Oswaldo Cruz Institute released a partial sequence from cerebral spinal fluid of Rio de Janeiro case, Zika1697_BR-RJ/2015, collected in mid-2015.

http://www.ncbi.nlm.nih.gov/nuccore/KT381874

 

LOCUS       KT381874                 238 bp    RNA     linear   VRL 14-FEB-2016
DEFINITION  Zika virus strain Zika1697_BR-RJ/2015 envelope protein gene,
            partial cds.
ACCESSION   KT381874
VERSION     KT381874.1  GI:987919162
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 238)
  AUTHORS   Sequeira,P.C., Mendonca,M.C.L., Brasil,P., Calvet,G., Alves,S.S.,
            Fabri,A.A., Araujo,E.S.M., Santos,F.B.D., Nogueira,R.M.R. and
            Filippis,A.M.B.
  TITLE     Detection of Zika RNA in cerebrospinal fluid (CSF) from a patient
            with neurological manifestations during Zika outbreak in Rio de
            Janeiro, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 238)
  AUTHORS   Sequeira,P.C., Mendonca,M.C.L., Brasil,P., Calvet,G., Alves,S.S.,
            Fabri,A.A., Araujo,E.S.M., Santos,F.B.D., Nogueira,R.M.R. and
            Filippis,A.M.B.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-AUG-2015) Oswaldo Cruz Institute, Oswaldo Cruz
            Foundation, Av. Brasil, 4365 - Pavilhao Helio e Peggy Pereira,
            B103, Rio de Janeiro, RJ 21045-900, Brazil
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..238
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Zika1697_BR-RJ/2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="2015"
                     /note="genotype: Asian"

LOCUS       KT381874                 238 bp    RNA     linear   VRL 14-FEB-2016
DEFINITION  Zika virus strain Zika1697_BR-RJ/2015 envelope protein gene,
            partial cds.
ACCESSION   KT381874
VERSION     KT381874.1  GI:987919162
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 238)
  AUTHORS   Sequeira,P.C., Mendonca,M.C.L., Brasil,P., Calvet,G., Alves,S.S.,
            Fabri,A.A., Araujo,E.S.M., Santos,F.B.D., Nogueira,R.M.R. and
            Filippis,A.M.B.
  TITLE     Detection of Zika RNA in cerebrospinal fluid (CSF) from a patient
            with neurological manifestations during Zika outbreak in Rio de
            Janeiro, Brazil
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 238)
  AUTHORS   Sequeira,P.C., Mendonca,M.C.L., Brasil,P., Calvet,G., Alves,S.S.,
            Fabri,A.A., Araujo,E.S.M., Santos,F.B.D., Nogueira,R.M.R. and
            Filippis,A.M.B.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-AUG-2015) Oswaldo Cruz Institute, Oswaldo Cruz
            Foundation, Av. Brasil, 4365 - Pavilhao Helio e Peggy Pereira,
            B103, Rio de Janeiro, RJ 21045-900, Brazil
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..238
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Zika1697_BR-RJ/2015"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil"
                     /collection_date="2015"
                     /note="genotype: Asian"
     CDS             <1..>238
                     /codon_start=2
                     /product="envelope protein"
                     /protein_id="AME17706.1"
                     /db_xref="GI:987919163"
                     /translation="CIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELV
                     TTTVSNMAEVRSYCYEVSISDMASDSRCPTQGEAY"
ORIGIN      
        1 gtgcatagga gtcagcaata gggactttgt ggaaggtatg tcaggtggga cttgggttga
       61 tgttgtcttg gaacatggag gttgtgtcac cgtaatggca caggacaaac cgactgtcga
      121 catagagctg gttacaacaa cagtcagcaa catggcggag gtaagatcct actgctatga
      181 ggtctccata tcagacatgg cttcggacag ccgctgccca acacaaggtg aagcctac

Sequences producing significant alignments:

Select:AllNone Selected:0

AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments

Sequences producing significant alignments:

Select for downloading or viewing reports	Description	Max score	Total score	Query cover	E value	Ident	Accession
Select seq gb|KT381874.1|	Zika virus strain Zika1697_BR-RJ/2015 envelope protein gene, partial cds	440	440	100%	5e-120	100%	KT381874.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU729218.1
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU761564.1
Select seq gb|KU740184.1|	Zika virus isolate GD01 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU740184.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	424	424	100%	5e-115	99%	KU527068.1
Select seq gb|KU646828.1|	Zika virus isolate Si322 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU646828.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU647676.1
Select seq gb|KU509998.1|	Zika virus strain Haiti/1225/2014, complete genome	424	424	100%	5e-115	99%	KU509998.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU365778.1
Select seq gb|KU312315.1|	Zika virus isolate Z1106027 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312315.1
Select seq gb|KU312314.1|	Zika virus isolate Z1106031 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312314.1
Select seq gb|KU312313.1|	Zika virus isolate Z1106032 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312313.1
Select seq gb|KM212966.1|	Zika virus isolate NC13(FP)-26112013-22072 glycoprotein gene, partial cds	424	424	100%	5e-115	99%	KM212966.1
Select seq gb|KJ579441.1|	Zika virus isolate PF13-CP221013c polyprotein gene, partial cds	424	424	100%	5e-115	99%	KJ579441.1
Select seq dbj|AB908162.1|	Zika virus gene for polyprotein, partial cds, strain: ZIKV Hu/Tahiti/01u/2014NIID	424	424	100%	5e-115	99%	AB908162.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	418	418	100%	2e-113	98%	KU744693.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	418	418	100%	2e-113	98%	KU497555.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	418	418	100%	2e-113	98%	KU707826.1
Select seq gb|KU646827.1|	Zika virus isolate Si323 polyprotein gene, partial cds	418	418	100%	2e-113	98%	KU646827.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU501216.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	418	418	100%	2e-113	98%	KU501215.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365780.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365779.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365777.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU312312.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	418	418	100%	2e-113	98%	KU321639.1
Select seq gb|KM212965.1|	Zika virus isolate NC13(FP)-20112013-22015 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212965.1
Select seq gb|KM212964.1|	Zika virus isolate NC14-17042014-4554 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212964.1
Select seq gb|KM212963.1|	Zika virus isolate NC14-23012014-250 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212963.1
Select seq gb|KJ634273.1|	Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds	418	418	100%	2e-113	98%	KJ634273.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KJ776791.1
Select seq gb|KJ680134.1|	Zika virus strain PF13-091213-121 polyprotein gene, partial cds	418	418	100%	2e-113	98%	KJ680134.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	412	412	100%	1e-111	98%	KU681081.3
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	412	412	100%	1e-111	98%	KF993678.1
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	412	412	100%	1e-111	98%	JN860885.1
Select seq gb|KU729217.1|	Zika virus isolate BeH823339 polyprotein gene, complete cds	407	407	100%	5e-110	97%	KU729217.1
Select seq gb|KU681082.3|	Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome	401	401	100%	2e-108	97%	KU681082.3
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	401	401	100%	2e-108	97%	EU545988.1
Select seq gb|KU686218.1|	Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds	392	392	95%	1e-105	98%	KU686218.1
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	351	351	100%	3e-93	93%	HQ234499.1
Select seq gb|HQ234500.1|	Zika virus isolate IbH_30656 polyprotein gene, partial cds	307	307	100%	6e-80	90%	HQ234500.1

Sequence map updated

https://www.google.com/maps/d/u/0/edit?mid=zv94AJqgUct4.kI8kcFySb4J0&hl=en

 

Sequences producing significant alignments:

Select:AllNone Selected:0

AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments

Sequences producing significant alignments:

Select for downloading or viewing reports	Description	Max score	Total score	Query cover	E value	Ident	Accession
Select seq gb|KT381874.1|	Zika virus strain Zika1697_BR-RJ/2015 envelope protein gene, partial cds	440	440	100%	5e-120	100%	KT381874.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	424	424	100%	5e-115	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	424	424	100%	5e-115	99%	KU853012.1
Select seq gb|KU844090.1|	Zika virus isolate Moscow-2016 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU844090.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU729218.1
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU761564.1
Select seq gb|KU740184.1|	Zika virus isolate GD01 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU740184.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	424	424	100%	5e-115	99%	KU527068.1
Select seq gb|KU646828.1|	Zika virus isolate Si322 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU646828.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU647676.1
Select seq gb|KU509998.1|	Zika virus strain Haiti/1225/2014, complete genome	424	424	100%	5e-115	99%	KU509998.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	424	424	100%	5e-115	99%	KU365778.1
Select seq gb|KU312315.1|	Zika virus isolate Z1106027 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312315.1
Select seq gb|KU312314.1|	Zika virus isolate Z1106031 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312314.1
Select seq gb|KU312313.1|	Zika virus isolate Z1106032 polyprotein gene, partial cds	424	424	100%	5e-115	99%	KU312313.1
Select seq gb|KM212966.1|	Zika virus isolate NC13(FP)-26112013-22072 glycoprotein gene, partial cds	424	424	100%	5e-115	99%	KM212966.1
Select seq gb|KJ579441.1|	Zika virus isolate PF13-CP221013c polyprotein gene, partial cds	424	424	100%	5e-115	99%	KJ579441.1
Select seq dbj|AB908162.1|	Zika virus gene for polyprotein, partial cds, strain: ZIKV Hu/Tahiti/01u/2014NIID	424	424	100%	5e-115	99%	AB908162.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	418	418	100%	2e-113	98%	KU820899.2
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU820897.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	418	418	100%	2e-113	98%	KU744693.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	418	418	100%	2e-113	98%	KU497555.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	418	418	100%	2e-113	98%	KU707826.1
Select seq gb|KU646827.1|	Zika virus isolate Si323 polyprotein gene, partial cds	418	418	100%	2e-113	98%	KU646827.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU501216.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	418	418	100%	2e-113	98%	KU501215.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365780.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365779.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU365777.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KU312312.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	418	418	100%	2e-113	98%	KU321639.1
Select seq gb|KM212965.1|	Zika virus isolate NC13(FP)-20112013-22015 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212965.1
Select seq gb|KM212964.1|	Zika virus isolate NC14-17042014-4554 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212964.1
Select seq gb|KM212963.1|	Zika virus isolate NC14-23012014-250 glycoprotein gene, partial cds	418	418	100%	2e-113	98%	KM212963.1
Select seq gb|KJ634273.1|	Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds	418	418	100%	2e-113	98%	KJ634273.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	418	418	100%	2e-113	98%	KJ776791.1
Select seq gb|KJ680134.1|	Zika virus strain PF13-091213-121 polyprotein gene, partial cds	418	418	100%	2e-113	98%	KJ680134.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	412	412	100%	1e-111	98%	KU681081.3
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	412	412	100%	1e-111	98%	KF993678.1
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	412	412	100%	1e-111	98%	JN860885.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	407	407	100%	5e-110	97%	KU729217.2
Select seq gb|KU681082.3|	Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome	401	401	100%	2e-108	97%	KU681082.3
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	401	401	100%	2e-108	97%	EU545988.1
Select seq gb|KU686218.1|	Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds	392	392	95%	2e-105	98%	KU686218.1
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	351	351	100%	3e-93	93%	HQ234499.1

Would you please share the alignment parameters that you used for this?

The entire fragment was used (238 BP)

Edited August 2, 201610 yr by niman

Check. Thanks!