Universidad el Bosque has released a partial Zika sequence, 

ZIKCOLSC67, from Colombia pregnant case co-infected with Dengue and chikinguya (collection Feb 2016).

LOCUS       KU954085                 240 bp ss-RNA     linear   VRL 23-MAR-2016
DEFINITION  Zika virus isolate ZIKCOLSC67 polyprotein gene, partial cds.
ACCESSION   KU954085
VERSION     KU954085.1  GI:1008913385
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 240)
  AUTHORS   Calvo,E.P. and Castellanos,J.E.
  TITLE     Dengue, chikungunya and Zika co-infection in a pregnant woman from
            Colombia
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 240)
  AUTHORS   Calvo,E.P. and Castellanos,J.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2016) Universidad el Bosque, Av. Cra 9 No. 131 A
            - 02 Edificio D, Bogota, Distrito Capital de Bogota 11001000,
            Colombia
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..240
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="ZIKCOLSC67"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Colombia"
                     /collection_date="Feb-2016"
     CDS             <1..>240
                     /codon_start=2
                     /product="polyprotein"
                     /protein_id="AMR39829.1"
                     /db_xref="GI:1008913386"
                     /translation="MILLIALAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVM
                     AQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMAR"
ORIGIN      
        1 catgatactg ctgattgccc tggcatacag catcaggtgc ataggagtca gcaataggga
       61 ctttgtggaa ggtatgtcag gtgggacttg ggttgatgtt gtcttggaac atggaggttg
      121 tgtcaccgta atggcacagg acaaaccgac tgtcgacata gagctggtta caacaacagt
      181 cagcaacatg gcggaggtaa gatcctactg ctatgaggca tcaatatcag acatggctcg

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|KU954085.1|	Zika virus isolate ZIKCOLSC67 polyprotein gene, partial cds	434	434	100%	5e-118	100%	KU954085.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	430	430	99%	6e-117	100%	KU922923.1
Select seq gb|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	425	425	99%	3e-115	99%	KU870645.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	425	425	99%	3e-115	99%	KU926310.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	425	425	99%	3e-115	99%	KU922960.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU820898.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU740184.2
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	425	425	99%	3e-115	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	425	425	99%	3e-115	99%	KU853012.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU729218.1
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU761564.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	425	425	99%	3e-115	99%	KU527068.1
Select seq gb|KU686218.1|	Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds	425	425	99%	3e-115	99%	KU686218.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU647676.1
Select seq gb|KU509998.1|	Zika virus strain Haiti/1225/2014, complete genome	425	425	99%	3e-115	99%	KU509998.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	425	425	99%	3e-115	99%	KU501215.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	425	425	99%	3e-115	99%	KU365778.1
Select seq gb|KU312314.1|	Zika virus isolate Z1106031 polyprotein gene, partial cds	425	425	99%	3e-115	99%	KU312314.1
Select seq gb|KU312313.1|	Zika virus isolate Z1106032 polyprotein gene, partial cds	425	425	99%	3e-115	99%	KU312313.1
Select seq dbj|AB908162.1|	Zika virus gene for polyprotein, partial cds, strain: ZIKV Hu/Tahiti/01u/2014NIID	425	425	99%	3e-115	99%	AB908162.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU955590.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU955589.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	421	421	99%	3e-114	99%	KU926309.1
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU866423.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	421	421	99%	3e-114	99%	KU820899.2
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU820897.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	421	421	99%	3e-114	99%	KU744693.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	421	421	99%	3e-114	99%	KU497555.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	421	421	99%	3e-114	99%	KU707826.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU501216.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU365780.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU365779.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU365777.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KU312312.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	421	421	99%	3e-114	99%	KU321639.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	421	421	99%	3e-114	99%	KJ776791.1
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	416	416	99%	1e-112	99%	KU955593.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	416	416	99%	1e-112	99%	KU681081.3
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	416	416	99%	1e-112	99%	JN860885.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	412	412	99%	2e-111	98%	KU729217.2
Select seq gb|KU681082.3|	Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome	412	412	99%	2e-111	98%	KU681082.3
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	412	412	99%	2e-111	98%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	407	407	99%	7e-110	98%	EU545988.1
Select seq gb|KM212966.1|	Zika virus isolate NC13(FP)-26112013-22072 glycoprotein gene, partial cds	405	405	94%	2e-109	99%	KM212966.1
Select seq gb|KM212965.1|	Zika virus isolate NC13(FP)-20112013-22015 glycoprotein gene, partial cds	401	401	94%	3e-108	99%	KM212965.1
Select seq gb|KM212964.1|	Zika virus isolate NC14-17042014-4554 glycoprotein gene, partial cds	401	401	94%	3e-108	99%	KM212964.1
Select seq gb|KM212963.1|	Zika virus isolate NC14-23012014-250 glycoprotein gene, partial cds	401	401	94%	3e-108	99%	KM212963.1
Select seq gb|KU844090.1|	Zika virus isolate Moscow-2016 polyprotein gene, partial cds	392	392	91%	1e-105	99%	KU844090.1
Select seq gb|KU312315.1|	Zika virus isolate Z1106027 polyprotein gene, partial cds	392	392	91%	1e-105	99%	KU312315.1
Select seq gb|KJ579441.1|	Zika virus isolate PF13-CP221013c polyprotein gene, partial cds	392	392	91%	1e-105	99%	KJ579441.1
Select seq gb|KJ680134.1|	Zika virus strain PF13-091213-121 polyprotein gene, partial cds	389	389	91%	2e-104	99%	KJ680134.1
Select seq gb|KU926326.1|	Zika virus isolate Zika 2235 Israel ex Colombia 2015 polyprotein gene, partial cds	374	374	86%	4e-100	100%	KU926326.1
Select seq gb|KU926325.1|	Zika virus isolate Zika 356 Israel ex Mexico 2016 polyprotein gene, partial cds	374	374	86%	4e-100	100%	KU926325.1
Select seq gb|KU926324.1|	Zika virus isolate Zika 352 Israel ex Vietnam 2016 polyprotein gene, partial cds	374	374	86%	4e-100	100%	KU926324.1
Select seq gb|KU926323.1|	Zika virus isolate Zika 269 Israel ex Colombia 2016 polyprotein gene, partial cds	374	374	86%	4e-100	100%	KU926323.1
Select seq gb|KU646828.1|	Zika virus isolate Si322 polyprotein gene, partial cds	374	374	86%	4e-100	100%	KU646828.1
Select seq gb|KU646827.1|	Zika virus isolate Si323 polyprotein gene, partial cds	369	369	86%	2e-98	99%	KU646827.1
Select seq gb|KJ634273.1|	Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds	369	369	86%	2e-98	99%	KJ634273.1
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	358	358	99%	3e-95	93%	HQ234499.1
Select seq gb|KT381874.1|	Zika virus strain Zika1697_BR-RJ/2015 envelope protein gene, partial cds	351	351	84%	5e-93	99%	KT381874.1

Zika sequence map update

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