niman Posted March 24, 2016 Report Share Posted March 24, 2016 (edited) Fundacao Oswaldo Cruz has released a full sequence from a Rio de Janiero patient isolated from saliva, Rio-S1, collected Jan 29, 2016.http://www.ncbi.nlm.nih.gov/nuccore/KU926310 Edited March 24, 2016 by niman Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 LOCUS KU926310 10805 bp ss-RNA linear VRL 21-MAR-2016 DEFINITION Zika virus isolate Rio-S1, complete genome. ACCESSION KU926310 VERSION KU926310.1 GI:1006593054 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10805) AUTHORS Bonaldo,M.C., Ribeiro,I.P., Lima,N.S., Santos,A.A.C., Raphael,L.M.S., Cruz,S.O.D., Mello,I.S., Furtado,N.D., Moura,E.E., Castro,M.G., Gerber,A.L., Almeida,L.G.P., Lourenco-de-Oliveira,R., Vasconcelos,A.T.R. and Brasil,P. TITLE Isolation of infective Zika virus from urine and saliva of patients in Brazil JOURNAL Unpublished REFERENCE 2 (bases 1 to 10805) AUTHORS Bonaldo,M.C., Ribeiro,I.P., Lima,N.S., Santos,A.A.C., Raphael,L.M.S., Cruz,S.O.D., Mello,I.S., Furtado,N.D., Moura,E.E., Castro,M.G., Gerber,A.L., Almeida,L.G.P., Lourenco-de-Oliveira,R., Vasconcelos,A.T.R. and Brasil,P. TITLE Direct Submission JOURNAL Submitted (16-MAR-2016) Laboratorio Nacional de Bioinformatica / Laboratorio Nacional de Computacao Cientifica, Laboratorio de Biologia Molecular de Flavivirus / Fundacao Oswaldo Cruz, Rua Getulio Vargas, 333, Petropolis, RJ 25651075, Brazil COMMENT ##Assembly-Data-START## Assembly Method :: Ray v. 2.2.0 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10805 /organism="Zika virus" /mol_type="genomic RNA" /isolate="Rio-S1" /isolation_source="saliva" /host="Homo sapiens" /db_xref="taxon:64320" /country="Brazil" /collection_date="29-Jan-2016" /note="passage details: Vero cells" 5'UTR 1..106 CDS 107..10378 /codon_start=1 /product="polyprotein" /protein_id="AMQ48982.1" /db_xref="GI:1006593055" /translation="MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI RMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKK RRGADTSVGIVGLLLTTAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQI MDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVT LPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKV IYLVMILLIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIE LVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWG NGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWF HDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAE MDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAG ADGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVG EKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFG AAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGC SVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSR MENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGK SYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLE CDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGI EESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTR GPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSVVTA GSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLA ILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQT AISALEGDLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGL ATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSE VLTAVGLICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKD AEVTGNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWY VYVKTGKRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMW HVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARN IQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAIT QGRREEETPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAP TRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLY IMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEV PERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKT KHQEWDFVVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQR RGRIGRNPNKPGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADK VAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIM EDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGATFGVMEALGTL PGHMTERFQEAIDNLAVLMRAETGSRPYKAAAAQLPETLETIMLLGLLGTVSLGIFFV LMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSP QDNQMAIIIMVAVGLLGLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPA SAWAIYAALTTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPL LMIGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIV VTDIDTMTIDPQVEKKMGQVLLIAVAVSSAILSRTAWGWGEAGALITAATSTLWEGSP NKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQ MSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPYGK VIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFH MAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMAGDWLEKRPGAFCIKVLCPYTSTMM ETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRP VKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHG SYEAPTQGSASSLINGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPD PQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAV EAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGA RFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWD TRISRFDLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQ DQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDR LKRMAVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHH FNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKT PVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLST QVRYLGEEGSTPGVL" mat_peptide 107..472 /product="anchored capsid protein C" mat_peptide 107..418 /product="capsid protein C" mat_peptide 473..976 /product="membrane glycoprotein precursor M" mat_peptide 473..751 /product="protein pr" mat_peptide 752..976 /product="membrane glycoprotein M" mat_peptide 977..2488 /product="envelope protein E" mat_peptide 2489..3544 /product="nonstructural protein NS1" mat_peptide 3545..4222 /product="nonstructural protein NS2A" mat_peptide 4223..4612 /product="nonstructural protein NS2B" mat_peptide 4613..6463 /product="nonstructural protein NS3" mat_peptide 6464..6844 /product="nonstructural protein NS4A" mat_peptide 6845..6913 /product="protein 2K" mat_peptide 6914..7666 /product="nonstructural protein NS4B" mat_peptide 7667..10375 /product="RNA-dependent RNA polymerase NS5" 3'UTR 10379..10805 ORIGIN 1 gttgttgatc tgtgtgaatc agactgcgac agttcgagtt tgaagcgaaa gctagcaaca 61 gtatcaacag gttttatttt ggatttggaa acgagagttt ctggtcatga aaaacccaaa 121 aaagaaatcc ggaggattcc ggattgtcaa tatgctaaaa cgcggagtag cccgtgtgag 181 cccctttggg ggcttgaaga ggctgccagc cggacttctg ctgggtcatg ggcccatcag 241 gatggtcttg gcgattctag cctttttgag attcacggca atcaagccat cactgggtct 301 catcaataga tggggttcag tggggaaaaa agaggctatg gaaataataa agaagttcaa 361 gaaagatctg gctgccatgc tgagaataat caatgctagg aaggagaaga agagacgagg 421 cgcagatact agtgtcggaa ttgttggcct cctgctgacc acagctatgg cagcggaggt 481 caccagacgt gggagtgcat actatatgta cttggacaga aacgatgctg gggaggccat 541 atcttttcca accacattgg ggatgaataa gtgttatata cagatcatgg atcttggaca 601 catgtgtgat gccaccatga gctatgaatg ccctatgctg gatgaggggg tggaaccaga 661 tgacgtcgat tgttggtgca acacgacgtc aacttgggtt gtgtacggaa cctgccatca 721 caaaaaaggt gaagcacgga gatctagaag agctgtgacg ctcccctccc attccactag 781 gaagctgcaa acgcggtcgc aaacctggtt ggaatcaaga gaatacacaa agcacttgat 841 tagagtcgaa aattggatat tcaggaaccc tggcttcgcg ttagcagcag ctgccatcgc 901 ttggcttttg ggaagctcaa cgagccaaaa agtcatatac ttggtcatga tactgctgat 961 tgccccggca tacagcatca ggtgcatagg agtcagcaat agggactttg tggaaggtat 1021 gtcaggtggg acttgggttg atgttgtctt ggaacatgga ggttgtgtca ccgtaatggc 1081 acaggacaaa ccgactgtcg acatagagct ggttacaaca acagtcagca acatggcgga 1141 ggtaagatcc tactgctatg aggcatcaat atcagacatg gcttcggaca gccgctgccc 1201 aacacaaggt gaagcctacc ttgacaagca atcagacact caatatgtct gcaaaagaac 1261 gttggtggac agaggctggg gaaatggatg tggacttttt ggcaaaggga gcctggtgac 1321 atgcgctaag tttgcatgct ccaagaaaat gaccgggaag agcatccagc cagagaatct 1381 ggagtaccgg ataatgctgt cagttcatgg ctcccagcac agtgggatga tcgttaatga 1441 cacaggacat gaaactgatg agaatagagc gaaggttgag ataacgccca attcaccaag 1501 agccgaagcc accctggggg gttttggaag cctaggactt gattgtgaac cgaggacagg 1561 ccttgacttt tcagatttgt attacttgac tatgaataac aagcattggt tggttcacaa 1621 ggagtggttc cacgacattc cattaccttg gcacgctggg gcagacaccg gaactccaca 1681 ctggaacaac aaagaagcac tggtagagtt caaggacgca catgccaaaa ggcaaactgt 1741 cgtggttcta gggagtcaag aaggagcagt tcacacggcc cttgctggag ctctggaggc 1801 tgagatggat ggtgcaaagg gaaggctgtc ctctggccac ttgaaatgtc gcctgaaaat 1861 ggataaactt agattgaagg gcgtgtcata ctccttgtgt accgcagcgt tcacattcac 1921 caagatcccg gctgaaacac tgcacgggac agtcacagtg gaggtacagt acgcaggggc 1981 agatggaccc tgcaaggttc cagctcagat ggcggtggac atgcaaactc tgaccccagt 2041 tgggaggttg ataaccgcca accccgtaat cactgaaagc actgagaact ctaagatgat 2101 gctggaactt gatccaccat ttggggactc ttacattgtc ataggagtcg gggagaagaa 2161 gatcacccac cactggcaca ggagtggcag caccattgga aaagcatttg aagccactgt 2221 gagaggtgcc aagagaatgg cagtcttggg agacacagcc tgggactttg gatcagttgg 2281 aggcgctctc aactcattgg gcaagggcat ccatcaaatt tttggagcag ctttcaaatc 2341 attgtttgga ggaatgtcct ggttctcaca aatcctcatt ggaacgttgc tgatgtggtt 2401 gggtctgaac acaaagaatg gatctatttc ccttatgtgc ttggccttag ggggagtgtt 2461 gatcttctta tccacagccg tctctgctga tgtggggtgc tcggtggact tctcaaagaa 2521 ggagacgaga tgcggtacag gggtgttcgt ctataacgac gttgaagcct ggagggatag 2581 gtacaagtac catcctgact ccccccgtag attggcagca gcagtcaagc aagcctggga 2641 agatggtatc tgcgggatct cctctgtttc aagaatggag aacatcatgt ggagatcagt 2701 agaaggggag ctcaacgcaa tcctggaaga gaatggagtt caactgacgg tcgttgtggg 2761 atctgtaaaa aaccccatgt ggagaggtcc acagagattg cccgtgcctg tgaacgagct 2821 gccccacggc tggaaggctt gggggaaatc gtacttcgtc agagcagcaa agacaaataa 2881 cagctttgtc gtggatggtg acacactgaa ggaatgccca ctcaaacata gagcatggaa 2941 cagctttctt gtggaggatc atgggttcgg ggtatttcac actagtgtct ggctcaaggt 3001 tagagaagat tattcattag agtgtgatcc agccgttatt ggaacagctg ttaagggaaa 3061 ggaggctgta cacagtgatc taggctactg gattgagagt gagaagaatg acacatggag 3121 gctgaagagg gcccatctga tcgagatgaa aacatgtgaa tggccaaagt cccacacatt 3181 gtggacagat ggaatagaag agagtgatct gatcataccc aagtctttag ctgggccact 3241 cagccatcac aataccagag agggctacag gacccaaatg aaagggccat ggcacagtga 3301 agagcttgaa attcggtttg aggaatgccc aggcactaag gtccacgtgg aggaaacatg 3361 tggaacaaga ggaccatctc tgagatcaac cactgcaagc ggaagggtga tcgaggaatg 3421 gtgctgcagg gagtgcacaa tgcccccact gtcgttccgg gctaaagatg gctgttggta 3481 tggaatggag ataaggccca ggaaagaacc agaaagcaac ttagtaaggt cagtggtgac 3541 tgcaggatca actgatcaca tggatcactt ctcccttgga gtgcttgtga ttctgctcat 3601 ggtgcaggaa gggctgaaga agagaatgac cacaaagatc atcataagca catcaatggc 3661 agtgctggta gctatgatcc tgggaggatt ttcaatgagt gacctggcta agcttgcaat 3721 tttgatgggt gccaccttcg cggaaatgaa cactggagga gatgtagctc atctggcgct 3781 gatagcggca ttcaaagtca gaccagcgtt gctggtatct ttcatcttca gagctaattg 3841 gacaccccgt gaaagcatgc tgctggcctt ggcctcgtgt cttttgcaaa ctgcgatctc 3901 cgccttggaa ggcgacctga tggttctcat caatggtttt gctttggcct ggttggcaat 3961 acgagcgatg gttgttccac gcactgataa catcaccttg gcaatcctgg ctgctctgac 4021 accactggcc cggggcacac tgcttgtggc gtggagagca ggccttgcta cttgcggggg 4081 gtttatgctc ctctctctga agggaaaagg cagtgtgaag aagaacttac catttgtcat 4141 ggccctggga ctaaccgctg tgaggctggt cgaccccatc aacgtggtgg gactgctgtt 4201 gctcacaagg agtgggaagc ggagctggcc ccctagcgaa gtactcacag ctgttggcct 4261 gatatgcgca ttggctggag ggttcgccaa ggcagatata gagatggctg ggcccatggc 4321 cgcggtcggt ctgctaattg tcagttacgt ggtctcagga aagagtgtgg acatgtacat 4381 tgaaagagca ggtgacatca catgggaaaa agatgcggaa gtcactggaa acagtccccg 4441 gctcgatgtg gcgctagatg agagtggtga tttctccctg gtggaggatg acggtccccc 4501 catgagagag atcatactca aggtggtcct gatgaccatc tgtggcatga acccaatagc 4561 catacccttt gcagctggag cgtggtacgt atacgtgaag actggaaaaa ggagtggtgc 4621 tctatgggat gtgcctgctc ccaaggaagt aaaaaagggg gagaccacag atggagtgta 4681 cagagtaatg actcgtagac tgctaggttc aacacaagtt ggagtgggag ttatgcaaga 4741 gggggtcttt cacactatgt ggcacgtcac aaaaggatcc gcgctgagaa gcggtgaagg 4801 gagacttgat ccatactggg gagatgtcaa gcaggatctg gtgtcatact gtggtccatg 4861 gaagctagat gccgcctggg acgggcacag cgaggtgcag ctcttggccg tgccccccgg 4921 agagagagcg aggaacatcc agactctgcc cggaatattt aagacaaagg atggggacat 4981 tggagcggtt gcgctggatt acccagcagg aacttcagga tctccaatcc tagacaagtg 5041 tgggagagtg ataggacttt atggcaatgg ggtcgtgatc aaaaatggga gttatgttag 5101 tgccatcacc caagggagga gggaggaaga gactcctgtt gagtgcttcg agccttcgat 5161 gctgaagaag aagcagctaa ctgtcttaga cttgcatcct ggagccggga aaaccaggag 5221 agttcttcct gaaatagtcc gtgaagccat aaaaacaaga ctccgtactg tgatcttagc 5281 tccaaccagg gttgtcgctg ctgaaatgga ggaagccctt agagggcttc cagtgcgtta 5341 tatgacaaca gcagtcaatg tcacccactc tggaacagaa atcgtcgact taatgtgcca 5401 tgccaccttc acttcacgtc tactacagcc aatcagagtc cccaactata atctgtatat 5461 tatggatgag gcccacttca cagatccctc aagcatagca gcaagaggat acatttcaac 5521 aagggttgag atgggcgagg cggctgccat cttcatgacc gccacgccac caggaacccg 5581 tgacgcattt ccggactcca actcaccaat tatggacacc gaagtggaag tcccagagag 5641 agcctggagc tcaggctttg attgggtgac ggatcattct ggaaaaacag tttggtttgt 5701 tccaagcgtg aggaacggca atgagatcgc agcttgtctg acaaaggctg gaaaacgggt 5761 catacagctc agcagaaaga cttttgagac agagttccag aaaacaaaac atcaagagtg 5821 ggactttgtc gtgacaactg acatttcaga gatgggcgcc aactttaaag ctgaccgtgt 5881 catagattcc aggagatgcc taaagccggt catacttgat ggcgagagag tcattctggc 5941 tggacccatg cctgtcacac atgccagcgc tgcccagagg agggggcgca taggcaggaa 6001 tcccaacaaa cctggagatg agtatctgta tggaggtggg tgcgcagaga ctgatgaaga 6061 ccatgcacac tggcttgaag caagaatgct ccttgacaat atttacctcc aagatggcct 6121 catagcctcg ctctatcgac ctgaggccga caaagtagca gccattgagg gagagttcaa 6181 gcttaggacg gagcaaagga agacctttgt ggaactcatg aaaagaggag atcttcctgt 6241 ttggctggcc tatcaggttg catctgccgg aataacctac acagatagaa gatggtgctt 6301 tgatggcacg accaacaaca ccataatgga agacagtgtg ccggcagagg tgtggaccag 6361 acacggagag aaaagagtgc tcaaaccgag gtggatggac gccagagttt gttcagatca 6421 tgcggccctg aagtcattca aggagtttgc cgctgggaaa agaggagcga cttttggagt 6481 gatggaagcc ctgggaacac tgccaggaca catgacagag agattccagg aagccattga 6541 caacctcgct gtgctcatgc gggcagagac tggaagcagg ccttacaaag ccgcggcggc 6601 ccaattgccg gagaccttag agaccattat gcttttggga ttgctgggaa cagtctcgtt 6661 gggaatcttt ttcgtcttga tgaggaacaa gggcataggg aagatgggct ttggaatggt 6721 gactcttggg gccagcgcat ggctcatgtg gctctcggaa attgagccag ccagaattgc 6781 atgtgtcctc attgttgtgt tcctattgct ggtggtgctc atacctgagc cagaaaagca 6841 aagatctccc caggacaacc aaatggcaat catcatcatg gtagcagtag gtcttctggg 6901 cttgattacc gccaatgaac tcggatggtt ggagagaaca aagagtgacc taagccatct 6961 aatgggaagg agagaggagg gagcaaccat aggattctca atggacattg acctgcggcc 7021 agcctcagct tgggccatct atgctgcctt gacaactttc attactccag ccgtccaaca 7081 tgcagtgacc acttcataca acaactactc cttaatggcg atggccacgc aagctggagt 7141 gttgtttggt atgggcaaag ggatgccatt ctacgcatgg gactttggag tcccgctgct 7201 aatgataggt tgctactcac aattaacacc cctgacccta atagtggcca tcattttgct 7261 cgtggcgcac tacatgtact tgatcccagg gctgcaggca gcagctgcgc gtgctgccca 7321 gaagagaacg gcagctggca tcatgaagaa ccctgttgtg gatggaatag tggtgactga 7381 cattgacaca atgacaattg acccccaagt ggagaaaaag atgggacagg tgctactcat 7441 agcagtagcc gtctccagcg ccatactgtc gcggaccgcc tgggggtggg gggaggctgg 7501 ggccctgatc acagccgcaa cttccacttt gtgggaaggc tctccgaaca agtactggaa 7561 ctcctctaca gccacttcac tgtgtaacat ttttagggga agttacttgg ctggagcttc 7621 tctaatctac acagtaacaa gaaacgctgg cttggtcaag agacgtgggg gtggaacagg 7681 agagaccctg ggagagaaat ggaaggcccg cttgaaccag atgtcggccc tggagttcta 7741 ctcctacaaa aagtcaggca tcaccgaggt gtgcagagaa gaggcccgcc gcgccctcaa 7801 ggacggtgtg gcaacgggag gccatgctgt gtcccgagga agtgcaaagc tgagatggtt 7861 agtggagcgg ggatacctgc agccctatgg aaaggtcatt gatcttggat gtggcagagg 7921 gggctggagt tactacgccg ccaccatccg caaagttcaa gaagtgaaag gatacacaaa 7981 aggaggccct ggtcatgaag aacccgtgtt ggtgcaaagc tatgggtgga acatagtccg 8041 tcttaagagt ggggtggacg tctttcatat ggcggctgag ccgtgtgaca cgttgctgtg 8101 tgacataggt gagtcatcat ctagtcctga agtggaagaa gcacggacgc tcagagtcct 8161 ctccatggcg ggggattggc ttgaaaaaag accaggagcc ttttgtataa aagtgttgtg 8221 cccatacacc agcaccatga tggaaaccct ggagcgactg cagcgtaggt atgggggagg 8281 actggtcaga gtgccactct cccgcaactc tacacatgag atgtactggg tctctggagc 8341 gaaaagcaac accataaaaa gtgtgtccac cacgagccag ctcctcttgg ggcgcatgga 8401 cgggcctagg aggccagtga aatatgagga ggatgtgaat ctcggctctg gcacgcgggc 8461 tgtggtaagc tgcgctgaag ctcccaacat gaagatcatt ggtaaccgca ttgaaaggat 8521 ccgcagtgag cacgcggaaa cgtggttctt tgacgagaac cacccatata ggacatgggc 8581 ttaccatgga agctatgagg cccccacaca agggtcagcg tcctctctaa taaacggggt 8641 tgtcaggctc ctgtcaaaac cctgggatgt ggtgactgga gtcacaggaa tagccatgac 8701 cgacaccaca ccgtatggtc agcaaagagt tttcaaggaa aaagtggaca ctagggtgcc 8761 agacccccaa gaaggcactc gtcaggttat gagcatggtc tcttcctggt tgtggaaaga 8821 gctaggcaaa cacaaacggc cacgagtctg taccaaagaa gagttcatca acaaggttcg 8881 tagcaatgca gcattagggg caatatttga agaggaaaaa gagtggaaga ctgcagtgga 8941 agctgtgaac gatccaaggt tctgggctct agtggacaag gaaagagagc accacctgag 9001 aggagagtgc cagagttgtg tgtacaacat gatgggaaaa agagaaaaga aacaagggga 9061 atttggaaag gccaagggca gccgcgccat ctggtatatg tggctagggg ctagatttct 9121 agagttcgaa gcccttggat tcttgaacga ggatcactgg atggggagag agaactcagg 9181 aggtggtgtt gaagggctgg gattacaaag actcggatat gtcctagaag agatgagtcg 9241 cataccagga ggaaggatgt atgcagatga cactgctggc tgggacaccc gcatcagcag 9301 gtttgatctg gagaatgaag ctctaatcac caaccaaatg gagaaagggc acagggcctt 9361 ggcattggcc ataatcaagt acacatacca aaacaaagtg gtaaaggtcc ttagaccagc 9421 tgaaaaaggg aaaacagtta tggacattat ttcgagacaa gaccaaaggg ggagcggaca 9481 agttgtcact tacgctctta acacatttac caatctagtg gtgcaactca ttcggaatat 9541 ggaggctgag gaagttctag agatgcaaga cttgtggctg ctgcggaggt cagagaaagt 9601 gaccaactgg ttgcagagca acggatggga taggctcaaa cgaatggcag tcagtggaga 9661 tgattgcgtt gtgaagccaa ttgatgatag gtttgcacat gccctcaggt tcttgaatga 9721 tatgggaaaa gttaggaagg acacacaaga gtggaaaccc tcaactggat gggacaactg 9781 ggaagaagtt ccgttttgct cccaccactt caacaagctc catctcaagg acgggaggtc 9841 cattgtggtt ccctgccgcc accaagatga actgattggc cgggcccgcg tctctccagg 9901 ggcgggatgg agcatccggg agactgcttg cctagcaaaa tcatatgcgc aaatgtggca 9961 gctcctttat ttccacagaa gggacctccg actgatggcc aatgccattt gttcatctgt 10021 gccagttgac tgggttccaa ctgggagaac tacctggtca atccatggaa agggagaatg 10081 gatgaccact gaagacatgc ttgtggtgtg gaacagagtg tggattgagg agaacgacca 10141 catggaagac aagaccccag ttacgaaatg gacagacatt ccctatttgg gaaaaaggga 10201 agacttgtgg tgtggatctc tcatagggca cagaccgcgc accacctggg ctgagaacat 10261 taaaaacaca gtcaacatgg tgcgcaggat cataggtgat gaagaaaagt acatggacta 10321 cctatccacc caagttcgct acttgggtga agaagggtct acacctggag tgctgtaagc 10381 accaatctta atgttgtcag gcctgctagt cagccacagc ttggggaaag ctgtgcagcc 10441 tgtgaccccc ccaggagaag ctgggaaacc aagcctatag tcaggccgag aacgccatgg 10501 cacggaagaa gccatgctgc ctgtgagccc ctcagaggac actgagtcaa aaaaccccac 10561 gcgcttggag gcgcaggatg ggaaaagaag gtggcgacct tccccaccct tcaatctggg 10621 gcctgaactg gagatcagct gtggatctcc agaagaggga ctagtggtta gaggagaccc 10681 cccggaaaac gcaaaacagc atattgacgc tgggaaagac cagagactcc atgagtttcc 10741 accacgctgg ccgccaggca cagatcgccg aatagcggcg gccggtgtgg ggaaatccat 10801 gggcc Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Sequences producing significant alignments:Select:AllNone Selected:0AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignmentsSequences producing significant alignments:Select for downloading or viewing reportsDescriptionMax scoreTotal scoreQuery coverE valueIdentAccessionSelect seq gb|KU509998.1|Zika virus strain Haiti/1225/2014, complete genome1838118381100%0.099%KU509998.1Select seq gb|KJ776791.1|Zika virus strain H/PF/2013 polyprotein gene, complete cds1837518375100%0.099%KJ776791.1Select seq gb|KU527068.1|Zika virus strain Natal RGN, complete genome1836618366100%0.099%KU527068.1Select seq gb|KU321639.1|Zika virus strain ZikaSPH2015, complete genome1836618366100%0.099%KU321639.1Select seq gb|KU729217.2|Zika virus isolate BeH823339 polyprotein gene, complete cds1835718357100%0.099%KU729217.2Select seq gb|KU729218.1|Zika virus isolate BeH828305 polyprotein gene, complete cds1835718357100%0.099%KU729218.1Select seq gb|KU707826.1|Zika virus isolate SSABR1, complete genome1835718357100%0.099%KU707826.1Select seq gb|KU365779.1|Zika virus strain BeH819966 polyprotein gene, complete cds1835718357100%0.099%KU365779.1Select seq gb|KU853013.1|Zika virus isolate Dominican Republic/2016/PD2, complete genome1834518345100%0.099%KU853013.1Select seq gb|KU501217.1|Zika virus strain 8375 polyprotein gene, complete cds1834518345100%0.099%KU501217.1Select seq gb|KU365780.1|Zika virus strain BeH815744 polyprotein gene, complete cds1834518345100%0.099%KU365780.1Select seq gb|KU853012.1|Zika virus isolate Dominican Republic/2016/PD1, complete genome1834318343100%0.099%KU853012.1Select seq gb|KU497555.1|Zika virus isolate Brazil-ZKV2015, complete genome183411834199%0.099%KU497555.1Select seq gb|KU647676.1|Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds1833918339100%0.099%KU647676.1Select seq gb|KU501216.1|Zika virus strain 103344 polyprotein gene, complete cds1833918339100%0.099%KU501216.1Select seq gb|KU365777.1|Zika virus strain BeH818995 polyprotein gene, complete cds1833918339100%0.099%KU365777.1Select seq gb|KU820897.1|Zika virus isolate FLR polyprotein gene, complete cds1833618336100%0.099%KU820897.1Select seq gb|KU365778.1|Zika virus strain BeH819015 polyprotein gene, complete cds1832718327100%0.099%KU365778.1Select seq gb|KU312312.1|Zika virus isolate Z1106033 polyprotein gene, complete cds1832718327100%0.099%KU312312.1Select seq gb|KU922960.1|Zika virus isolate MEX/InDRE/Sm/2016, complete genome1832118321100%0.099%KU922960.1Select seq gb|KU922923.1|Zika virus isolate MEX/InDRE/Lm/2016, complete genome1831818318100%0.099%KU922923.1Select seq gb|KU501215.1|Zika virus strain PRVABC59, complete genome1831818318100%0.099%KU501215.1Select seq gb|KU820898.1|Zika virus isolate GZ01 polyprotein gene, complete cds1830018300100%0.099%KU820898.1Select seq gb|KU740184.2|Zika virus isolate GD01 polyprotein gene, complete cds1829118291100%0.099%KU740184.2Select seq gb|KU761564.1|Zika virus isolate GDZ16001 polyprotein gene, complete cds1829118291100%0.099%KU761564.1Select seq gb|KU820899.2|Zika virus isolate ZJ03, complete genome1827318273100%0.099%KU820899.2Select seq gb|KU866423.1|Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds1816418164100%0.099%KU866423.1Select seq gb|KU744693.1|Zika virus isolate VE_Ganxian, complete genome1813218132100%0.099%KU744693.1Select seq gb|KU681081.3|Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome1804218042100%0.099%KU681081.3Select seq gb|JN860885.1|Zika virus isolate FSS13025 polyprotein gene, partial cds177351773599%0.098%JN860885.1Select seq gb|KF993678.1|Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds176881768898%0.099%KF993678.1Select seq gb|EU545988.1|Zika virus polyprotein gene, complete cds1759817598100%0.098%EU545988.1Select seq gb|KU681082.3|Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome1743417434100%0.098%KU681082.3Select seq gb|HQ234499.1|Zika virus isolate P6-740 polyprotein gene, partial cds164511645199%0.096%HQ234499.1Select seq gb|KF383115.1|Zika virus strain ArB1362 polyprotein gene, complete cds1329313293100%0.089%KF383115.1Select seq gb|KF268949.1|Zika virus isolate ARB15076 polyprotein gene, complete cds1328813288100%0.089%KF268949.1Select seq gb|KF268948.1|Zika virus isolate ARB13565 polyprotein gene, complete cds1328813288100%0.089%KF268948.1Select seq gb|KF268950.1|Zika virus isolate ARB7701 polyprotein gene, complete cds1328113281100%0.089%KF268950.1Select seq gb|KU720415.1|Zika virus strain MR 766 polyprotein gene, complete cds1327713277100%0.089%KU720415.1Select seq gb|HQ234498.1|Zika virus isolate MR_766 polyprotein gene, partial cds132721327299%0.089%HQ234498.1Select seq gb|DQ859059.1|Zika virus strain MR 766 polyprotein gene, complete cds1327013270100%0.089%DQ859059.1Select seq gb|KF383119.1|Zika virus strain ArD158084 polyprotein gene, complete cds1325913259100%0.089%KF383119.1Select seq dbj|LC002520.1|Zika virus genomic RNA, complete genome, strain: MR766-NIID1325413254100%0.089%LC002520.1Select seq gb|KF383116.1|Zika virus strain ArD7117 polyprotein gene, complete cds1323913239100%0.089%KF383116.1Select seq gb|HQ234501.1|Zika virus isolate ArD_41519 polyprotein gene, partial cds132321323299%0.089%HQ234501.1Select seq gb|AY632535.2|Zika virus strain MR 766, complete genome1319613196100%0.089%AY632535.2Select seq gb|HQ234500.1|Zika virus isolate IbH_30656 polyprotein gene, partial cds131471314799%0.088%HQ234500.1Select seq gb|KF383117.1|Zika virus strain ArD128000 polyprotein gene, complete cds1313313133100%0.088%KF383117.1Select seq gb|KF383118.1|Zika virus strain ArD157995 polyprotein gene, complete cds1293613004100%0.088%KF383118.1Select seq gb|KF383121.1|Zika virus strain ArD158095 polyprotein gene, partial cds128551285597%0.089%KF383121.1Select seq gb|KF383120.1|Zika virus strain ArD142623 nonfunctional polyprotein gene, partial sequence108441084497%0.084%KF383120.1Select seq gb|KU312314.1|Zika virus isolate Z1106031 polyprotein gene, partial cds4958495827%0.099%KU312314.1Select seq gb|KU312313.1|Zika virus isolate Z1106032 polyprotein gene, partial cds4931493127%0.099%KU312313.1Select seq gb|KU646828.1|Zika virus isolate Si322 polyprotein gene, partial cds4632463225%0.099%KU646828.1Select seq gb|KU646827.1|Zika virus isolate Si323 polyprotein gene, partial cds4623462325%0.099%KU646827.1Select seq gb|KU312315.1|Zika virus isolate Z1106027 polyprotein gene, partial cds3416341618%0.099%KU312315.1Select seq gb|KU740199.1|Zika virus isolate VE_Ganxian2016 polyprotein gene, partial cds3214321417%0.099%KU740199.1Select seq gb|DQ859064.1|Spondweni virus strain SM-6 V-1 polyprotein gene, complete cds2863419595%0.071%DQ859064.1Select seq gb|KJ634273.1|Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds2677267714%0.099%KJ634273.1Select seq gb|KU686218.1|Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds2051205111%0.099%KU686218.1Select seq gb|KU179098.1|Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds2021202111%0.099%KU179098.1Select seq gb|KM078936.1|Zika virus strain CHI1410214 NS5 protein gene, partial cds175217529%0.099%KM078936.1Select seq gb|KM078961.1|Zika virus strain CHI2612114 NS5 protein gene, partial cds174817489%0.099%KM078961.1Select seq gb|KM078930.1|Zika virus strain CHI2283714 NS5 protein gene, partial cds174617469%0.099%KM078930.1Select seq gb|KM078971.1|Zika virus strain CHI2613014 NS5 protein gene, partial cds174517459%0.099%KM078971.1Select seq gb|KM078970.1|Zika virus strain CHI2490414 NS5 protein gene, partial cds174517459%0.099%KM078970.1Select seq gb|KM078933.1|Zika virus strain CHI1058514 NS5 protein gene, partial cds174517459%0.099%KM078933.1Select seq gb|KM078929.1|Zika virus strain CHI1805214 NS5 protein gene, partial cds174317439%0.099%KM078929.1Select seq gb|KJ873160.1|Zika virus isolate NC14-03042014-3481 nonstructural protein 5 gene, partial cds160216028%0.099%KJ873160.1Select seq gb|KJ873161.1|Zika virus isolate NC14-02042014-3220 nonstructural protein 5 gene, partial cds142014207%0.099%KJ873161.1Select seq gb|KM851039.1|Zika virus strain SV0127/14 nonstructural protein 5 gene, partial cds138213827%0.099%KM851039.1Select seq gb|KU556802.1|Zika virus isolate MEX/InDRE/14/2015 NS5 protein gene, partial cds134613467%0.099%KU556802.1Select seq gb|KM851038.1|Zika virus strain CPC-0740 nonstructural protein 5 gene, partial cds134613467%0.098%KM851038.1Select seq gb|AF013415.1|Zika virus strain MR-766 NS5 protein (NS5) gene, partial cds1306130610%0.088%AF013415.1Select seq gb|KT200609.1|Zika virus isolate BR/949/15 NS5 gene, partial cds124512456%0.099%KT200609.1Select seq gb|KU232300.1|Zika virus isolate 067ZV_PEBR15 NS5 protein gene, partial cds124012406%0.099%KU232300.1Select seq gb|KU232290.1|Zika virus isolate 036ZV_PEBR15 NS5 protein gene, partial cds123112316%0.099%KU232290.1Select seq gb|KU232297.1|Zika virus isolate 049ZV_PEBR15 NS5 protein gene, partial cds122912296%0.099%KU232297.1Select seq gb|KU232294.1|Zika virus isolate 061ZV_PEBR15 NS5 protein gene, partial cds122012206%0.099%KU232294.1Select seq gb|KU232292.1|Zika virus isolate 054ZV_PEBR15 NS5 protein gene, partial cds121812186%0.099%KU232292.1Select seq gb|KU232298.1|Zika virus isolate 050ZV_PEBR15 NS5 protein gene, partial cds121412146%0.099%KU232298.1Select seq gb|KU232296.1|Zika virus isolate 045ZV_PEBR15 NS5 protein gene, partial cds121112116%0.099%KU232296.1Select seq gb|KU232293.1|Zika virus isolate 057ZV_PEBR15 NS5 protein gene, partial cds121112116%0.099%KU232293.1Select seq gb|KU232295.1|Zika virus isolate 068ZV_PEBR15 NS5 protein gene, partial cds120512056%0.099%KU232295.1Select seq gb|KU232288.1|Zika virus isolate 001ZV_PEBR15 NS5 protein gene, partial cds119511956%0.099%KU232288.1Select seq gb|KU232289.1|Zika virus isolate 020ZV_PEBR15 NS5 protein gene, partial cds119111916%0.099%KU232289.1Select seq gb|KU232299.1|Zika virus isolate 015ZV_PEBR15 NS5 protein gene, partial cds118711876%0.099%KU232299.1Select seq gb|KU232291.1|Zika virus isolate 051ZV_PEBR15 NS5 protein gene, partial cds118611866%0.099%KU232291.1Select seq gb|KU758878.1|Zika virus polyprotein gene, partial cds113311336%0.099%KU758878.1Select seq gb|KF270886.1|Zika virus strain CCB-870 envelope glycoprotein gene, partial cds108610868%0.089%KF270886.1Select seq gb|KU867812.1|Zika virus isolate Jiangxi.CHN/01/2016 nonstructural protein 5 gene, partial cds101810185%0.0100%KU867812.1 Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Sequence maphttps://www.google.com/maps/d/u/0/edit?mid=zv94AJqgUct4.kI8kcFySb4J0&hl=en Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 Link to comment Share on other sites More sharing options...
niman Posted March 24, 2016 Author Report Share Posted March 24, 2016 S1 Table Clinical symptomsPatient1234Onset date01/11/1601/24/1601/22/1601/31/16Days after symptoms onset *3251Days after rash onset *<1**111Rash duration5 days6 days2 days2 daysRash typeMacularMacular and maculo-papularMaculo-papularMaculo-papularLow grade fever(duration)-+ (2 days)+ (4 days)-Headache--+-Retro-orbital pain--+-Photophobia--NI-Fatigue/ malaise-++-Myalgia-++-Arthralgia(region)+ (wrist and elbows)-+ (large and small joints)-Arthritis----Anorexia--+-Nausea/ vomiting--+-Diarrhea----Abdominal pain----Dysuria----Bleeding/ petechia----Dizziness/ light headedness----Pruritus+-++Paresthesias+---Conjunctivitis----Edema(local/site)+ (hands)---Lymphadenopathy(local/ site)----EnanthemNI-NI-Respiratory symptoms----Jaundice----Seizures----* Regarding the date of sample collection; **the collection date was in the first day of rash manifestation S2 TableClinical symptomsPatient56789Onset date01/26/1601/26/1601/31/1601/31/1601/28/16Days after sypmtons onset *23125Days after rash onset *2<1122Rash duration 20 days 4 days5 days6 days3 daysRash typeMacularMaculo-papularMaculo-papularMacular and maculo-papularMaculo-papularLow grade fever(duration)-+ (1 day)-+ (2 days)-Headache+--++Retro-orbital pain+--++Photophobia+---+Fatigue/ malaise++-+-Myalgia++--+Arthralgia(region)-+ (wrists, ankles, knees, hands)-+ (large and small joints)-Arthritis-----Anorexia++---Nausea/ vomiting+----Diarrhea+----Abdominal pain-+---Dysuria-----Bleeding/ petechia ----Dizziness/ light headedness+----Pruritus+++++Paresthesias++---Conjunctivitis++--+Edema+ (feet and hands) +(hands)-+-Lymphadenopathy(local/ site)+(Cervical and auricular)---+(cervical)Enanthem-----Respiratory symptoms +--+-Jaundice-----Seizures-----* Regarding the date of sample collection; **the collection date was in the first day of rash manifestation S3 Table Social-demographic dataPatient1234GenderfemalefemalemalefemaleAge36302442Gestational age (weeks)1833NA21Family members illness--+-Partner illness--NI-Repellent spray use++NI+Previous DENV infection+-NI-Domicile in Rio de Janeiro StateDuque de CaxiasNova IguaçuRio de JaneiroDuque de CaxiasNA – not applicable; NI- not informed S4 Table Social demographic dataPatient56789Gender femalemalefemalefemalefemaleAge3068202722Gestational age (weeks)NANA172120Family members illness-+---Partner illness-----Repellent spray use+-+++Previous DENV infection++-+-Domicile in Rio de Janeiro StateRio de JaneiroRio de JaneiroRio de JaneiroDuque de CaxiasRio de JaneiroNA – not applicable; NI- not informed Link to comment Share on other sites More sharing options...
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