niman Posted April 17, 2016 Report Share Posted April 17, 2016 University of Florida has released a partial Zika 2014 envelope sequence A/Haiti/1227/2014 which is distinct from other 2014 envelope sequences from Haiti. This sequence shares a polymorphisms with two sequences from Mexico and one from Martinique,suggesting Haiti seeded Zika into multiple countries in the Americas,including Brazil.All four Haiti sequences (three from 2014 and 1 from 2016) have an identical NS5 sequence.which has not been reported in any sequence from Brazil. Link to comment Share on other sites More sharing options...
niman Posted April 17, 2016 Author Report Share Posted April 17, 2016 LOCUS KX062044 349 bp ss-RNA linear VRL 14-APR-2016 DEFINITION Zika virus isolate Haiti/1227/2014 envelope protein gene, partial cds. ACCESSION KX062044 VERSION KX062044.1 GI:1018266330 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 349) AUTHORS Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A., Okech,B.A. and Loeb,J.C. TITLE Envelope protein gene sequences of two different Zika virus isolates from blood drawn in 2014 from Haitian children JOURNAL Unpublished REFERENCE 2 (bases 1 to 349) AUTHORS Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A., Okech,B.A. and Loeb,J.C. TITLE Direct Submission JOURNAL Submitted (12-APR-2016) Environmental and Global Health, University of Florida - Gainesville, 1225 Center Drive, Room 4155, Gainesville, FL 32610, USA COMMENT ##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..349 /organism="Zika virus" /mol_type="genomic RNA" /isolate="Haiti/1227/2014" /isolation_source="plasma" /host="Homo sapiens" /db_xref="taxon:64320" /country="Haiti" /collection_date="15-Dec-2014" /identified_by="John Lednicky" CDS <1..>349 /codon_start=1 /product="envelope protein" /protein_id="AMY50629.1" /db_xref="GI:1018266331" /translation="EALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGR LSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKV PAQMAVDMQTLTPV" ORIGIN 1 gaagcactgg tagagttcaa ggacgcacat gccaaaaggc aaactgtcgt ggttctaggg 61 agtcaagaag gagcagttca cacggccctt gctggagctc tggaggctga gatggatggt 121 gcaaagggaa ggctgtcctc tggccacttg aaatgtcgcc tgaaaatgga taaacttaga 181 ttgaagggcg tgtcatactc cttgtgtacc gcagcgttca cattcaccaa gatcccggct 241 gaaacactgc acgggacagt cacagtggag gtacagtacg cagggacaga tggaccttgc 301 aaggttccag cccagatggc ggtggacatg caaactctga ccccagttg Link to comment Share on other sites More sharing options...
niman Posted April 17, 2016 Author Report Share Posted April 17, 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|KU922960.1|Zika virus isolate MEX/InDRE/Sm/2016, complete genome645645100%0.0100%KU922960.1Select seq gb|KU922923.1|Zika virus isolate MEX/InDRE/Lm/2016, complete genome645645100%0.0100%KU922923.1Select seq gb|KU647676.1|Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds645645100%0.0100%KU647676.1Select seq gb|KU963796.1|Zika virus isolate SZ-WIV01 polyprotein gene, complete cds640640100%8e-18099%KU963796.1Select seq gb|KU509998.2|Zika virus strain Haiti/1225/2014, complete genome640640100%8e-18099%KU509998.2Select seq gb|KU991811.1|Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds640640100%8e-18099%KU991811.1Select seq gb|KU955589.1|Zika virus isolate Z16006 polyprotein gene, complete cds640640100%8e-18099%KU955589.1Select seq gb|KU926309.1|Zika virus isolate Rio-U1, complete genome640640100%8e-18099%KU926309.1Select seq gb|KU866423.1|Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds640640100%8e-18099%KU866423.1Select seq gb|KU853013.1|Zika virus isolate Dominican Republic/2016/PD2, complete genome640640100%8e-18099%KU853013.1Select seq gb|KU853012.1|Zika virus isolate Dominican Republic/2016/PD1, complete genome640640100%8e-18099%KU853012.1Select seq gb|KU820899.2|Zika virus isolate ZJ03, complete genome640640100%8e-18099%KU820899.2Select seq gb|KU820897.1|Zika virus isolate FLR polyprotein gene, complete cds640640100%8e-18099%KU820897.1Select seq gb|KU681081.3|Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome640640100%8e-18099%KU681081.3Select seq gb|KU527068.1|Zika virus strain Natal RGN, complete genome640640100%8e-18099%KU527068.1Select seq gb|KU646828.1|Zika virus isolate Si322 polyprotein gene, partial cds640640100%8e-18099%KU646828.1Select seq gb|KU321639.1|Zika virus strain ZikaSPH2015, complete genome640640100%8e-18099%KU321639.1Select seq gb|KJ776791.1|Zika virus strain H/PF/2013 polyprotein gene, complete cds640640100%8e-18099%KJ776791.1Select seq gb|KU870645.1|Zika virus isolate FB-GWUH-2016, complete genome634634100%4e-17899%KU870645.1Select seq gb|KU729217.2|Zika virus isolate BeH823339 polyprotein gene, complete cds634634100%4e-17899%KU729217.2Select seq gb|KU729218.1|Zika virus isolate BeH828305 polyprotein gene, complete cds634634100%4e-17899%KU729218.1Select seq gb|KU497555.1|Zika virus isolate Brazil-ZKV2015, complete genome634634100%4e-17899%KU497555.1Select seq gb|KU707826.1|Zika virus isolate SSABR1, complete genome634634100%4e-17899%KU707826.1Select seq gb|KU501217.1|Zika virus strain 8375 polyprotein gene, complete cds634634100%4e-17899%KU501217.1Select seq gb|KU501216.1|Zika virus strain 103344 polyprotein gene, complete cds634634100%4e-17899%KU501216.1Select seq gb|KU501215.1|Zika virus strain PRVABC59, complete genome634634100%4e-17899%KU501215.1Select seq gb|KU365780.1|Zika virus strain BeH815744 polyprotein gene, complete cds634634100%4e-17899%KU365780.1Select seq gb|KU365779.1|Zika virus strain BeH819966 polyprotein gene, complete cds634634100%4e-17899%KU365779.1Select seq gb|KU365778.1|Zika virus strain BeH819015 polyprotein gene, complete cds634634100%4e-17899%KU365778.1Select seq gb|KU365777.1|Zika virus strain BeH818995 polyprotein gene, complete cds634634100%4e-17899%KU365777.1Select seq gb|KU312315.1|Zika virus isolate Z1106027 polyprotein gene, partial cds634634100%4e-17899%KU312315.1Select seq gb|KU312312.1|Zika virus isolate Z1106033 polyprotein gene, complete cds634634100%4e-17899%KU312312.1Select seq gb|KJ634273.1|Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds634634100%4e-17899%KJ634273.1Select seq gb|KU940228.1|Zika virus isolate Bahia07, partial genome628628100%2e-17699%KU940228.1Select seq gb|KU940224.1|Zika virus isolate Bahia09, partial genome628628100%2e-17699%KU940224.1Select seq gb|KU955593.1|Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome628628100%2e-17699%KU955593.1Select seq gb|KU955590.1|Zika virus isolate Z16019 polyprotein gene, complete cds628628100%2e-17699%KU955590.1Select seq gb|KU926310.1|Zika virus isolate Rio-S1, complete genome628628100%2e-17699%KU926310.1Select seq gb|KU820898.1|Zika virus isolate GZ01 polyprotein gene, complete cds628628100%2e-17699%KU820898.1Select seq gb|KU740184.2|Zika virus isolate GD01 polyprotein gene, complete cds628628100%2e-17699%KU740184.2Select seq gb|KU761564.1|Zika virus isolate GDZ16001 polyprotein gene, complete cds628628100%2e-17699%KU761564.1Select seq gb|KU646827.1|Zika virus isolate Si323 polyprotein gene, partial cds628628100%2e-17699%KU646827.1Select seq gb|KU312314.1|Zika virus isolate Z1106031 polyprotein gene, partial cds628628100%2e-17699%KU312314.1Select seq gb|KU312313.1|Zika virus isolate Z1106032 polyprotein gene, partial cds628628100%2e-17699%KU312313.1Select seq gb|JN860885.1|Zika virus isolate FSS13025 polyprotein gene, partial cds628628100%2e-17699%JN860885.1Select seq gb|EU545988.1|Zika virus polyprotein gene, complete cds628628100%2e-17699%EU545988.1Select seq gb|KU744693.1|Zika virus isolate VE_Ganxian, complete genome612612100%2e-17198%KU744693.1Select seq gb|KF993678.1|Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds612612100%2e-17198%KF993678.1Select seq gb|KU681082.3|Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome606606100%8e-17098%KU681082.3Select seq gb|HQ234499.1|Zika virus isolate P6-740 polyprotein gene, partial cds568568100%4e-15896%HQ234499.1Select seq gb|KR816334.1|Zika virus isolate BR/UFBA/LabViro/Ex1 envelope protein gene, partial cds56256287%2e-15699%KR816334.1Select seq gb|KR816333.1|Zika virus isolate BR/UFBA/LabViro/23 envelope protein gene, partial cds56056087%6e-15699%KR816333.1Select seq gb|KR815989.1|Zika virus isolate 15095 envelope protein gene, partial cds56056086%6e-156100%KR815989.1Select seq gb|KR816335.1|Zika virus isolate BR/UFBA/LabViro/18 envelope protein gene, partial cds55655687%8e-15599%KR816335.1Select seq gb|KU940227.1|Zika virus isolate Bahia08, partial genome53453486%4e-14899%KU940227.1 Link to comment Share on other sites More sharing options...
niman Posted April 18, 2016 Author Report Share Posted April 18, 2016 Sequence map updatehttps://www.google.com/maps/d/u/1/edit?mid=zv94AJqgUct4.kI8kcFySb4J0&hl=en Link to comment Share on other sites More sharing options...
niman Posted April 20, 2016 Author Report Share Posted April 20, 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|KX062044.1|Zika virus isolate Haiti/1227/2014 envelope protein gene, partial cds645645100%0.0100%KX062044.1Select seq gb|KU922960.1|Zika virus isolate MEX/InDRE/Sm/2016, complete genome645645100%0.0100%KU922960.1Select seq gb|KU922923.1|Zika virus isolate MEX/InDRE/Lm/2016, complete genome645645100%0.0100%KU922923.1Select seq gb|KU647676.1|Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds645645100%0.0100%KU647676.1Select seq gb|KX062045.1|Zika virus isolate Haiti/1230/2014 envelope protein gene, partial cds640640100%8e-18099%KX062045.1Select seq gb|KX051563.1|Zika virus isolate Haiti/1/2016, complete genome640640100%8e-18099%KX051563.1Select seq gb|KU509998.3|Zika virus strain Haiti/1225/2014, complete genome640640100%8e-18099%KU509998.3Select seq gb|KU963796.1|Zika virus isolate SZ-WIV01 polyprotein gene, complete cds640640100%8e-18099%KU963796.1Select seq gb|KU991811.1|Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds640640100%8e-18099%KU991811.1Select seq gb|KU955589.1|Zika virus isolate Z16006 polyprotein gene, complete cds640640100%8e-18099%KU955589.1Select seq gb|KU926309.1|Zika virus isolate Rio-U1, complete genome640640100%8e-18099%KU926309.1Select seq gb|KU866423.1|Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds640640100%8e-18099%KU866423.1Select seq gb|KU853013.1|Zika virus isolate Dominican Republic/2016/PD2, complete genome640640100%8e-18099%KU853013.1Select seq gb|KU853012.1|Zika virus isolate Dominican Republic/2016/PD1, complete genome640640100%8e-18099%KU853012.1Select seq gb|KU820899.2|Zika virus isolate ZJ03, complete genome640640100%8e-18099%KU820899.2Select seq gb|KU820897.1|Zika virus isolate FLR polyprotein gene, complete cds640640100%8e-18099%KU820897.1Select seq gb|KU681081.3|Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome640640100%8e-18099%KU681081.3Select seq gb|KU527068.1|Zika virus strain Natal RGN, complete genome640640100%8e-18099%KU527068.1Select seq gb|KU646828.1|Zika virus isolate Si322 polyprotein gene, partial cds640640100%8e-18099%KU646828.1Select seq gb|KU321639.1|Zika virus strain ZikaSPH2015, complete genome640640100%8e-18099%KU321639.1Select seq gb|KJ776791.1|Zika virus strain H/PF/2013 polyprotein gene, complete cds640640100%8e-18099%KJ776791.1Select seq gb|KU870645.1|Zika virus isolate FB-GWUH-2016, complete genome634634100%4e-17899%KU870645.1Select seq gb|KU729217.2|Zika virus isolate BeH823339 polyprotein gene, complete cds634634100%4e-17899%KU729217.2Select seq gb|KU729218.1|Zika virus isolate BeH828305 polyprotein gene, complete cds634634100%4e-17899%KU729218.1Select seq gb|KU497555.1|Zika virus isolate Brazil-ZKV2015, complete genome634634100%4e-17899%KU497555.1Select seq gb|KU707826.1|Zika virus isolate SSABR1, complete genome634634100%4e-17899%KU707826.1Select seq gb|KU501217.1|Zika virus strain 8375 polyprotein gene, complete cds634634100%4e-17899%KU501217.1Select seq gb|KU501216.1|Zika virus strain 103344 polyprotein gene, complete cds634634100%4e-17899%KU501216.1Select seq gb|KU501215.1|Zika virus strain PRVABC59, complete genome634634100%4e-17899%KU501215.1Select seq gb|KU365780.1|Zika virus strain BeH815744 polyprotein gene, complete cds634634100%4e-17899%KU365780.1Select seq gb|KU365779.1|Zika virus strain BeH819966 polyprotein gene, complete cds634634100%4e-17899%KU365779.1Select seq gb|KU365778.1|Zika virus strain BeH819015 polyprotein gene, complete cds634634100%4e-17899%KU365778.1Select seq gb|KU365777.1|Zika virus strain BeH818995 polyprotein gene, complete cds634634100%4e-17899%KU365777.1Select seq gb|KU312315.1|Zika virus isolate Z1106027 polyprotein gene, partial cds634634100%4e-17899%KU312315.1Select seq gb|KU312312.1|Zika virus isolate Z1106033 polyprotein gene, complete cds634634100%4e-17899%KU312312.1Select seq gb|KJ634273.1|Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds634634100%4e-17899%KJ634273.1Select seq gb|KX056898.1|Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds628628100%2e-17699%KX056898.1Select seq gb|KU940228.1|Zika virus isolate Bahia07, partial genome628628100%2e-17699%KU940228.1Select seq gb|KU940224.1|Zika virus isolate Bahia09, partial genome628628100%2e-17699%KU940224.1Select seq gb|KU955593.1|Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome628628100%2e-17699%KU955593.1Select seq gb|KU955590.1|Zika virus isolate Z16019 polyprotein gene, complete cds628628100%2e-17699%KU955590.1Select seq gb|KU926310.1|Zika virus isolate Rio-S1, complete genome628628100%2e-17699%KU926310.1Select seq gb|KU820898.1|Zika virus isolate GZ01 polyprotein gene, complete cds628628100%2e-17699%KU820898.1Select seq gb|KU740184.2|Zika virus isolate GD01 polyprotein gene, complete cds628628100%2e-17699%KU740184.2Select seq gb|KU761564.1|Zika virus isolate GDZ16001 polyprotein gene, complete cds628628100%2e-17699%KU761564.1Select seq gb|KU646827.1|Zika virus isolate Si323 polyprotein gene, partial cds628628100%2e-17699%KU646827.1Select seq gb|KU312314.1|Zika virus isolate Z1106031 polyprotein gene, partial cds628628100%2e-17699%KU312314.1Select seq gb|KU312313.1|Zika virus isolate Z1106032 polyprotein gene, partial cds628628100%2e-17699%KU312313.1Select seq gb|JN860885.1|Zika virus isolate FSS13025 polyprotein gene, partial cds628628100%2e-17699%JN860885.1Select seq gb|EU545988.1|Zika virus polyprotein gene, complete cds628628100%2e-17699%EU545988.1Select seq gb|KU744693.1|Zika virus isolate VE_Ganxian, complete genome612612100%2e-17198%KU744693.1Select seq gb|KF993678.1|Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds612612100%2e-17198%KF993678.1Select seq gb|KU681082.3|Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome606606100%8e-17098%KU681082.3Select seq gb|HQ234499.1|Zika virus isolate P6-740 polyprotein gene, partial cds568568100%4e-15896%HQ234499.1Select seq gb|KR816334.1|Zika virus isolate BR/UFBA/LabViro/Ex1 envelope protein gene, partial cds56256287%2e-15699%KR816334.1Select seq gb|KR816333.1|Zika virus isolate BR/UFBA/LabViro/23 envelope protein gene, partial cds56056087%6e-15699%KR816333.1Select seq gb|KR815989.1|Zika virus isolate 15095 envelope protein gene, partial cds56056086%6e-156100%KR815989.1Select seq gb|KR816335.1|Zika virus isolate BR/UFBA/LabViro/18 envelope protein gene, partial cds55655687%8e-15599%KR816335.1Select seq gb|KU940227.1|Zika virus isolate Bahia08, partial genome53453486%4e-14899%KU940227.1 Link to comment Share on other sites More sharing options...
niman Posted April 20, 2016 Author Report Share Posted April 20, 2016 Zika virus envelope protein gene, partial cds.PopSet: 1018266330GenBank FASTAGo to:Study DetailsEnvelope protein gene sequences of two different Zika virus isolates from blood drawn in 2014 from Haitian children.Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A., Okech,B.A. and Loeb,J.C. Go to:Sequences in this data setKX062045.1Zika virus isolate Haiti/1230/2014 envelope protein gene, partial cdsKX062044.1Zika virus isolate Haiti/1227/2014 envelope protein gene, partial cdshttp://www.ncbi.nlm.nih.gov/popset?DbFrom=nuccore&Cmd=Link&LinkName=nuccore_popset&IdsFromResult=1018266330 Link to comment Share on other sites More sharing options...
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