First 2016 Zika Sequence From United States Resident

[niman]

Although confirmation of over 300 US Zika cases in 2015/2016 have been reported, including 278 on the CDC update page of confirmations in the US, no sequences have been released from US residents collected in 2015/2016.

Today a full sequence was accessible at Genbank.  The name of the sequence, FB-GWUH/2016 suggests it was collected on February 2, 2016 from a fetal brain at George Washington University Hospital, which is reflected in the "USA" origin from "fetal brain", as cited on the characterization page.

Moreover, the characterization sheet indicates that the patient was thought to have been infected in Guatemala, which is fully supported by the relatedness to the two Zika sequences at Genbank from Guatemala.

This data matches "Patient B" described in the CDC MMWR on pregnant Zika confirmed US residents, as well as a media report describing a Washington DC resident infected in Central America, who elected to terminate her pregnancy after Zika was confirmed in amniotic fluid and sonograms and MRI confirmed severe microcephaly in the fetus.

Although the CDC MMWR described the radiological confirmation of microcephaly and the patient was Zika confirmed by PCR,this case has not been cited in the WHO SitRep on confirmed microcephaly cases (the only US case is the full term infant in Hawaii).

Edited March 26, 2016 by niman

[niman]

LOCUS       KU870645               10798 bp    RNA     linear   VRL 22-MAR-2016
DEFINITION  Zika virus isolate FB-GWUH-2016, complete genome.
ACCESSION   KU870645
VERSION     KU870645.1  GI:1006593136
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10798)
  AUTHORS   Driggers,R.W., Ho,C.-Y., Korhonen,E.M., Kuivanen,S.,
            Jaaskelainen,A.J., Smura,T., Rosenberg,A., Hill,A., DeBiasi,R.,
            Vezina,G., Timofeev,J., Rodriguez,F.J., Levanov,L., Razak,J.,
            Iyengar,P., Hennenfent,A., Kennedy,R., Lanciotti,R., du Plessis,A.
            and Vapalahti,O.
  TITLE     Zika virus infection with prolonged maternal viremia and fetal
            brain abnormalities
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10798)
  AUTHORS   Smura,T., Korhonen,E., Kuivanen,S. and Vapalahti,O.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-MAR-2016) Department of Virology, University of
            Helsinki, Haartmaninkatu 3, Helsinki 00280, Finland
FEATURES             Location/Qualifiers
     source          1..10798
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="FB-GWUH-2016"
                     /isolation_source="fetal brain"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="USA"
                     /collection_date="02-Feb-2016"
                     /note="putative country of infection: Guatemala;
                     passage details: SK-N-SH"

http://www.ncbi.nlm.nih.gov/nuccore/KU870645

 

[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|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	18420	18420	100%	0.0	99%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	18417	18417	100%	0.0	99%	KU501216.1
Select seq gb|KU509998.1|	Zika virus strain Haiti/1225/2014, complete genome	18375	18375	100%	0.0	99%	KU509998.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	18372	18372	100%	0.0	99%	KJ776791.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	18363	18363	100%	0.0	99%	KU707826.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	18363	18363	100%	0.0	99%	KU365779.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	18363	18363	100%	0.0	99%	KU321639.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	18357	18357	100%	0.0	99%	KU926309.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	18354	18354	100%	0.0	99%	KU729218.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	18348	18348	100%	0.0	99%	KU365780.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	18345	18345	100%	0.0	99%	KU365777.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	18336	18336	100%	0.0	99%	KU647676.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	18330	18330	100%	0.0	99%	KU365778.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	18330	18330	100%	0.0	99%	KU312312.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	18327	18327	100%	0.0	99%	KU729217.2
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	18327	18327	99%	0.0	99%	KU497555.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	18327	18327	100%	0.0	99%	KU527068.1
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	18321	18321	100%	0.0	99%	KU820897.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	18321	18321	100%	0.0	99%	KU501215.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	18318	18318	100%	0.0	99%	KU922960.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	18312	18312	100%	0.0	99%	KU926310.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	18312	18312	100%	0.0	99%	KU922923.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	18303	18303	100%	0.0	99%	KU820898.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	18303	18303	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	18303	18303	100%	0.0	99%	KU853012.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	18294	18294	100%	0.0	99%	KU740184.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	18294	18294	100%	0.0	99%	KU761564.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	18267	18267	100%	0.0	99%	KU820899.2
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	18159	18159	100%	0.0	99%	KU866423.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	18137	18137	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	18029	18029	100%	0.0	99%	KU681081.3
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	17730	17730	99%	0.0	98%	JN860885.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	17676	17676	98%	0.0	99%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	17567	17567	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	17429	17429	100%	0.0	98%	KU681082.3
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	16397	16397	99%	0.0	95%	HQ234499.1
Select seq gb|KU720415.1|	Zika virus strain MR 766 polyprotein gene, complete cds	13286	13286	100%	0.0	89%	KU720415.1
Select seq gb|HQ234498.1|	Zika virus isolate MR_766 polyprotein gene, partial cds	13281	13281	99%	0.0	89%	HQ234498.1
Select seq gb|KF383115.1|	Zika virus strain ArB1362 polyprotein gene, complete cds	13275	13275	100%	0.0	89%	KF383115.1
Select seq gb|KF268949.1|	Zika virus isolate ARB15076 polyprotein gene, complete cds	13270	13270	100%	0.0	89%	KF268949.1
Select seq gb|KF268948.1|	Zika virus isolate ARB13565 polyprotein gene, complete cds	13270	13270	100%	0.0	89%	KF268948.1
Select seq dbj|LC002520.1|	Zika virus genomic RNA, complete genome, strain: MR766-NIID	13263	13263	100%	0.0	89%	LC002520.1
Select seq gb|KF268950.1|	Zika virus isolate ARB7701 polyprotein gene, complete cds	13263	13263	100%	0.0	89%	KF268950.1
Select seq gb|KF383119.1|	Zika virus strain ArD158084 polyprotein gene, complete cds	13259	13259	100%	0.0	89%	KF383119.1
Select seq gb|DQ859059.1|	Zika virus strain MR 766 polyprotein gene, complete cds	13243	13243	100%	0.0	89%	DQ859059.1
Select seq gb|KF383116.1|	Zika virus strain ArD7117 polyprotein gene, complete cds	13230	13230	100%	0.0	89%	KF383116.1
Select seq gb|HQ234501.1|	Zika virus isolate ArD_41519 polyprotein gene, partial cds	13214	13214	99%	0.0	89%	HQ234501.1
Select seq gb|AY632535.2|	Zika virus strain MR 766, complete genome	13205	13205	100%	0.0	89%	AY632535.2
Select seq gb|KF383117.1|	Zika virus strain ArD128000 polyprotein gene, complete cds	13160	13160	100%	0.0	88%	KF383117.1
Select seq gb|HQ234500.1|	Zika virus isolate IbH_30656 polyprotein gene, partial cds	13144	13144	99%	0.0	88%	HQ234500.1
Select seq gb|KF383118.1|	Zika virus strain ArD157995 polyprotein gene, complete cds	12945	13013	100%	0.0	88%	KF383118.1
Select seq gb|KF383121.1|	Zika virus strain ArD158095 polyprotein gene, partial cds	12855	12855	97%	0.0	89%	KF383121.1
Select seq gb|KF383120.1|	Zika virus strain ArD142623 nonfunctional polyprotein gene, partial sequence	10877	10877	97%	0.0	84%	KF383120.1
Select seq gb|KU312314.1|	Zika virus isolate Z1106031 polyprotein gene, partial cds	4967	4967	27%	0.0	99%	KU312314.1
Select seq gb|KU312313.1|	Zika virus isolate Z1106032 polyprotein gene, partial cds	4940	4940	27%	0.0	99%	KU312313.1
Select seq gb|KU646828.1|	Zika virus isolate Si322 polyprotein gene, partial cds	4655	4655	25%	0.0	99%	KU646828.1
Select seq gb|KU646827.1|	Zika virus isolate Si323 polyprotein gene, partial cds	4646	4646	25%	0.0	99%	KU646827.1
Select seq gb|KU312315.1|	Zika virus isolate Z1106027 polyprotein gene, partial cds	3440	3440	18%	0.0	99%	KU312315.1
Select seq gb|KU740199.1|	Zika virus isolate VE_Ganxian2016 polyprotein gene, partial cds	3214	3214	17%	0.0	99%	KU740199.1
Select seq gb|DQ859064.1|	Spondweni virus strain SM-6 V-1 polyprotein gene, complete cds	2879	4206	95%	0.0	71%	DQ859064.1
Select seq gb|KJ634273.1|	Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds	2695	2695	14%	0.0	99%	KJ634273.1
Select seq gb|KU686218.1|	Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds	2042	2042	11%	0.0	99%	KU686218.1
Select seq gb|KU179098.1|	Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds	2021	2021	11%	0.0	99%	KU179098.1
Select seq gb|KM078936.1|	Zika virus strain CHI1410214 NS5 protein gene, partial cds	1752	1752	9%	0.0	99%	KM078936.1
Select seq gb|KM078961.1|	Zika virus strain CHI2612114 NS5 protein gene, partial cds	1748	1748	9%	0.0	99%	KM078961.1
Select seq gb|KM078930.1|	Zika virus strain CHI2283714 NS5 protein gene, partial cds	1746	1746	9%	0.0	99%	KM078930.1
Select seq gb|KM078971.1|	Zika virus strain CHI2613014 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078971.1
Select seq gb|KM078970.1|	Zika virus strain CHI2490414 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078970.1
Select seq gb|KM078933.1|	Zika virus strain CHI1058514 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078933.1
Select seq gb|KM078929.1|	Zika virus strain CHI1805214 NS5 protein gene, partial cds	1743	1743	9%	0.0	99%	KM078929.1
Select seq gb|KJ873160.1|	Zika virus isolate NC14-03042014-3481 nonstructural protein 5 gene, partial cds	1602	1602	8%	0.0	99%	KJ873160.1
Select seq gb|KJ873161.1|	Zika virus isolate NC14-02042014-3220 nonstructural protein 5 gene, partial cds	1420	1420	7%	0.0	99%	KJ873161.1
Select seq gb|KM851039.1|	Zika virus strain SV0127/14 nonstructural protein 5 gene, partial cds	1388	1388	7%	0.0	99%	KM851039.1
Select seq gb|KM851038.1|	Zika virus strain CPC-0740 nonstructural protein 5 gene, partial cds	1352	1352	7%	0.0	98%	KM851038.1
Select seq gb|KU556802.1|	Zika virus isolate MEX/InDRE/14/2015 NS5 protein gene, partial cds	1346	1346	7%	0.0	99%	KU556802.1
Select seq gb|AF013415.1|	Zika virus strain MR-766 NS5 protein (NS5) gene, partial cds	1306	1306	10%	0.0	88%	AF013415.1
Select seq gb|KU232300.1|	Zika virus isolate 067ZV_PEBR15 NS5 protein gene, partial cds	1240	1240	6%	0.0	99%	KU232300.1
Select seq gb|KT200609.1|	Zika virus isolate BR/949/15 NS5 gene, partial cds	1240	1240	6%	0.0	99%	KT200609.1
Select seq gb|KU232290.1|	Zika virus isolate 036ZV_PEBR15 NS5 protein gene, partial cds	1231	1231	6%	0.0	99%	KU232290.1
Select seq gb|KU232297.1|	Zika virus isolate 049ZV_PEBR15 NS5 protein gene, partial cds	1229	1229	6%	0.0	99%	KU232297.1
Select seq gb|KU232294.1|	Zika virus isolate 061ZV_PEBR15 NS5 protein gene, partial cds	1220	1220	6%	0.0	99%	KU232294.1
Select seq gb|KU232292.1|	Zika virus isolate 054ZV_PEBR15 NS5 protein gene, partial cds	1218	1218	6%	0.0	99%	KU232292.1
Select seq gb|KU232298.1|	Zika virus isolate 050ZV_PEBR15 NS5 protein gene, partial cds	1214	1214	6%	0.0	99%	KU232298.1
Select seq gb|KU232296.1|	Zika virus isolate 045ZV_PEBR15 NS5 protein gene, partial cds	1211	1211	6%	0.0	99%	KU232296.1
Select seq gb|KU232293.1|	Zika virus isolate 057ZV_PEBR15 NS5 protein gene, partial cds	1211	1211	6%	0.0	99%	KU232293.1
Select seq gb|KU232295.1|	Zika virus isolate 068ZV_PEBR15 NS5 protein gene, partial cds	1205	1205	6%	0.0	99%	KU232295.1
Select seq gb|KU232288.1|	Zika virus isolate 001ZV_PEBR15 NS5 protein gene, partial cds	1195	1195	6%	0.0	99%	KU232288.1
Select seq gb|KU232289.1|	Zika virus isolate 020ZV_PEBR15 NS5 protein gene, partial cds	1191	1191	6%	0.0	99%	KU232289.1
Select seq gb|KU232299.1|	Zika virus isolate 015ZV_PEBR15 NS5 protein gene, partial cds	1187	1187	6%	0.0	99%	KU232299.1
Select seq gb|KU232291.1|	Zika virus isolate 051ZV_PEBR15 NS5 protein gene, partial cds	1186	1186	6%	0.0	99%	KU232291.1
Select seq gb|KU758878.1|	Zika virus polyprotein gene, partial cds	1130	1130	6%	0.0	98%	KU758878.1
Select seq gb|KF270886.1|	Zika virus strain CCB-870 envelope glycoprotein gene, partial cds	1068	1068	8%	0.0	88%	KF270886.1
Select seq gb|KU867812.1|	Zika virus isolate Jiangxi.CHN/01/2016 nonstructural protein 5 gene, partial cds	1018	1018	5%	0.0	100%	KU867812.1
Select seq gb|AF372422.1|AF372422	Zika virus envelope protein (E) gene, partial cds	1011	1011	8%	0.0	86%	AF372422.1
Select seq gb|KF270887.1|	Zika virus strain CCB-870 NS3 protein gene, partial cds	991	991	7%	0.0	88%	KF270887.1
Select seq gb|KF383022.1|	Zika virus strain ArD127988 envelope protein gene, partial cds	975	975	7%	0.0	89%	KF383022.1
Select seq gb|EF158064.1|	St. Louis encephalitis virus strain GML 902612 polyprotein gene, partial cds	975	1977	64%	0.0	70%	EF158064.1
Select seq gb|KF383026.1|	Zika virus strain ArD127994 envelope protein gene, partial cds	971	971	7%	0.0	89%	KF383026.1
Select seq gb|EU303241.1|	Zika virus note MR766 (p4 15/9/76) nonstructural protein 5 (NS5) gene, partial cds	971	971	7%	0.0	88%	EU303241.1
Select seq gb|KF383032.1|	Zika virus strain ArD30101 envelope protein gene, partial cds	962	962	7%	0.0	88%	KF383032.1
Select seq gb|KF383037.1|	Zika virus strain ArA506 envelope protein gene, partial cds	957	957	7%	0.0	88%	KF383037.1
Select seq gb|KF383034.1|	Zika virus strain ArD30156 envelope protein gene, partial cds	957	957	7%	0.0	88%	KF383034.1
Select seq gb|KF383029.1|	Zika virus strain ArD165522 envelope protein gene, partial cds	957	957	7%	0.0	88%	KF383029.1
Select seq gb|KF383033.1|	Zika virus strain AnD30332 envelope protein gene, partial cds	953	953	7%	0.0	88%	KF383033.1
Select seq gb|KF383036.1|	Zika virus strain ArA975 envelope protein gene, partial cds	951	951	7%	0.0	88%	KF383036.1
Select seq gb|JX041632.1|	West Nile virus strain Ig2266, complete genome	939	1789	58%	0.0	69%	JX041632.1
Select seq gb|KF383028.1|	Zika virus strain ArD165531 envelope protein gene, partial cds	935	935	7%	0.0	88%	KF383028.1
Select seq gb|KF383039.1|	Zika virus strain HD78788 envelope protein gene, partial cds	933	933	7%	0.0	88%	KF383039.1
Select seq gb|GQ851605.1|	West Nile virus strain G16146 polyprotein gene, complete cds	931	1846	54%	0.0	69%	GQ851605.1
Select seq gb|KF383031.1|	Zika virus strain ArD9957 envelope protein gene, partial cds	930	930	7%	0.0	87%	KF383031.1
Select seq gb|KF383038.1|	Zika virus strain ArA986 envelope protein gene, partial cds	924	924	7%	0.0	87%	KF383038.1
Select seq gb|KF383046.1|	Zika virus strain ArA982 envelope protein gene, partial cds	915	915	7%	0.0	87%	KF383046.1
Select seq gb|KT823415.1|	St. Louis encephalitis virus strain RT 121B polyprotein gene, complete cds	908	1902	65%	0.0	69%	KT823415.1
Select seq gb|FJ753286.2|	St. Louis encephalitis virus strain CbaAr-4005, complete genome	908	1923	65%	0.0	69%	FJ753286.2
Select seq gb|KF383045.1|	Zika virus strain ArA27106 envelope protein gene, partial cds	902	902	7%	0.0	87%	KF383045.1
Select seq gb|KF383103.1|	Zika virus strain ArA986 nonstructural protein 5 gene, partial cds	897	897	6%	0.0	88%	KF383103.1
Select seq gb|KF383086.1|	Zika virus strain ArA975 nonstructural protein 5 gene, partial cds	897	897	6%	0.0	88%	KF383086.1
Select seq gb|KF383043.1|	Zika virus strain ArA27443 envelope protein gene, partial cds	897	897	7%	0.0	87%	KF383043.1
Select seq gb|KF383035.1|	Zika virus strain MR1429 envelope protein gene, partial cds	897	897	7%	0.0	86%	KF383035.1
Select seq gb|KF383041.1|	Zika virus strain ArA27290 envelope protein gene, partial cds	893	893	7%	0.0	86%	KF383041.1
Select seq gb|KF383042.1|	Zika virus strain ArA27096 envelope protein gene, partial cds	888	888	7%	0.0	86%	KF383042.1
Select seq gb|KF383104.1|	Zika virus strain ArA982 nonstructural protein 5 gene, partial cds	865	865	6%	0.0	87%	KF383104.1
Select seq gb|KF383085.1|	Zika virus strain ArD9957 nonstructural protein 5 gene, partial cds	865	865	6%	0.0	87%	KF383085.1
Select seq gb|KF383040.1|	Zika virus strain ArA27101 envelope protein gene, partial cds	863	863	7%	0.0	85%	KF383040.1
Select seq gb|KF383106.1|	Zika virus strain ArA27443 nonstructural protein 5 gene, partial cds	861	861	6%	0.0	87%	KF383106.1
Select seq gb|KF383114.1|	Zika virus strain AnD30332 nonstructural protein 5 gene, partial cds	856	856	6%	0.0	87%	KF383114.1
Select seq gb|KF383107.1|	Zika virus strain ArA27407 nonstructural protein 5 gene, partial cds	856	856	6%	0.0	87%	KF383107.1
Select seq gb|KF383088.1|	Zika virus strain ArD30101 nonstructural protein 5 gene, partial cds	856	856	6%	0.0	87%	KF383088.1
Select seq gb|KF383087.1|	Zika virus strain ArD30156 nonstructural protein 5 gene, partial cds	852	852	6%	0.0	87%	KF383087.1
Select seq gb|KF383089.1|	Zika virus strain ArD165531 nonstructural protein 5 gene, partial cds	838	838	6%	0.0	86%	KF383089.1
Select seq gb|KF383101.1|	Zika virus strain ArD127710 nonstructural protein 5 gene, partial cds	834	834	6%	0.0	86%	KF383101.1
Select seq gb|KF383097.1|	Zika virus strain ArD127994 nonstructural protein 5 gene, partial cds	834	834	6%	0.0	86%	KF383097.1
Select seq gb|KF383099.1|	Zika virus strain ArD127987 nonstructural protein 5 gene, partial cds	829	829	6%	0.0	86%	KF383099.1
Select seq dbj|AB908162.1|	Zika virus gene for polyprotein, partial cds, strain: ZIKV Hu/Tahiti/01u/2014NIID	829	829	4%	0.0	99%	AB908162.1
Select seq gb|KF383098.1|	Zika virus strain ArD127988 nonstructural protein 5 gene, partial cds	825	825	6%	0.0	86%	KF383098.1
Select seq gb|KU872850.1|	Zika virus isolate Dominican Rep-Rus-2016, NS2 partial cds	814	814	4%	0.0	99%	KU872850.1

[niman]

[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|KU870645.1|	Zika virus isolate FB-GWUH-2016, complete genome	18525	18525	100%	0.0	100%	KU870645.1
Select seq gb|KU501217.1|	Zika virus strain 8375 polyprotein gene, complete cds	18420	18420	100%	0.0	99%	KU501217.1
Select seq gb|KU501216.1|	Zika virus strain 103344 polyprotein gene, complete cds	18417	18417	100%	0.0	99%	KU501216.1
Select seq gb|KU509998.1|	Zika virus strain Haiti/1225/2014, complete genome	18375	18375	100%	0.0	99%	KU509998.1
Select seq gb|KJ776791.1|	Zika virus strain H/PF/2013 polyprotein gene, complete cds	18372	18372	100%	0.0	99%	KJ776791.1
Select seq gb|KU707826.1|	Zika virus isolate SSABR1, complete genome	18363	18363	100%	0.0	99%	KU707826.1
Select seq gb|KU365779.1|	Zika virus strain BeH819966 polyprotein gene, complete cds	18363	18363	100%	0.0	99%	KU365779.1
Select seq gb|KU321639.1|	Zika virus strain ZikaSPH2015, complete genome	18363	18363	100%	0.0	99%	KU321639.1
Select seq gb|KU926309.1|	Zika virus isolate Rio-U1, complete genome	18357	18357	100%	0.0	99%	KU926309.1
Select seq gb|KU729218.1|	Zika virus isolate BeH828305 polyprotein gene, complete cds	18354	18354	100%	0.0	99%	KU729218.1
Select seq gb|KU365780.1|	Zika virus strain BeH815744 polyprotein gene, complete cds	18348	18348	100%	0.0	99%	KU365780.1
Select seq gb|KU365777.1|	Zika virus strain BeH818995 polyprotein gene, complete cds	18345	18345	100%	0.0	99%	KU365777.1
Select seq gb|KU647676.1|	Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds	18336	18336	100%	0.0	99%	KU647676.1
Select seq gb|KU365778.1|	Zika virus strain BeH819015 polyprotein gene, complete cds	18330	18330	100%	0.0	99%	KU365778.1
Select seq gb|KU312312.1|	Zika virus isolate Z1106033 polyprotein gene, complete cds	18330	18330	100%	0.0	99%	KU312312.1
Select seq gb|KU729217.2|	Zika virus isolate BeH823339 polyprotein gene, complete cds	18327	18327	100%	0.0	99%	KU729217.2
Select seq gb|KU497555.1|	Zika virus isolate Brazil-ZKV2015, complete genome	18327	18327	99%	0.0	99%	KU497555.1
Select seq gb|KU527068.1|	Zika virus strain Natal RGN, complete genome	18327	18327	100%	0.0	99%	KU527068.1
Select seq gb|KU820897.1|	Zika virus isolate FLR polyprotein gene, complete cds	18321	18321	100%	0.0	99%	KU820897.1
Select seq gb|KU501215.1|	Zika virus strain PRVABC59, complete genome	18321	18321	100%	0.0	99%	KU501215.1
Select seq gb|KU922960.1|	Zika virus isolate MEX/InDRE/Sm/2016, complete genome	18318	18318	100%	0.0	99%	KU922960.1
Select seq gb|KU926310.1|	Zika virus isolate Rio-S1, complete genome	18312	18312	100%	0.0	99%	KU926310.1
Select seq gb|KU922923.1|	Zika virus isolate MEX/InDRE/Lm/2016, complete genome	18312	18312	100%	0.0	99%	KU922923.1
Select seq gb|KU820898.1|	Zika virus isolate GZ01 polyprotein gene, complete cds	18303	18303	100%	0.0	99%	KU820898.1
Select seq gb|KU853013.1|	Zika virus isolate Dominican Republic/2016/PD2, complete genome	18303	18303	100%	0.0	99%	KU853013.1
Select seq gb|KU853012.1|	Zika virus isolate Dominican Republic/2016/PD1, complete genome	18303	18303	100%	0.0	99%	KU853012.1
Select seq gb|KU955590.1|	Zika virus isolate Z16019 polyprotein gene, complete cds	18300	18300	100%	0.0	99%	KU955590.1
Select seq gb|KU740184.2|	Zika virus isolate GD01 polyprotein gene, complete cds	18294	18294	100%	0.0	99%	KU740184.2
Select seq gb|KU761564.1|	Zika virus isolate GDZ16001 polyprotein gene, complete cds	18294	18294	100%	0.0	99%	KU761564.1
Select seq gb|KU955589.1|	Zika virus isolate Z16006 polyprotein gene, complete cds	18267	18267	100%	0.0	99%	KU955589.1
Select seq gb|KU820899.2|	Zika virus isolate ZJ03, complete genome	18267	18267	100%	0.0	99%	KU820899.2
Select seq gb|KU866423.1|	Zika virus isolate Zika virus/SZ01/2016 polyprotein gene, complete cds	18159	18159	100%	0.0	99%	KU866423.1
Select seq gb|KU744693.1|	Zika virus isolate VE_Ganxian, complete genome	18137	18137	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	18029	18029	100%	0.0	99%	KU681081.3
Select seq gb|KU955593.1|	Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome	17732	17732	100%	0.0	98%	KU955593.1
Select seq gb|JN860885.1|	Zika virus isolate FSS13025 polyprotein gene, partial cds	17730	17730	99%	0.0	98%	JN860885.1
Select seq gb|KF993678.1|	Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds	17676	17676	98%	0.0	99%	KF993678.1
Select seq gb|EU545988.1|	Zika virus polyprotein gene, complete cds	17567	17567	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	17429	17429	100%	0.0	98%	KU681082.3
Select seq gb|HQ234499.1|	Zika virus isolate P6-740 polyprotein gene, partial cds	16397	16397	99%	0.0	95%	HQ234499.1
Select seq gb|KU720415.1|	Zika virus strain MR 766 polyprotein gene, complete cds	13286	13286	100%	0.0	89%	KU720415.1
Select seq gb|HQ234498.1|	Zika virus isolate MR_766 polyprotein gene, partial cds	13281	13281	99%	0.0	89%	HQ234498.1
Select seq gb|KF383115.1|	Zika virus strain ArB1362 polyprotein gene, complete cds	13275	13275	100%	0.0	89%	KF383115.1
Select seq gb|KU955595.1|	Zika virus isolate Zika virus/A.taylori-tc/SEN/1984/41671-DAK, complete genome	13272	13272	100%	0.0	89%	KU955595.1
Select seq gb|KF268949.1|	Zika virus isolate ARB15076 polyprotein gene, complete cds	13270	13270	100%	0.0	89%	KF268949.1
Select seq gb|KF268948.1|	Zika virus isolate ARB13565 polyprotein gene, complete cds	13270	13270	100%	0.0	89%	KF268948.1
Select seq gb|KU955592.1|	Zika virus isolate Zika virus/A.taylori-tc/SEN/1984/41662-DAK, complete genome	13263	13263	100%	0.0	89%	KU955592.1
Select seq dbj|LC002520.1|	Zika virus genomic RNA, complete genome, strain: MR766-NIID	13263	13263	100%	0.0	89%	LC002520.1
Select seq gb|KF268950.1|	Zika virus isolate ARB7701 polyprotein gene, complete cds	13263	13263	100%	0.0	89%	KF268950.1
Select seq gb|KF383119.1|	Zika virus strain ArD158084 polyprotein gene, complete cds	13259	13259	100%	0.0	89%	KF383119.1
Select seq gb|KU955594.1|	Zika virus isolate Zika virus/M.mulatta-tc/UGA/1947/MR-766, complete genome	13247	13247	100%	0.0	89%	KU955594.1
Select seq gb|KU955591.1|	Zika virus isolate Zika virus/A.africanus-tc/SEN/1984/41525-DAK, complete genome	13245	13245	100%	0.0	89%	KU955591.1
Select seq gb|DQ859059.1|	Zika virus strain MR 766 polyprotein gene, complete cds	13243	13243	100%	0.0	89%	DQ859059.1
Select seq gb|KF383116.1|	Zika virus strain ArD7117 polyprotein gene, complete cds	13230	13230	100%	0.0	89%	KF383116.1
Select seq gb|HQ234501.1|	Zika virus isolate ArD_41519 polyprotein gene, partial cds	13214	13214	99%	0.0	89%	HQ234501.1
Select seq gb|AY632535.2|	Zika virus strain MR 766, complete genome	13205	13205	100%	0.0	89%	AY632535.2
Select seq gb|KF383117.1|	Zika virus strain ArD128000 polyprotein gene, complete cds	13160	13160	100%	0.0	88%	KF383117.1
Select seq gb|HQ234500.1|	Zika virus isolate IbH_30656 polyprotein gene, partial cds	13144	13144	99%	0.0	88%	HQ234500.1
Select seq gb|KF383118.1|	Zika virus strain ArD157995 polyprotein gene, complete cds	12945	13013	100%	0.0	88%	KF383118.1
Select seq gb|KF383121.1|	Zika virus strain ArD158095 polyprotein gene, partial cds	12855	12855	97%	0.0	89%	KF383121.1
Select seq gb|KF383120.1|	Zika virus strain ArD142623 nonfunctional polyprotein gene, partial sequence	10877	10877	97%	0.0	84%	KF383120.1
Select seq gb|KU312314.1|	Zika virus isolate Z1106031 polyprotein gene, partial cds	4967	4967	27%	0.0	99%	KU312314.1
Select seq gb|KU312313.1|	Zika virus isolate Z1106032 polyprotein gene, partial cds	4940	4940	27%	0.0	99%	KU312313.1
Select seq gb|KU646828.1|	Zika virus isolate Si322 polyprotein gene, partial cds	4655	4655	25%	0.0	99%	KU646828.1
Select seq gb|KU646827.1|	Zika virus isolate Si323 polyprotein gene, partial cds	4646	4646	25%	0.0	99%	KU646827.1
Select seq gb|KU312315.1|	Zika virus isolate Z1106027 polyprotein gene, partial cds	3440	3440	18%	0.0	99%	KU312315.1
Select seq gb|KU740199.1|	Zika virus isolate VE_Ganxian2016 polyprotein gene, partial cds	3214	3214	17%	0.0	99%	KU740199.1
Select seq gb|DQ859064.1|	Spondweni virus strain SM-6 V-1 polyprotein gene, complete cds	2879	4206	95%	0.0	71%	DQ859064.1
Select seq gb|KJ634273.1|	Zika virus strain CK-ISL 2014 E protein (E) gene, partial cds	2695	2695	14%	0.0	99%	KJ634273.1
Select seq gb|KU686218.1|	Zika virus isolate MEX/InDRE/14/2015 polyprotein gene, partial cds	2042	2042	11%	0.0	99%	KU686218.1
Select seq gb|KU179098.1|	Zika virus isolate JMB-185 nonstructural protein 5 gene, partial cds	2021	2021	11%	0.0	99%	KU179098.1
Select seq gb|KM078936.1|	Zika virus strain CHI1410214 NS5 protein gene, partial cds	1752	1752	9%	0.0	99%	KM078936.1
Select seq gb|KM078961.1|	Zika virus strain CHI2612114 NS5 protein gene, partial cds	1748	1748	9%	0.0	99%	KM078961.1
Select seq gb|KM078930.1|	Zika virus strain CHI2283714 NS5 protein gene, partial cds	1746	1746	9%	0.0	99%	KM078930.1
Select seq gb|KM078971.1|	Zika virus strain CHI2613014 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078971.1
Select seq gb|KM078970.1|	Zika virus strain CHI2490414 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078970.1
Select seq gb|KM078933.1|	Zika virus strain CHI1058514 NS5 protein gene, partial cds	1745	1745	9%	0.0	99%	KM078933.1
Select seq gb|KM078929.1|	Zika virus strain CHI1805214 NS5 protein gene, partial cds	1743	1743	9%	0.0	99%	KM078929.1
Select seq gb|KJ873160.1|	Zika virus isolate NC14-03042014-3481 nonstructural protein 5 gene, partial cds	1602	1602	8%	0.0	99%	KJ873160.1
Select seq gb|KJ873161.1|	Zika virus isolate NC14-02042014-3220 nonstructural protein 5 gene, partial cds	1420	1420	7%	0.0	99%	KJ873161.1
Select seq gb|KM851039.1|	Zika virus strain SV0127/14 nonstructural protein 5 gene, partial cds	1388	1388	7%	0.0	99%	KM851039.1
Select seq gb|KM851038.1|	Zika virus strain CPC-0740 nonstructural protein 5 gene, partial cds	1352	1352	7%	0.0	98%	KM851038.1
Select seq gb|KU556802.1|	Zika virus isolate MEX/InDRE/14/2015 NS5 protein gene, partial cds	1346	1346	7%	0.0	99%	KU556802.1
Select seq gb|AF013415.1|	Zika virus strain MR-766 NS5 protein (NS5) gene, partial cds	1306	1306	10%	0.0	88%	AF013415.1
Select seq gb|KU232300.1|	Zika virus isolate 067ZV_PEBR15 NS5 protein gene, partial cds	1240	1240	6%	0.0	99%	KU232300.1
Select seq gb|KT200609.1|	Zika virus isolate BR/949/15 NS5 gene, partial cds	1240	1240	6%	0.0	99%	KT200609.1
Select seq gb|KU232290.1|	Zika virus isolate 036ZV_PEBR15 NS5 protein gene, partial cds	1231	1231	6%	0.0	99%	KU232290.1
Select seq gb|KU232297.1|	Zika virus isolate 049ZV_PEBR15 NS5 protein gene, partial cds	1229	1229	6%	0.0	99%	KU232297.1
Select seq gb|KU232294.1|	Zika virus isolate 061ZV_PEBR15 NS5 protein gene, partial cds	1220	1220	6%	0.0	99%	KU232294.1
Select seq gb|KU232292.1|	Zika virus isolate 054ZV_PEBR15 NS5 protein gene, partial cds	1218	1218	6%	0.0	99%	KU232292.1
Select seq gb|KU232298.1|	Zika virus isolate 050ZV_PEBR15 NS5 protein gene, partial cds	1214	1214	6%	0.0	99%	KU232298.1
Select seq gb|KU232296.1|	Zika virus isolate 045ZV_PEBR15 NS5 protein gene, partial cds	1211	1211	6%	0.0	99%	KU232296.1
Select seq gb|KU232293.1|	Zika virus isolate 057ZV_PEBR15 NS5 protein gene, partial cds	1211	1211	6%	0.0	99%	KU232293.1
Select seq gb|KU232295.1|	Zika virus isolate 068ZV_PEBR15 NS5 protein gene, partial cds	1205	1205	6%	0.0	99%	KU232295.1
Select seq gb|KU232288.1|	Zika virus isolate 001ZV_PEBR15 NS5 protein gene, partial cds	1195	1195	6%	0.0	99%	KU232288.1
Select seq gb|KU232289.1|	Zika virus isolate 020ZV_PEBR15 NS5 protein gene, partial cds	1191	1191	6%	0.0	99%	KU232289.1
Select seq gb|KU232299.1|	Zika virus isolate 015ZV_PEBR15 NS5 protein gene, partial cds	1187	1187	6%	0.0	99%	KU232299.1
Select seq gb|KU232291.1|	Zika virus isolate 051ZV_PEBR15 NS5 protein gene, partial cds	1186	1186	6%	0.0	99%	KU232291.1

[niman]

Zika Virus Infection with Prolonged Maternal Viremia and Fetal Brain Abnormalities

Rita W. Driggers, M.D., Cheng-Ying Ho, M.D., Ph.D., Essi M. Korhonen, M.Sc., Suvi Kuivanen, M.Sc., Anne J. Jääskeläinen, Ph.D., Teemu Smura, Ph.D., Avi Rosenberg, M.D., Ph.D., D. Ashley Hill, M.D., Roberta L. DeBiasi, M.D., Gilbert Vezina, M.D., Julia Timofeev, M.D., Fausto J. Rodriguez, M.D., Lev Levanov, Ph.D., Jennifer Razak, M.G.C., C.G.C, Preetha Iyengar, M.D., Andrew Hennenfent, D.V.M., M.P.H., Richard Kennedy, M.D., Robert Lanciotti, Ph.D., Adre du Plessis, M.B., Ch.B., M.P.H., and Olli Vapalahti, M.D., Ph.D.

March 30, 2016DOI: 10.1056/NEJMoa1601824

http://www.nejm.org/doi/full/10.1056/NEJMoa1601824#t=article

[niman]

CASE REPORT

A 33-year-old Finnish woman who was in the 11th week of gestation was on holiday in Mexico, Guatemala, and Belize with her husband in late November 2015. (Details are provided in Section 1.0 of the Supplementary Appendix, available with the full text of this article at NEJM.org.) During their travels, she and her husband recalled being bitten by mosquitoes, particularly in Guatemala. One day after her arrival at her current residence in Washington, D.C., she became ill with ocular pain, myalgia, and mild fever (maximum, 37.5°C), which lasted for 5 days. On the second day of fever, a rash developed (Figure 1FIGURE 1Timeline of Symptoms and Radiographic and Laboratory Studies., and Fig. S5 in the Supplementary Appendix). Her husband was concomitantly reporting similar symptoms. Serologic analysis that was performed 4 weeks after the onset of illness while she was on a trip to her native Finland was positive for IgG antibodies and negative for IgM antibodies against dengue virus. Subsequent serologic analysis was positive for both IgG and IgM antibodies against ZIKV, findings that were compatible with acute or recent ZIKV infection. Serologic analysis for the presence of chikungunya virus was negative. The patient had been vaccinated against tick-borne encephalitis and yellow fever more than 10 years earlier.

Fetal ultrasonography that was performed at 13, 16, and 17 weeks of gestation (1, 4, and 5 weeks after the resolution of symptoms) showed no evidence of microcephaly or intracranial calcifications. However, there was a decrease in the fetal head circumference from the 47th percentile at 16 weeks to the 24th percentile at 20 weeks.

At 16 weeks of gestation, the presence of flavivirus in serum was detected on nested reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay, and sequencing showed identity to Central American epidemic strains of ZIKV. The finding was confirmed with a specific ZIKV quantitative RT-PCR assay (Table S2 in the Supplementary Appendix). The Division of Vector-Borne Diseases Arbovirus Diagnostic Laboratory at the CDC reported serologic evidence of infection at 17 weeks of gestation, with serum positivity for ZIKV IgM and a titer of more than 1:2560 on a plaque-reduction neutralization test. On the basis of these results, the patient sought more thorough assessment of the fetus.

Fetal ultrasonography at 19 weeks of gestation showed abnormal intracranial anatomy (Figure 2FIGURE 2Fetal Ultrasonography at 19 Weeks of Gestation., and Fig. S1 in the Supplementary Appendix). The cerebral mantle appeared to be thin with increased extra-axial spaces. Both frontal horns were enlarged with heterogeneous, predominantly echogenic material present in the frontal horn and body of the left lateral ventricle, a finding that raised concern about intraventricular hemorrhage. Dilation and upward displacement of the third ventricle, dilation of the frontal horns of the lateral ventricles, concave medial borders of the lateral ventricles, and the absence of the cavum septum pellucidum suggested agenesis of the corpus callosum. No parenchymal calcifications were seen. The head circumference measured in the 24th percentile for gestational age. The remainder of the fetal anatomy was normal.

Fetal MRI at 20 weeks of gestation showed diffuse atrophy of the cerebral mantle, which was most severe in the frontal and parietal lobes, with the anterior temporal lobes least affected (Figure 3FIGURE 3Magnetic Resonance Imaging of the Fetal Brain at 19 Weeks of Gestation.). The normal lamination pattern of the cerebral mantle was absent, and the subplate zone was largely undetectable. The corpus callosum was significantly shorter than expected for gestational age, with an anterior–posterior length of 14 mm (expected range, 18 to 22).18,19 The cavum septum pellucidum was very small. The lateral ventricles were mildly enlarged, as was the third ventricle, with a transverse diameter measuring 2.5 mm (average measurement at gestational age, 1.75 mm [range, 1.1 to 2.3]).18 The fourth ventricle was normal. The volume of the choroid plexus was unusually prominent, without evidence of hemorrhage. No focal destructive lesions were identified within the cerebral cortex or white matter. The cerebellum was normal in appearance and size. Given the grave prognosis, the patient elected to terminate the pregnancy at 21 weeks of gestation.