative of ZIKV infection. PCR products (362 bp) were sequenced at the ACTGene Analises Moleculares, Alvorada, Rio Grande do Sul (Porto Allegre, Brazil), and sequences were deposited in GenBank under accession nos. KR816333–KR816336.

All patients were negative by RT-PCR for DENV, Mayaro virus, and WNV. Samples from 7 (29.2%) patients were positive by RT-PCR for ZIKV (369-bp fragment) and from 3 (12.5%) patients for CHIKV (305-bp fragment). There was no simultaneous detection of ZIKV and CHIKV. Most (85.7%) patients positive for ZIKV were women; they had a median age of 28 years and no history of international travel. Patients positive for ZIKV sought medical care after a 4-day (range 1–5 days) history of rash, myalgias, arthralgias, or fever. Three patients had IgG against DENV, which is consistent with a previous DENV infection, and none of the 7 ZIKV-positive patients had a positive response for DENV.

Mean laboratory findings for patients with acute ZIKV infection were a leukocyte count of 3,750 cells/mm3 (range 2,790 cells/mm3–6,150 cells/mm3) and a platelet count of 180,000 platelets/mm3 (range 151,000 platelets/mm3–274,000 platelets/mm3). The mean C-reactive protein level was 16.3 mg/L (range 0.9 mg/L–19.7 mg/L). Sign and symptom duration was 1–5 days, and most patients had a maculopapular rash, myalgias, fever, and headache. Arthralgia was seen less frequently.

ZIKV infections were assessed by sequencing partial ZIKV envelope gene regions of isolates. Phylogenetic analysis rooted with Spondwei virus showed that ZIKV sequences obtained belonged to the Asian lineage and showed 99% identity with a sequence from a ZIKV isolate from French Polynesia (KJ776791) (10).

We report ZIKV infection in Brazil in association with an ongoing outbreak of an acute maculoexantematic illness. Although the patient population samples were not randomly selected, 42% (10/24) of the patients were positive for ZIKV (n = 7) or CHIKV (n = 3) and had maculopapular rash, fever, myalgias and headache. After detection of ZIKV in Bahia, many cases have been identified in other states (http://www.promedmail.org, archive no. 20152015602.343.1158).

Cases of infection with DENV, CHIKV, and ZIKV in Brazil and elsewhere will make diagnosis based on clinical and epidemiologic grounds unreliable. These issues show the need for laboratory confirmation of these arboviral infections. More studies are needed to address the effects of these concurrent arboviruses infections in Brazil.

 
 
Gubio S. Campos, Antonio C. Bandeira, and Silvia I. SardiComments to Author 
Author affiliations: Federal University of Bahia, Salvador, Bahia, Brazil (G.S. Campos, S.I. Sardi); Hospital Aliança, Salvador (A.C. Bandeira)

Acknowledgment

This study was supported by Fundação de Amparo a Pesquisa do Estado da Bahia.

References

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Table

Suggested citation for this article: Campos GS, Bandeira AC, Sardi SI. Zika virus outbreak, Bahia, Brazil [letter]. Emerg Infect Dis. 2015 Oct [date cited]. http://dx.doi.org/10.3201/eid2110.150847

DOI: 10.3201/eid2110.150847

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