Haiti 2016 Zika Recombinant Signals Origin In Americas

[niman]

The recently released detail in PLOS NTD confirm that the 2014 Zika sequences in Haiti were due to local transmission.  Although the UF authors note the similarities (identity) with 31 of 51 NS5 sequences from Easter Island (collected between Mach and May,2014), the don't address the 2016 sequence (from a US resident infected in Haiti).

 

The 2016 NS5 sequence is identical to the 2014 Haiti sequences, but most of the 2016 polymorphisms match the 2016 sequences from Natal, Brazil (from the brain of the aborted fetus in Slovenia).

 

The 2016 Haiti sequence ,Haiti/1/2016,is a clear recombinant, which was created by recombination between the 2014 Haiti sequence, Haiti/1225/2014 and the 2016 sequence from Brazil via Slovenia, Natal RGN.

Edited April 25, 2016 by niman

[niman]

The first patient was a 15 year-old boy who presented to the clinic on December 12, 2014, with a history of subjective fever, headache, and generalized arthralgias, myalgias and asthenia. When seen, temperature was 37 degrees C, with a pulse of 92 and respiratory rate of 24, weight 51.5 Kg. He had no rash, and physical exam was unremarkable. The second patient was a 7 year-old girl who was seen on December 15, 2014 at the clinic for subjective nocturnal fever, abdominal pain, anorexia, and cough. Temperature was 37 degrees C, pulse 116, RR 28, and weight 22.8 Kg. There was no rash, and physical exam was again unremarkable. The third patient was an asymptomatic 4 year-old boy who came in December 17, 2014 for follow up after being treated for tonsillitis on November 25, when he had presented with a fever of 39 degrees C. In none of the cases would it have been possible to have identified the illness as a ZIKV infection based on clinical presentation, rather than DENV or CHIKV (and, as indicated, one child was simultaneously infected with DENV).

http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004687

 

[niman]

In tissue culture, viral agents from all three patients induced subtle CPE within 4–8 days post-inoculation of human (A549, HeLa, and MRC-5) and more pronounced CPE in simian (LLC-MK2 and Vero E6) cells incubated at either 33° and 37°C.

[niman]

 the recent epidemic outbreaks in South America are probably the result of a limited introduction from French Polynesia via Easter Island no more than 3–4 year ago.

[niman]

LOCUS       KU509998               10807 bp    RNA     linear   VRL 11-APR-2016
DEFINITION  Zika virus strain Haiti/1225/2014, complete genome.
ACCESSION   KU509998
VERSION     KU509998.3  GI:1016563098
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Morris,J.G. Jr., Beau De Rochars,V.M., Elbadry,M.A.,
            Okech,B.A. and Loeb,J.C.
  TITLE     Zika virus from a Haitian, December 2014
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10807)
  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 (10-JAN-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
REFERENCE   3  (bases 1 to 10807)
  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 (30-MAR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
  REMARK    Sequence update by submitter
REFERENCE   4  (bases 1 to 10807)
  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 (11-APR-2016) Environmental and Global Health, University
            of Florida - Gainesville, 1225 Center Drive, Room 4155,
            Gainesville, FL 32610, USA
  REMARK    Sequence update by submitter
COMMENT     On Apr 11, 2016 this sequence version replaced gi:1012306669.
            
            ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10807
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Haiti/1225/2014"
                     /isolation_source="plasma"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Haiti"
                     /collection_date="12-Dec-2014"

http://www.ncbi.nlm.nih.gov/nuccore/KU509998

 

[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|KU509998.3|	Zika virus strain Haiti/1225/2014, complete genome	18525	18525	100%	0.0	100%	KU509998.3
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	18502	18502	100%	0.0	99%	KU321639.1
Select seq gb|KX051563.1|	Zika virus isolate Haiti/1/2016, complete genome	18480	18480	100%	0.0	99%	KX051563.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	18447	18447	100%	0.0	99%	KJ776791.1
Select seq gb|KU991811.1|	Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds	18429	18429	100%	0.0	99%	KU991811.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	18420	18420	100%	0.0	99%	KU729218.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	18420	18420	100%	0.0	99%	KU707826.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	18420	18420	100%	0.0	99%	KU365779.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	18408	18408	100%	0.0	99%	KU926309.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	18408	18408	100%	0.0	99%	KU365780.1
Select seq gb|KU940228.1|	Zika virus isolate Bahia07, partial genome	18402	18402	100%	0.0	99%	KU940228.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	18402	18402	100%	0.0	99%	KU527068.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	18402	18402	100%	0.0	99%	KU647676.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	18402	18402	100%	0.0	99%	KU365777.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	18399	18399	100%	0.0	99%	KU501217.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	18395	18395	99%	0.0	99%	KU497555.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	18393	18393	100%	0.0	99%	KU729217.2
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	18393	18393	100%	0.0	99%	KU501216.1
Select seq gb|KX087102.1|	Zika virus strain ZIKV/Homo sapiens/COL/FLR/2015, complete genome	18390	18390	100%	0.0	99%	KX087102.1
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	18390	18390	100%	0.0	99%	KU820897.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	18390	18390	100%	0.0	99%	KU365778.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	18390	18390	100%	0.0	99%	KU312312.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	18384	18384	100%	0.0	99%	KU922960.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	18381	18381	100%	0.0	99%	KU926310.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	18381	18381	100%	0.0	99%	KU922923.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	18381	18381	100%	0.0	99%	KU501215.1
Select seq gb|KX087101.1|	Zika virus strain ZIKV/Homo sapiens/PRI/PRVABC59/2015, complete genome	18375	18375	100%	0.0	99%	KX087101.1
Select seq gb|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	18375	18375	100%	0.0	99%	KU870645.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	18372	18372	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	18370	18370	100%	0.0	99%	KU853012.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	18363	18363	100%	0.0	99%	KU820898.1
Select seq gb|KX117076.1|	Zika virus isolate Zhejiang04, complete genome	18357	18357	100%	0.0	99%	KX117076.1
Select seq gb|KX056898.1|	Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds	18357	18357	100%	0.0	99%	KX056898.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	18357	18357	100%	0.0	99%	KU955590.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	18354	18354	100%	0.0	99%	KU740184.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	18354	18354	100%	0.0	99%	KU761564.1
Select seq gb|KU963796.1|	Zika virus isolate SZ-WIV01 polyprotein gene, complete cds	18348	18348	100%	0.0	99%	KU963796.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	18345	18345	100%	0.0	99%	KU955589.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	18345	18345	100%	0.0	99%	KU820899.2
Select seq gb|KU940224.1|	Zika virus isolate Bahia09, partial genome	18309	18309	99%	0.0	99%	KU940224.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	18258	18258	100%	0.0	99%	KU744693.1
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	18236	18236	100%	0.0	99%	KU866423.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	18105	18105	100%	0.0	99%	KU681081.3
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	17798	17798	100%	0.0	98%	KU955593.1
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	17798	17798	99%	0.0	98%	JN860885.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	17751	17751	98%	0.0	99%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	17643	17643	100%	0.0	98%	EU545988.1

[niman]

LOCUS       KX059013                1024 bp    cRNA    linear   VRL 12-APR-2016
DEFINITION  Zika virus isolate Haiti/1227/2014 NS5 gene, partial cds.
ACCESSION   KX059013
VERSION     KX059013.1  GI:1016884666
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 1024)
  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..1024
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /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"

http://www.ncbi.nlm.nih.gov/nuccore/KX059013

 

[niman]

LOCUS       KX059014                1024 bp    cRNA    linear   VRL 12-APR-2016
DEFINITION  Zika virus isolate Haiti/1230/2014 NS5 gene, partial cds.
ACCESSION   KX059014
VERSION     KX059014.1  GI:1016884668
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 1024)
  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..1024
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /isolate="Haiti/1230/2014"
                     /isolation_source="plasma"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Haiti"
                     /collection_date="17-Dec-2014"
                     /identified_by="John Lednicky"

http://www.ncbi.nlm.nih.gov/nuccore/KX059014

 

[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|KX059014.1|	Zika virus isolate Haiti/1230/2014 NS5 gene, partial cds	1761	1761	100%	0.0	100%	KX059014.1
Select seq gb|KX059013.1|	Zika virus isolate Haiti/1227/2014 NS5 gene, partial cds	1761	1761	100%	0.0	100%	KX059013.1
Select seq gb|KX051563.1|	Zika virus isolate Haiti/1/2016, complete genome	1761	1761	100%	0.0	100%	KX051563.1
Select seq gb|KU509998.3|	Zika virus strain Haiti/1225/2014, complete genome	1761	1761	100%	0.0	100%	KU509998.3
Select seq gb|KM078936.1|	Zika virus strain CHI1410214 NS5 protein gene, partial cds	1761	1761	100%	0.0	100%	KM078936.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	1761	1761	100%	0.0	100%	KJ776791.1
Select seq gb|KM078961.1|	Zika virus strain CHI2612114 NS5 protein gene, partial cds	1757	1757	100%	0.0	99%	KM078961.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	1755	1755	100%	0.0	99%	KU497555.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	1755	1755	100%	0.0	99%	KU647676.1
Select seq gb|KM078930.1|	Zika virus strain CHI2283714 NS5 protein gene, partial cds	1755	1755	100%	0.0	99%	KM078930.1
Select seq gb|KM078971.1|	Zika virus strain CHI2613014 NS5 protein gene, partial cds	1754	1754	100%	0.0	99%	KM078971.1
Select seq gb|KM078970.1|	Zika virus strain CHI2490414 NS5 protein gene, partial cds	1754	1754	100%	0.0	99%	KM078970.1
Select seq gb|KM078933.1|	Zika virus strain CHI1058514 NS5 protein gene, partial cds	1754	1754	100%	0.0	99%	KM078933.1
Select seq gb|KX087102.1|	Zika virus strain ZIKV/Homo sapiens/COL/FLR/2015, complete genome	1752	1752	100%	0.0	99%	KX087102.1
Select seq gb|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	1752	1752	100%	0.0	99%	KU870645.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	1752	1752	100%	0.0	99%	KU926310.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	1752	1752	100%	0.0	99%	KU729217.2
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	1752	1752	100%	0.0	99%	KU820897.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	1752	1752	100%	0.0	99%	KU321639.1
Select seq gb|KM078929.1|	Zika virus strain CHI1805214 NS5 protein gene, partial cds	1752	1752	100%	0.0	99%	KM078929.1
Select seq gb|KX087101.1|	Zika virus strain ZIKV/Homo sapiens/PRI/PRVABC59/2015, complete genome	1746	1746	100%	0.0	99%	KX087101.1
Select seq gb|KU991811.1|	Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU991811.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	1746	1746	100%	0.0	99%	KU926309.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	1746	1746	100%	0.0	99%	KU922960.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	1746	1746	100%	0.0	99%	KU922923.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	1746	1746	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	1746	1746	100%	0.0	99%	KU853012.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	1746	1746	100%	0.0	99%	KU707826.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	1746	1746	100%	0.0	99%	KU527068.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU501216.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	1746	1746	100%	0.0	99%	KU501215.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU365780.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU365779.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	1746	1746	100%	0.0	99%	KU365777.1
Select seq gb|KX117076.1|	Zika virus isolate Zhejiang04, complete genome	1743	1743	100%	0.0	99%	KX117076.1
Select seq gb|KU940228.1|	Zika virus isolate Bahia07, partial genome	1743	1743	100%	0.0	99%	KU940228.1
Select seq gb|KU940224.1|	Zika virus isolate Bahia09, partial genome	1743	1743	100%	0.0	99%	KU940224.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	1743	1743	100%	0.0	99%	KU820898.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	1743	1743	100%	0.0	99%	KU729218.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	1743	1743	100%	0.0	99%	KU312312.1
Select seq gb|KX056898.1|	Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KX056898.1
Select seq gb|KU963796.1|	Zika virus isolate SZ-WIV01 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU963796.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU955590.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU955589.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU740184.2
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	1737	1737	100%	0.0	99%	KU820899.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU761564.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	1737	1737	100%	0.0	99%	KU744693.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	1737	1737	100%	0.0	99%	KU365778.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	1734	1734	100%	0.0	99%	KF993678.1
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	1719	1719	100%	0.0	99%	KU866423.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	1719	1719	100%	0.0	99%	KU681081.3
Select seq gb|KU179098.1|	Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds	1710	1710	98%	0.0	99%	KU179098.1
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	1689	1689	100%	0.0	98%	KU955593.1
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	1689	1689	100%	0.0	98%	JN860885.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	1689	1689	100%	0.0	98%	EU545988.1
Select seq gb|KU681082.3|	Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome	1665	1665	100%	0.0	98%	KU681082.3
Select seq gb|KJ873160.1|	Zika virus isolate NC14-03042014-3481 nonstructural protein 5 gene, partial cds	1611	1611	91%	0.0	100%	KJ873160.1
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	1530	1530	100%	0.0	95%	HQ234499.1
Select seq gb|KJ873161.1|	Zika virus isolate NC14-02042014-3220 nonstructural protein 5 gene, partial cds	1429	1429	81%	0.0	100%	KJ873161.1
Select seq gb|KU985087.1|	Zika virus isolate MEX/InDRE/Zika-2/2015 nonstructural protein 5 gene, partial cds	1353	1353	77%	0.0	99%	KU985087.1
Select seq gb|KM851039.1|	Zika virus strain SV0127/14 nonstructural protein 5 gene, partial cds	1348	1348	78%	0.0	99%	KM851039.1
Select seq gb|KU556802.1|	Zika virus isolate MEX/InDRE/14/2015 NS5 protein gene, partial cds	1346	1346	76%	0.0	99%	KU556802.1
Select seq gb|KM851038.1|	Zika virus strain CPC-0740 nonstructural protein 5 gene, partial cds	1312	1312	78%	0.0	98%	KM851038.1

[niman]

LOCUS       KX051563               10807 bp    cRNA    linear   VRL 19-APR-2016
DEFINITION  Zika virus isolate Haiti/1/2016, complete genome.
ACCESSION   KX051563
VERSION     KX051563.1  GI:1016884664
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10807)
  AUTHORS   Lednicky,J.A., Crooke,H.R., White,S.K., Loeb,J.C., Iovine,N.M. and
            Morris,J.G. Jr.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-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..10807
                     /organism="Zika virus"
                     /mol_type="viral cRNA"
                     /isolate="Haiti/1/2016"
                     /isolation_source="saliva and urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="USA"
                     /collection_date="05-Feb-2016"
                     /identified_by="John Lednicky and Sarah White"
                     /note="passage details: one passage in LLC-MK2 cells"

http://www.ncbi.nlm.nih.gov/nuccore/KX051563

 

[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|KX051563.1|	Zika virus isolate Haiti/1/2016, complete genome	18969	18969	100%	0.0	100%	KX051563.1
Select seq gb|KU509998.3|	Zika virus strain Haiti/1225/2014, complete genome	18914	18914	100%	0.0	99%	KU509998.3
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	18886	18886	100%	0.0	99%	KU321639.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	18864	18864	100%	0.0	99%	KU527068.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	18853	18853	100%	0.0	99%	KJ776791.1
Select seq gb|KU991811.1|	Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds	18831	18831	100%	0.0	99%	KU991811.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	18820	18820	100%	0.0	99%	KU729218.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	18820	18820	100%	0.0	99%	KU707826.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	18820	18820	100%	0.0	99%	KU365779.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	18803	18803	100%	0.0	99%	KU926309.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	18803	18803	100%	0.0	99%	KU365780.1
Select seq gb|KU940228.1|	Zika virus isolate Bahia07, partial genome	18798	18798	100%	0.0	99%	KU940228.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	18798	18798	100%	0.0	99%	KU647676.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	18798	18798	100%	0.0	99%	KU365777.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	18792	18792	100%	0.0	99%	KU501217.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	18788	18788	99%	0.0	99%	KU497555.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	18787	18787	100%	0.0	99%	KU729217.2
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	18787	18787	100%	0.0	99%	KU501216.1
Select seq gb|KX087102.1|	Zika virus strain ZIKV/Homo sapiens/COL/FLR/2015, complete genome	18781	18781	100%	0.0	99%	KX087102.1
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU820897.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU365778.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU312312.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	18776	18776	100%	0.0	99%	KU922960.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	18770	18770	100%	0.0	99%	KU926310.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	18770	18770	100%	0.0	99%	KU922923.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	18770	18770	100%	0.0	99%	KU501215.1
Select seq gb|KX087101.1|	Zika virus strain ZIKV/Homo sapiens/PRI/PRVABC59/2015, complete genome	18764	18764	100%	0.0	99%	KX087101.1
Select seq gb|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	18764	18764	100%	0.0	99%	KU870645.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	18759	18759	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	18757	18757	100%	0.0	99%	KU853012.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	18748	18748	100%	0.0	99%	KU820898.1
Select seq gb|KX117076.1|	Zika virus isolate Zhejiang04, complete genome	18742	18742	100%	0.0	99%	KX117076.1
Select seq gb|KX056898.1|	Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds	18742	18742	100%	0.0	99%	KX056898.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	18742	18742	100%	0.0	99%	KU955590.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	18737	18737	100%	0.0	99%	KU740184.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	18737	18737	100%	0.0	99%	KU761564.1
Select seq gb|KU963796.1|	Zika virus isolate SZ-WIV01 polyprotein gene, complete cds	18731	18731	100%	0.0	99%	KU963796.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	18726	18726	100%	0.0	99%	KU955589.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	18726	18726	100%	0.0	99%	KU820899.2
Select seq gb|KU940224.1|	Zika virus isolate Bahia09, partial genome	18700	18700	99%	0.0	99%	KU940224.1
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	18593	18593	100%	0.0	99%	KU866423.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	18587	18587	100%	0.0	99%	KU744693.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	18432	18432	100%	0.0	99%	KU681081.3
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	18063	18063	99%	0.0	98%	JN860885.1
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	18061	18061	100%	0.0	98%	KU955593.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	18046	18046	98%	0.0	99%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	17871	17871	100%	0.0	98%	EU545988.1

[niman]

LOCUS       KU527068               10808 bp    RNA     linear   VRL 11-FEB-2016
DEFINITION  Zika virus strain Natal RGN, complete genome.
ACCESSION   KU527068
VERSION     KU527068.1  GI:982894594
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10808)
  AUTHORS   Mlakar,J., Korva,M., Tul,N., Popovic,M., Poljsak-Prijatelj,M.,
            Mraz,J., Kolenc,M., Resman Rus,K., Vesnaver Vipotnik,T., Fabjan
            Vodusek,V., Vizjak,A., Pizem,J., Petrovec,M. and Avsic Zupanc,T.
  TITLE     Zika Virus Associated with Microcephaly
  JOURNAL   N. Engl. J. Med. (2016) In press
   PUBMED   26862926
  REMARK    Publication Status: Available-Online prior to print
REFERENCE   2  (bases 1 to 10808)
  AUTHORS   Avsic Zupanc,T. and Korva,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JAN-2016) Institute of Microbiology and Immunology,
            University of Ljubljana, Faculty of Medicine, Vrazov trg 2,
            Ljubljana 1000, Slovenia
FEATURES             Location/Qualifiers
     source          1..10808
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /strain="Natal RGN"
                     /isolation_source="fetus' brain autopsy"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="Brazil: Rio Grande do Norte, Natal"
                     /collection_date="2015"

http://www.ncbi.nlm.nih.gov/nuccore/KU527068

 

[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|KU527068.1|	Zika virus strain Natal RGN, complete genome	18969	18969	100%	0.0	100%	KU527068.1
Select seq gb|KX051563.1|	Zika virus isolate Haiti/1/2016, complete genome	18864	18864	100%	0.0	99%	KX051563.1
Select seq gb|KU509998.3|	Zika virus strain Haiti/1225/2014, complete genome	18820	18820	100%	0.0	99%	KU509998.3
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	18803	18803	100%	0.0	99%	KU321639.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	18803	18803	100%	0.0	99%	KJ776791.1
Select seq gb|KU991811.1|	Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds	18792	18792	100%	0.0	99%	KU991811.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU729217.2
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU729218.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	18781	18781	100%	0.0	99%	KU707826.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	18781	18781	100%	0.0	99%	KU365779.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	18776	18776	100%	0.0	99%	KU926310.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	18764	18764	100%	0.0	99%	KU926309.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	18764	18764	100%	0.0	99%	KU501217.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	18764	18764	100%	0.0	99%	KU365780.1
Select seq gb|KU940228.1|	Zika virus isolate Bahia07, partial genome	18759	18759	100%	0.0	99%	KU940228.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	18759	18759	100%	0.0	99%	KU647676.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	18759	18759	100%	0.0	99%	KU501216.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	18759	18759	100%	0.0	99%	KU365777.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	18753	18753	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	18752	18752	100%	0.0	99%	KU853012.1
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	18750	18750	99%	0.0	99%	KU497555.1
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	18742	18742	100%	0.0	99%	KU820897.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	18742	18742	100%	0.0	99%	KU365778.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	18742	18742	100%	0.0	99%	KU312312.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	18737	18737	100%	0.0	99%	KU922960.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	18731	18731	100%	0.0	99%	KU922923.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	18731	18731	100%	0.0	99%	KU501215.1
Select seq gb|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	18726	18726	100%	0.0	99%	KU870645.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	18709	18709	100%	0.0	99%	KU820898.1
Select seq gb|KX056898.1|	Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds	18703	18703	100%	0.0	99%	KX056898.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	18703	18703	100%	0.0	99%	KU955590.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	18698	18698	100%	0.0	99%	KU740184.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	18698	18698	100%	0.0	99%	KU761564.1
Select seq gb|KU963796.1|	Zika virus isolate SZ-WIV01 polyprotein gene, complete cds	18681	18681	100%	0.0	99%	KU963796.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	18676	18676	100%	0.0	99%	KU955589.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	18676	18676	100%	0.0	99%	KU820899.2
Select seq gb|KU940224.1|	Zika virus isolate Bahia09, partial genome	18661	18661	99%	0.0	99%	KU940224.1
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	18543	18543	100%	0.0	99%	KU866423.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	18515	18515	100%	0.0	99%	KU744693.1
Select seq gb|KU681081.3|	Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome	18382	18382	100%	0.0	99%	KU681081.3
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	18013	18013	99%	0.0	98%	JN860885.1
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	18011	18011	100%	0.0	98%	KU955593.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	17996	17996	98%	0.0	99%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	17821	17821	100%	0.0	98%	EU545988.1
Select seq gb|KU681082.3|	Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome	17634	17634	100%	0.0	98%	KU681082.3
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	16377	16377	99%	0.0	95%	HQ234499.1