Partial Zika Sequence From Rio de Janeiro Brazil CSF

[niman]

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

 

[niman]

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  JOURNAL   Unpublished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"

[niman]

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

[niman]

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

[niman]

Sequence map updated

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

 

[niman]

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

[Christian Olsen]

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

[niman]

The entire fragment was used (238 BP)

Edited August 2, 2016 by niman

[Christian Olsen]

Check. Thanks!