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SARS-CoV2 BA.2.86 Derivative Sequences Map

Pinellas Co Zika Sequence Matches Miami Dade

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niman Grand Master

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The Pinellas Co Zika active investigation has been closed.  However, although the precise location of Zika transmission was not identified, media reports noted that the case was a firefighter who worked in Hillsborough County (Tampa Bay), whose travel prior to disease onset was limited to Pinellas and Hillsborough Counties, which include Clearwater and St Petersburgh in Pinellas County as well as Tampa Bay in Hillisborough County.  These sites are over 200 miles northwest of the outbreaks in Miami Dade (Wynwood and Miami Beach).

The Andersen Lab at Scripps Clinic has been sequencing samples from humans and mosquitoes in Florida.  Five of these sequences (3 human and 3 mosquito) have been released at Genbank and all five of these sequences fall into a well defined sub-clade, which includes full or partial Zika sequences from French Guyana, Dominican Republic, and Guadeloupe.

In addition to the five full sequences at Genbank, the Anderson Lab has been posting additional sequences at their website.  The recent update of the summary table (Location of Infection column) indicated that one of these sequences (ZM 39) was from the case in Pinellas County.

The sequence relationship to the sequences from Miami Dade County raises concerns that Zika in Florida mosquitoes is widespread and has been circulating in Florida well in advance of reports of local transmission.

 

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Samples

Scripps ID Patient ID Sample type Quality score % Coverage Location of infection
ZF1 001 Saliva *** 99.71 Martinique
ZF8 008 Urine *** 90.07 Puerto Rico
ZF10 010 Urine **** 97.69 Cuba
ZF16 016 Urine *** 99.88 Puerto Rico
ZF21 021 Urine *** 97.45 "Dade County Florida"
ZF22 022 Urine *** 97.77 "Dade County Florida"
ZF30 030 Urine *** 99.75 "Dade County Florida"
ZF32 032 Urine *** 99.75 "Dade County Florida"
ZF38 038 Urine *** 99.76 Dade
ZF39 039 Urine **** 99.75 "Pinellas County Florida"
ZL2 Hu0015 Saliva *** 99.75 "Dade County Florida"
ZM1 7501 Mosquito **** 99.75 "Dade County Florida"
ZM2 7719 Mosquito **** 99.74 "Dade County Florida"
ZM3 7727 Mosquito **** 99.83 "Dade County Florida"
ZM4 16-10416 Mosquito **** 99.72 Dade - Miami Beach
ZM5 16-3125 Mosquito ** 96.63 Dade - Miami Beach
ZC188 423568715 Serum **** 98.26 Columbia
ZC192 423401315 Serum **** 98.36 Columbia
ZC204 424439915 Serum **** 99.74 Columbia
ZC207 423217515 Serum **** 96.68 Columbia
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Sequence MetaData

Scripps ID Patient ID Sample type Quality score % Coverage Average Depth Onset Collection Days post onset Local or travel Location of infection GE/ul RNA GE/mL sample Sequencing status Consensus name Merged Bam File
ZF1 001 Saliva *** 99.71 46616.27 2016.03.18 2016.03.22 4 Travel Martinique 11 3.3E+03 coding-complete ZF1_01Sa_XX_2016-03-22 usa_ex_martinique ZF1.c1.Sa.a1.l1.l3.l4.r1
ZF8 008 Urine *** 90.07 35012.49 2016.06.15 2016.06.21 6 Travel Puerto Rico 4 1.1E+03 coding-complete ZF8_08U_XX_2016-06-21 usa_ex_puerto_rico ZF8.c1.UR.a1.l1.l2.r1
ZF10 010 Urine **** 97.69 55330.48 2016.06.17 2016.06.22 5 Local? Cuba 213 6.1E+04 coding-complete ZF10_10U_KX842499 2016-06-22 usa_ex_cuba ZF10.c1.UR.a1.l1.r1
ZF16 016 Urine *** 99.88 75158.72 2016.06.28 2016.07.03 5 Travel Puerto Rico 14 4.0E+03 coding-complete ZF16_16U_XX_2016-07-03 usa_ex_puerto_rico ZF16.c1.UR.a1.l1.l2.l3.l4.l5.r1
ZF21 021 Urine *** 97.45 52361.36 2016.07.09 2016.07.19 10 Local "Dade County Florida" 50 1.4E+04 coding-complete ZF21_21U_XX_2016-07-19 usa ZF21.c1.UR.a1.l1.l2.l3.r1
ZF22 022 Urine *** 97.77 51135.60 2016.07.16 2016.07.16 6 Local "Dade County Florida" 11 3.0E+03 coding-complete ZF22_22U_XX_2016-07-16 usa ZF22.c1.UR.a1.l1.l2.l3.l4.r1
ZF30 030 Urine *** 99.75 57779.63 2016.07.31 2016.08.02 2 Local "Dade County Florida" 36 1.0E+04 coding-complete ZF30_30U_XX_2016-08-02 usa ZF30.c1.UR.a1.l1.l2.l3.r1
ZF32 032 Urine *** 99.75 51483.94 2016.07.29 2016.08.05 7 Local "Dade County Florida" 75 2.1E+04 coding-complete ZF32_32U_XX_2016-08-05 usa ZF32.c1.UR.a1.l1.l2.l3.r1
ZF38 038 Urine *** 99.76 81750.77 2016.08.04 2016.08.05 1 Local Dade 38 1.1E+04 coding-complete ZF38_38U_XX_2016-08-05 usa ZF38.c1.UR.a1.l1.l2.l3.l4.r1
ZF39 039 Urine **** 99.75 70253.99 2016.08.12 2016.08.17 5 Local "Pinellas County Florida" 1276 3.6E+05 coding-complete ZF39_39U_XX_2016-08-17 usa ZF39.c1.UR.a1.l1.l2.l3.r1
ZL2 Hu0015 Saliva *** 99.75 89934.25 2016.08.19 2016.08.24 5 Local "Dade County Florida" 38 21610.23 coding-complete ZL2_Hu0015_KX832731 2016-08-22 usa ZL2.c1.SA.a1.l1.l2.r1
ZM1 7501 Mosquito **** 99.75 141038.31   2016.08.22   Local "Dade County Florida" 4563 9.1E+06 coding-complete Ae-aegypti_ZM1_7501_KX838904_2016-08-22_usa ZM1.c1.MO.a1.l1.l2.r1
ZM2 7719 Mosquito **** 99.74 137263.85   2016.08.23   Local "Dade County Florida" 279 5.6E+05 coding-complete Ae-aegypti_ZM2_7719_KX838905_2016-08-23_usa ZM2.c1.MO.a1.l1.l2.r1
ZM3 7727 Mosquito **** 99.83 139787.57   2016.08.23   Local "Dade County Florida" 22549 4.5E+07 coding-complete Ae-aegypti_ZM3_7727_KX838906_2016-08-23_usa ZM3.c1.MO.a1.l1.l2.r1
ZM4 16-10416 Mosquito **** 99.72 45505.39   2016.09.04   Local Dade - Miami Beach 102 4.4E+04 coding-complete Ae-aegypti_ZM4_16-10416_XX_2016-09-04_usa ZM4.c1.MO.a1.l1.l2.r1
ZM5 16-3125 Mosquito ** 96.63 5365.36   2016.09.09   Local Dade - Miami Beach 447 1.9E+05 missing part of 5' Ae-aegypti_ZM5_16-3125_XX_2016-09-09_usa ZM5.c1.MO.a1.l1.l2.r1
ZC188 423568715 Serum **** 98.26 29394.90   2016.01.16     Columbia 36 1.5E+04 coding-complete ZC188_423568715_XX_2016-01-16_colombia ZC188.c1.SR.a1.l3.l4.r1
ZC192 423401315 Serum **** 98.36 30396.29   2016.01.07     Columbia 39 1.7E+04 coding-complete ZC192_423401315_XX_2016-01-07_colombia ZC192.c1.SR.a1.l3.l4.r1
ZC204 424439915 Serum **** 99.74 29003.25   2016.01.06     Columbia 48 2.1E+04 coding-complete ZC204_424439915_XX_2016-01-05_colombia ZC204.c1.SR.a1.l1.l2.r1
ZC207 423217515 Serum **** 96.68 19477.70   2016.01.09     Columbia 16 6.7E+04 coding-complete ZC207_423217515_XX_2016-01-09_colombia ZC207.c1.SR.a1.l1.l2.r1

Quality 

**** Complete coding sequence, no apparent contamination in aligned bam file
*** Complete coding sequence, some contamination in aligned bam file (confident in consensus)
**  Partial coding sequence, no apparent contamination in aligned bam file
*   Partial coding sequence, some contamination in aligned bam file
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 README.md
@@ -7,20 +7,20 @@
    | :--- | :--- | :--- | :--- | :--- | :--- |
    | ZF1 | 001 | Saliva | *** | 99.71 | Martinique |
    | ZF8 | 008 | Urine | *** | 90.07 | Puerto Rico |
    -| ZF10 | 010 | Urine | **** | 97.69 | Cuba |
    +| ZF10 | 010 | Urine | **** | 97.69 | USA |
    | ZF16 | 016 | Urine | *** | 99.88 | Puerto Rico |
    -| ZF21 | 021 | Urine | *** | 97.45 | "Dade County Florida" |
    -| ZF22 | 022 | Urine | *** | 97.77 | "Dade County Florida" |
    -| ZF30 | 030 | Urine | *** | 99.75 | "Dade County Florida" |
    -| ZF32 | 032 | Urine | *** | 99.75 | "Dade County Florida" |
    -| ZF38 | 038 | Urine | *** | 99.76 | Dade |
    -| ZF39 | 039 | Urine | **** | 99.75 | "Pinellas County Florida" |
    -| ZL2 | Hu0015 | Saliva | *** | 99.75 | "Dade County Florida" |
    -| ZM1 | 7501 | Mosquito | **** | 99.75 | "Dade County Florida" |
    -| ZM2 | 7719 | Mosquito | **** | 99.74 | "Dade County Florida" |
    -| ZM3 | 7727 | Mosquito | **** | 99.83 | "Dade County Florida" |
    -| ZM4 | 16-10416 | Mosquito | **** | 99.72 | Dade - Miami Beach |
    -| ZM5 | 16-3125 | Mosquito | ** | 96.63 | Dade - Miami Beach |
    +| ZF21 | 021 | Urine | *** | 97.45 | USA |
    +| ZF22 | 022 | Urine | *** | 97.77 | USA |
    +| ZF30 | 030 | Urine | *** | 99.75 | USA |
    +| ZF32 | 032 | Urine | *** | 99.75 | USA |
    +| ZF38 | 038 | Urine | *** | 99.76 | USA |
    +| ZF39 | 039 | Urine | **** | 99.75 | USA |
    +| ZL2 | Hu0015 | Saliva | *** | 99.75 | USA |
    +| ZM1 | 7501 | Mosquito | **** | 99.75 | USA |
    +| ZM2 | 7719 | Mosquito | **** | 99.74 | USA |
    +| ZM3 | 7727 | Mosquito | **** | 99.83 | USA |
    +| ZM4 | 16-10416 | Mosquito | **** | 99.72 | USA |
    +| ZM5 | 16-3125 | Mosquito | ** | 96.63 | USA |
    | ZC188 | 423568715 | Serum | **** | 98.26 | Columbia |
    | ZC192 | 423401315 | Serum | **** | 98.36 | Columbia |
    | ZC204 | 424439915 | Serum | **** | 99.74 | Columbia |
 

 View
26  consensus_sequences/README.md
@@ -4,20 +4,20 @@
    | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- | :--- |
    | ZF1 | 001 | Saliva | *** | 99.71 | 46616.27 | 2016.03.18 | 2016.03.22 | 4 | Travel | Martinique | 11 | 3.3E+03 | coding-complete | ZF1_01Sa_XX_2016-03-22 usa_ex_martinique | ZF1.c1.Sa.a1.l1.l3.l4.r1 |
    | ZF8 | 008 | Urine | *** | 90.07 | 35012.49 | 2016.06.15 | 2016.06.21 | 6 | Travel | Puerto Rico | 4 | 1.1E+03 | coding-complete | ZF8_08U_XX_2016-06-21 usa_ex_puerto_rico | ZF8.c1.UR.a1.l1.l2.r1 |
    -| ZF10 | 010 | Urine | **** | 97.69 | 55330.48 | 2016.06.17 | 2016.06.22 | 5 | Local? | Cuba | 213 | 6.1E+04 | coding-complete | ZF10_10U_KX842499 2016-06-22 usa_ex_cuba | ZF10.c1.UR.a1.l1.r1 |
    +| ZF10 | 010 | Urine | **** | 97.69 | 55330.48 | 2016.06.17 | 2016.06.22 | 5 | Local? | USA | 213 | 6.1E+04 | coding-complete | ZF10_10U_KX842499 2016-06-22 usa_ex_USA | ZF10.c1.UR.a1.l1.r1 |
    | ZF16 | 016 | Urine | *** | 99.88 | 75158.72 | 2016.06.28 | 2016.07.03 | 5 | Travel | Puerto Rico | 14 | 4.0E+03 | coding-complete | ZF16_16U_XX_2016-07-03 usa_ex_puerto_rico | ZF16.c1.UR.a1.l1.l2.l3.l4.l5.r1 |
    -| ZF21 | 021 | Urine | *** | 97.45 | 52361.36 | 2016.07.09 | 2016.07.19 | 10 | Local | "Dade County Florida" | 50 | 1.4E+04 | coding-complete | ZF21_21U_XX_2016-07-19 usa | ZF21.c1.UR.a1.l1.l2.l3.r1 |
    -| ZF22 | 022 | Urine | *** | 97.77 | 51135.60 | 2016.07.16 | 2016.07.16 | 6 | Local | "Dade County Florida" | 11 | 3.0E+03 | coding-complete | ZF22_22U_XX_2016-07-16 usa | ZF22.c1.UR.a1.l1.l2.l3.l4.r1 |
    -| ZF30 | 030 | Urine | *** | 99.75 | 57779.63 | 2016.07.31 | 2016.08.02 | 2 | Local | "Dade County Florida" | 36 | 1.0E+04 | coding-complete | ZF30_30U_XX_2016-08-02 usa | ZF30.c1.UR.a1.l1.l2.l3.r1 |
    -| ZF32 | 032 | Urine | *** | 99.75 | 51483.94 | 2016.07.29 | 2016.08.05 | 7 | Local | "Dade County Florida" | 75 | 2.1E+04 | coding-complete | ZF32_32U_XX_2016-08-05 usa | ZF32.c1.UR.a1.l1.l2.l3.r1 |
    -| ZF38 | 038 | Urine | *** | 99.76 | 81750.77 | 2016.08.04 | 2016.08.05 | 1 | Local | Dade | 38 | 1.1E+04 | coding-complete | ZF38_38U_XX_2016-08-05 usa | ZF38.c1.UR.a1.l1.l2.l3.l4.r1 |
    -| ZF39 | 039 | Urine | **** | 99.75 | 70253.99 | 2016.08.12 | 2016.08.17 | 5 | Local | "Pinellas County Florida" | 1276 | 3.6E+05 | coding-complete | ZF39_39U_XX_2016-08-17 usa | ZF39.c1.UR.a1.l1.l2.l3.r1 |
    -| ZL2 | Hu0015 | Saliva | *** | 99.75 | 89934.25 | 2016.08.19 | 2016.08.24 | 5 | Local | "Dade County Florida" | 38 | 21610.23 | coding-complete | ZL2_Hu0015_KX832731 2016-08-22 usa | ZL2.c1.SA.a1.l1.l2.r1 |
    -| ZM1 | 7501 | Mosquito | **** | 99.75 | 141038.31 | | 2016.08.22 | | Local | "Dade County Florida" | 4563 | 9.1E+06 | coding-complete | Ae-aegypti_ZM1_7501_KX838904_2016-08-22_usa | ZM1.c1.MO.a1.l1.l2.r1 |
    -| ZM2 | 7719 | Mosquito | **** | 99.74 | 137263.85 | | 2016.08.23 | | Local | "Dade County Florida" | 279 | 5.6E+05 | coding-complete | Ae-aegypti_ZM2_7719_KX838905_2016-08-23_usa | ZM2.c1.MO.a1.l1.l2.r1 |
    -| ZM3 | 7727 | Mosquito | **** | 99.83 | 139787.57 | | 2016.08.23 | | Local | "Dade County Florida" | 22549 | 4.5E+07 | coding-complete | Ae-aegypti_ZM3_7727_KX838906_2016-08-23_usa | ZM3.c1.MO.a1.l1.l2.r1 |
    -| ZM4 | 16-10416 | Mosquito | **** | 99.72 | 45505.39 | | 2016.09.04 | | Local | Dade - Miami Beach | 102 | 4.4E+04 | coding-complete | Ae-aegypti_ZM4_16-10416_XX_2016-09-04_usa | ZM4.c1.MO.a1.l1.l2.r1 |
    -| ZM5 | 16-3125 | Mosquito | ** | 96.63 | 5365.36 | | 2016.09.09 | | Local | Dade - Miami Beach | 447 | 1.9E+05 | missing part of 5' | Ae-aegypti_ZM5_16-3125_XX_2016-09-09_usa | ZM5.c1.MO.a1.l1.l2.r1 |
    +| ZF21 | 021 | Urine | *** | 97.45 | 52361.36 | 2016.07.09 | 2016.07.19 | 10 | Local | USA | 50 | 1.4E+04 | coding-complete | ZF21_21U_XX_2016-07-19 usa | ZF21.c1.UR.a1.l1.l2.l3.r1 |
    +| ZF22 | 022 | Urine | *** | 97.77 | 51135.60 | 2016.07.16 | 2016.07.16 | 6 | Local | USA | 11 | 3.0E+03 | coding-complete | ZF22_22U_XX_2016-07-16 usa | ZF22.c1.UR.a1.l1.l2.l3.l4.r1 |
    +| ZF30 | 030 | Urine | *** | 99.75 | 57779.63 | 2016.07.31 | 2016.08.02 | 2 | Local | USA | 36 | 1.0E+04 | coding-complete | ZF30_30U_XX_2016-08-02 usa | ZF30.c1.UR.a1.l1.l2.l3.r1 |
    +| ZF32 | 032 | Urine | *** | 99.75 | 51483.94 | 2016.07.29 | 2016.08.05 | 7 | Local | USA | 75 | 2.1E+04 | coding-complete | ZF32_32U_XX_2016-08-05 usa | ZF32.c1.UR.a1.l1.l2.l3.r1 |
    +| ZF38 | 038 | Urine | *** | 99.76 | 81750.77 | 2016.08.04 | 2016.08.05 | 1 | Local | USA | 38 | 1.1E+04 | coding-complete | ZF38_38U_XX_2016-08-05 usa | ZF38.c1.UR.a1.l1.l2.l3.l4.r1 |
    +| ZF39 | 039 | Urine | **** | 99.75 | 70253.99 | 2016.08.12 | 2016.08.17 | 5 | Local | USA | 1276 | 3.6E+05 | coding-complete | ZF39_39U_XX_2016-08-17 usa | ZF39.c1.UR.a1.l1.l2.l3.r1 |
    +| ZL2 | Hu0015 | Saliva | *** | 99.75 | 89934.25 | 2016.08.19 | 2016.08.24 | 5 | Local | USA | 38 | 21610.23 | coding-complete | ZL2_Hu0015_KX832731 2016-08-22 usa | ZL2.c1.SA.a1.l1.l2.r1 |
    +| ZM1 | 7501 | Mosquito | **** | 99.75 | 141038.31 | | 2016.08.22 | | Local | USA | 4563 | 9.1E+06 | coding-complete | Ae-aegypti_ZM1_7501_KX838904_2016-08-22_usa | ZM1.c1.MO.a1.l1.l2.r1 |
    +| ZM2 | 7719 | Mosquito | **** | 99.74 | 137263.85 | | 2016.08.23 | | Local | USA | 279 | 5.6E+05 | coding-complete | Ae-aegypti_ZM2_7719_KX838905_2016-08-23_usa | ZM2.c1.MO.a1.l1.l2.r1 |
    +| ZM3 | 7727 | Mosquito | **** | 99.83 | 139787.57 | | 2016.08.23 | | Local | USA | 22549 | 4.5E+07 | coding-complete | Ae-aegypti_ZM3_7727_KX838906_2016-08-23_usa | ZM3.c1.MO.a1.l1.l2.r1 |
    +| ZM4 | 16-10416 | Mosquito | **** | 99.72 | 45505.39 | | 2016.09.04 | | Local | USA | 102 | 4.4E+04 | coding-complete | Ae-aegypti_ZM4_16-10416_XX_2016-09-04_usa | ZM4.c1.MO.a1.l1.l2.r1 |
    +| ZM5 | 16-3125 | Mosquito | ** | 96.63 | 5365.36 | | 2016.09.09 | | Local | USA | 447 | 1.9E+05 | missing part of 5' | Ae-aegypti_ZM5_16-3125_XX_2016-09-09_usa | ZM5.c1.MO.a1.l1.l2.r1 |
    | ZC188 | 423568715 | Serum | **** | 98.26 | 29394.90 | | 2016.01.16 | | | Columbia | 36 | 1.5E+04 | coding-complete | ZC188_423568715_XX_2016-01-16_colombia | ZC188.c1.SR.a1.l3.l4.r1 |
    | ZC192 | 423401315 | Serum | **** | 98.36 | 30396.29 | | 2016.01.07 | | | Columbia | 39 | 1.7E+04 | coding-complete | ZC192_423401315_XX_2016-01-07_colombia | ZC192.c1.SR.a1.l3.l4.r1 |
    | ZC204 | 424439915 | Serum | **** | 99.74 | 29003.25 | | 2016.01.06 | | | Columbia | 48 | 2.1E+04 | coding-complete | ZC204_424439915_XX_2016-01-05_colombia | ZC204.c1.SR.a1.l1.l2.r1 |
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LOCUS       KX922707               10609 bp    RNA     linear   VRL 05-OCT-2016
DEFINITION  Zika virus isolate ZIKV/Homo_sapiens/USA/2016/FL039U polyprotein
            gene, complete cds.
ACCESSION   KX922707
VERSION     KX922707.1  GI:1071930518
DBLINK      BioProject: PRJNA342539
            BioSample: SAMN05853066
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10609)
  AUTHORS   Grubaugh,N., Tan,A., Gangavarupu,K., Oliveira,G.,
            Robles-Sikisaka,R., Cone,M., Kopp,E., Hogan,K., Cannons,A.,
            Michael,S., Isern,S. and Andersen,K.
  TITLE     Zika virus sequences from Florida, USA, 2016
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10609)
  AUTHORS   Grubaugh,N., Tan,A., Gangavarupu,K., Oliveira,G.,
            Robles-Sikisaka,R., Cone,M., Kopp,E., Hogan,K., Cannons,A.,
            Michael,S., Isern,S. and Andersen,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-SEP-2016) Department of Immunology and Microbial
            Science, The Scripps Research Institute, 10550 North Torrey Pines
            Road, IMM-210, La Jolla, CA 92037, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: NovoAlign v. V3.04
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10609
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="ZIKV/Homo_sapiens/USA/2016/FL039U"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="USA: Florida"
                     /collection_date="17-Aug-2016"
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LOCUS       KX922707               10609 bp    RNA     linear   VRL 05-OCT-2016
DEFINITION  Zika virus isolate ZIKV/Homo_sapiens/USA/2016/FL039U polyprotein
            gene, complete cds.
ACCESSION   KX922707
VERSION     KX922707.1  GI:1071930518
DBLINK      BioProject: PRJNA342539
            BioSample: SAMN05853066
KEYWORDS    .
SOURCE      Zika virus
  ORGANISM  Zika virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus.
REFERENCE   1  (bases 1 to 10609)
  AUTHORS   Grubaugh,N., Tan,A., Gangavarupu,K., Oliveira,G.,
            Robles-Sikisaka,R., Cone,M., Kopp,E., Hogan,K., Cannons,A.,
            Michael,S., Isern,S. and Andersen,K.
  TITLE     Zika virus sequences from Florida, USA, 2016
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10609)
  AUTHORS   Grubaugh,N., Tan,A., Gangavarupu,K., Oliveira,G.,
            Robles-Sikisaka,R., Cone,M., Kopp,E., Hogan,K., Cannons,A.,
            Michael,S., Isern,S. and Andersen,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-SEP-2016) Department of Immunology and Microbial
            Science, The Scripps Research Institute, 10550 North Torrey Pines
            Road, IMM-210, La Jolla, CA 92037, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: NovoAlign v. V3.04
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10609
                     /organism="Zika virus"
                     /mol_type="genomic RNA"
                     /isolate="ZIKV/Homo_sapiens/USA/2016/FL039U"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:64320"
                     /country="USA: Florida"
                     /collection_date="17-Aug-2016"
     CDS             81..10352
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="AOS90224.1"
                     /db_xref="GI:1071930519"
                     /translation="MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPI
                     RMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKK
                     RRGADTSVGIVGLLLTTAMAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQI
                     MDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVT
                     LPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKV
                     IYLVMILLIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIE
                     LVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWG
                     NGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET
                     DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWF
                     HDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAE
                     MDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAG
                     TDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVG
                     EKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFG
                     AAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSADVGC
                     SVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAVKQAWEDGICGISSVSR
                     MENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGK
                     SYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLE
                     CDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGI
                     EESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVHVEETCGTR
                     GPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLVRSVVTA
                     GSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDLAKLA
                     ILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLLQT
                     AISALEGDLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGL
                     ATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSE
                     VLTAVGLICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKD
                     AEVTGNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWY
                     VYVKTGKRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMW
                     HVTKGSALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARN
                     IQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAIT
                     QGRREEETPVECFEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAP
                     TRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLY
                     IMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEV
                     PERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKT
                     KHQEWDFVVTTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQR
                     RGRIGRNPNKPGDEYLYGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADK
                     VAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIM
                     EDSVPAEVWTRHGEKRVLKPRWMDARVCSDHAALKSFKEFAAGKRGAAFGVMEALGTL
                     PGHMTERFQEAIDNLAVLMRAETGSRPYKAAAAQLPETLETIMLLGLLGTVSLGIFFV
                     LMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIPEPEKQRSP
                     QDNQMAIIIMVAVGLLGLITANELGWLERTKSDLSHLMGRREEGATIGFSMDIDLRPA
                     SAWAIYAALTTFITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDFGVPL
                     LMIGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIV
                     VTDIDTMTIDPQVEKKMGQVLLIAVAVSSAILSRTAWGWGEAGALITAATSTLWEGSP
                     NKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRRGGGTGETLGEKWKARLNQ
                     MSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPYGK
                     VIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIVRLKSGVDVFH
                     MAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMM
                     ETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRP
                     VKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHG
                     SYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPD
                     PQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAV
                     EAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGA
                     RFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWD
                     TRISRFDLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQ
                     DQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDR
                     LKRMAVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHH
                     FNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRR
                     DLRLMANAICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKT
                     PVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGEEEKYMDYLST
                     QVRYLGEEGSTPGVL"
ORIGIN      
        1 cgacagttcg agtttgaagc gaaagctagc aacagtatca acaggtttta ttttggattt
       61 ggaaacgaga gtttctggtc atgaaaaacc caaaaaagaa atccggagga ttccggattg
      121 tcaatatgct aaaacgcgga gtagcccgtg tgagcccctt tgggggcttg aagaggctgc
      181 cagccggact tctgctgggt catgggccca tcaggatggt cttggcgatt ctagcctttt
      241 tgagattcac ggcaatcaag ccatcactgg gtctcatcaa tagatggggt tcagtgggga
      301 aaaaagaggc tatggaaata ataaagaagt tcaagaaaga tctggctgcc atgctgagaa
      361 taatcaatgc taggaaggag aagaagagac gaggcgcaga tactagtgtc ggaattgttg
      421 gcctcctgct gaccacagct atggcagcgg aggtcactag acgtgggagt gcatactaca
      481 tgtacttgga cagaaacgat gctggggagg ccatatcttt tccaaccaca ttggggatga
      541 ataagtgtta tatacagatc atggatcttg gacacatgtg tgatgccacc atgagctatg
      601 aatgccctat gctggatgag ggggtggaac cagatgacgt cgattgttgg tgcaacacga
      661 cgtcaacttg ggttgtgtac ggaacctgcc atcacaaaaa aggtgaagca cggagatcta
      721 gaagagctgt gacgctcccc tcccattcca ctaggaagct gcaaacgcgg tcgcaaacct
      781 ggttggaatc aagagaatac acaaagcact tgattagagt cgaaaattgg atattcagga
      841 accctggctt cgcgttagca gcagctgcca tcgcttggct tttgggaagc tcaacgagcc
      901 aaaaagtcat atacttggtc atgatactgc tgattgcccc ggcatacagc atcaggtgca
      961 taggagtcag caatagggac tttgtggaag gtatgtcagg tgggacttgg gttgatgttg
     1021 tcttggaaca tggaggttgt gtcaccgtaa tggcacagga caaaccgact gtcgacatag
     1081 agctggttac aacaacagtc agcaacatgg cggaggtaag atcctactgc tatgaggcat
     1141 caatatcaga catggcttcg gacagccgct gcccaacaca aggtgaagcc taccttgaca
     1201 agcaatcaga cactcaatat gtctgcaaaa gaacgttagt ggacagaggc tggggaaatg
     1261 gatgtggact ttttggcaaa gggagcctgg tgacatgcgc taagtttgca tgctccaaga
     1321 aaatgaccgg gaagagcatc cagccagaga atctggagta ccggataatg ctgtcagttc
     1381 atggctccca gcacagtggg atgatcgtta atgacacagg acatgaaact gatgagaata
     1441 gagcgaaggt tgagataacg cccaattcac caagagccga agccaccctg gggggttttg
     1501 gaagcctagg acttgattgt gaaccgagga caggccttga cttttcagat ttgtattact
     1561 tgactatgaa taacaagcac tggttggttc acaaggagtg gttccacgac attccattac
     1621 cttggcacgc tggggcagac accggaactc cacactggaa caacaaagaa gcactggtag
     1681 agttcaagga cgcacatgcc aaaaggcaaa ctgtcgtggt tctagggagt caagaaggag
     1741 cagttcacac ggcccttgct ggagctctgg aggctgagat ggatggtgca aagggaaggc
     1801 tgtcctctgg ccacttgaaa tgtcgcctga aaatggataa acttagattg aagggcgtgt
     1861 catactcctt gtgtaccgca gcgttcacat tcaccaagat cccggctgaa acactgcacg
     1921 ggacagtcac agtggaggta cagtacgcag ggacagatgg accttgcaag gttccagctc
     1981 agatggcggt ggacatgcaa actctgaccc cagttgggag gttgataacc gccaaccccg
     2041 taatcactga aagcactgag aactctaaga tgatgctgga acttgatcca ccatttgggg
     2101 actcttacat tgtcatagga gtcggggaga agaagatcac ccaccactgg cacaggagtg
     2161 gcagcaccat tggaaaagca tttgaagcca ctgtgagagg tgccaagaga atggcagtct
     2221 tgggagacac agcctgggac tttggatcag ttggaggcgc tctcaactca ttgggcaagg
     2281 gcatccatca aatttttgga gcagctttca aatcattgtt tggaggaatg tcctggttct
     2341 cacaaatcct cattggaacg ttgctgatgt ggttgggtct gaacacaaag aatggatcta
     2401 tttccctcat gtgcttggcc ttagggggag tgttgatctt cttatccaca gccgtctctg
     2461 ctgatgtggg gtgctcggtg gacttctcaa agaaggagac gagatgcggt acaggggtgt
     2521 tcgtctataa cgacgttgaa gcctggaggg acaggtacaa gtaccatcct gactcccccc
     2581 gtagattggc agcagcagtc aagcaagcct gggaagatgg tatctgcggg atctcctctg
     2641 tttcaagaat ggaaaacatc atgtggagat cagtagaagg ggagctcaat gcaatcctgg
     2701 aagagaatgg agttcaactg acggtcgttg tgggatctgt aaaaaacccc atgtggagag
     2761 gtccacagag attgcccgtg cctgtgaacg agctgcccca cggctggaag gcttggggga
     2821 aatcgtactt cgttagagca gcaaagacaa ataacagctt tgtcgtggat ggtgacacac
     2881 tgaaggaatg cccactcaaa catagagcat ggaacagctt tcttgtggag gatcatgggt
     2941 tcggggtatt tcacactagt gtctggctca aggttagaga agattattca ttagagtgtg
     3001 atccagccgt tattggaaca gctgttaagg gaaaggaggc tgtacacagt gatctaggct
     3061 actggattga gagtgagaag aatgacacat ggaggctgaa gagggcccat ctgatcgaga
     3121 tgaaaacatg tgaatggcca aagtcccaca cattgtggac agatggaata gaagagagtg
     3181 atctgatcat acccaagtct ttagctgggc cactcagcca ccacaatacc agagagggct
     3241 ataggaccca aatgaaaggg ccatggcaca gtgaagagct tgaaattcgg tttgaggaat
     3301 gcccaggcac taaggtccac gtggaggaaa catgtggaac aagaggacca tctctgagat
     3361 caaccactgc aagcggaagg gtgatcgagg aatggtgctg cagggagtgc acaatgcccc
     3421 cactgtcgtt ccgggctaaa gatggctgtt ggtatggaat ggagataagg cccaggaaag
     3481 aaccagaaag caacttagta aggtcagtgg tgactgcagg atcaactgat cacatggatc
     3541 acttctccct tggagtgctt gtgattctgc tcatggtgca ggaagggctg aagaagagaa
     3601 tgaccacaaa gatcatcata agcacatcaa tggcagtgct ggtagctatg atcctgggag
     3661 gattttcaat gagtgacctg gctaagcttg caattttgat gggtgccacc ttcgcggaaa
     3721 tgaacactgg aggagatgta gctcatctgg cgctgatagc ggcattcaaa gtcagaccag
     3781 cgttgctggt atctttcatc ttcagagcta attggacacc ccgtgaaagc atgctgctgg
     3841 ccttggcctc gtgtcttttg caaactgcga tctccgcctt ggaaggcgac ctgatggttc
     3901 tcatcaatgg ttttgctttg gcctggttgg caatacgagc gatggttgtt ccacgcactg
     3961 ataacatcac cttggcaatc ctggctgctc tgacaccact ggcccggggc acactgcttg
     4021 tggcgtggag agcaggcctt gctacttgcg gggggtttat gctcctctct ctgaagggaa
     4081 aaggcagtgt gaagaagaac ttaccatttg tcatggccct gggactaacc gctgtgaggc
     4141 tggtcgaccc catcaacgtg gtgggactgc tgttgctcac aaggagtggg aagcggagct
     4201 ggccccctag cgaagtactc acagctgttg gcctgatatg cgcattggct ggagggttcg
     4261 ccaaggcaga tatagagatg gctgggccca tggccgcagt cggtctgcta attgtcagtt
     4321 acgtggtctc aggaaagagt gtggacatgt acattgaaag agcaggtgac atcacatggg
     4381 aaaaagatgc ggaagtcact ggaaacagtc cccggctcga tgtggcgcta gatgagagtg
     4441 gtgatttctc cctggtagag gatgacggtc cccccatgag agagatcata ctcaaggtgg
     4501 tcctgatgac catctgtggc atgaacccaa tagccatacc ctttgcagct ggagcgtggt
     4561 acgtatacgt gaagactgga aaaaggagtg gtgctctatg ggatgtgcct gctcccaagg
     4621 aagtaaaaaa gggggagacc acagatggag tgtacagagt aatgactcgt agactgctag
     4681 gttcaacaca agttggagtg ggagttatgc aagagggggt ctttcacact atgtggcacg
     4741 tcacaaaagg atccgcgctg agaagcggtg aagggagact tgatccatac tggggagatg
     4801 tcaagcagga tctggtgtca tactgtggtc catggaagct agatgccgcc tgggacgggc
     4861 acagcgaggt gcagctcttg gccgtgcccc ccggagagag agcgaggaac atccagactc
     4921 tgcccggaat atttaagaca aaggatgggg acattggagc ggttgcgctg gattacccag
     4981 caggaacttc aggatctcca atcctagaca agtgtgggag agtgatagga ctttatggca
     5041 atggggtcgt gatcaaaaat gggagttatg ttagtgccat cacccaaggg aggagggagg
     5101 aagagactcc tgttgagtgc ttcgagcctt cgatgctgaa gaagaagcag ctaactgtct
     5161 tagacttgca tcctggagct gggaaaacca ggagagttct tcctgaaata gtccgtgaag
     5221 ctataaaaac aagactccgt actgtgatct tagctccaac cagggttgtc gctgctgaaa
     5281 tggaggaagc ccttagaggg cttccagtgc gttatatgac aacagcagtc aatgtcaccc
     5341 attctggaac agaaatcgtc gacttaatgt gccatgccac cttcacttca cgtctactac
     5401 agccaatcag agtccccaac tataatctgt atattatgga tgaggcccac ttcacagatc
     5461 cctcaagtat agcagcaaga ggatacattt caacaagggt tgagatgggc gaggcggctg
     5521 ccatcttcat gaccgccacg ccaccaggaa cccgtgacgc atttccggac tccaactcac
     5581 caattatgga caccgaagtg gaagtcccag agagagcctg gagctcaggc tttgattggg
     5641 tgacggatca ctctggaaaa acagtttggt ttgttccaag cgtgaggaac ggcaatgaga
     5701 tcgcagcttg tctgacaaag gctggaaaac gggtcataca gctcagcaga aagacttttg
     5761 agacagagtt ccagaaaaca aaacatcaag agtgggactt tgtcgtgaca accgacattt
     5821 cagagatggg cgccaacttt aaagctgacc gtgtcataga ttccaggaga tgcctaaagc
     5881 cggtcatact tgatggcgag agagtcattc tggctggacc catgcctgtc acacatgcca
     5941 gcgctgccca gaggaggggg cgcataggca ggaatcccaa caaacctgga gatgagtatc
     6001 tgtatggagg tgggtgcgca gagactgacg aagaccatgc acactggctt gaagcaagaa
     6061 tgctccttga caatatttac ctccaagatg gcctcatagc ctcgctctat cgacctgagg
     6121 ccgacaaagt agcagccatt gagggagagt tcaagcttag gacggagcaa aggaagacct
     6181 ttgtggaact catgaaaaga ggagatcttc ctgtttggct ggcctatcag gttgcatctg
     6241 ccggaataac ttacacagat agaagatggt gctttgatgg cacgaccaac aacaccataa
     6301 tggaagacag tgtgccggca gaggtgtgga ccagacacgg agagaaaaga gtgctcaaac
     6361 cgaggtggat ggacgccaga gtttgttcag atcatgcggc cctgaagtca ttcaaggagt
     6421 ttgccgctgg gaaaagagga gcggcttttg gagtgatgga agccctggga acactgccag
     6481 gacacatgac agagagattc caggaagcca ttgacaacct cgctgtgctc atgcgggcag
     6541 agactggaag caggccttac aaagccgcgg cggcccaatt gccggagacc ctagagacca
     6601 ttatgctttt ggggttgctg ggaacagtct cgctgggaat ctttttcgtc ttgatgagga
     6661 acaagggcat agggaagatg ggctttggaa tggtgactct tggggccagc gcatggctca
     6721 tgtggctctc ggaaattgag ccagccagaa ttgcatgtgt cctcattgtt gtgttcctac
     6781 tgctggtggt gctcatacct gagccagaaa agcaaagatc tccccaggac aaccaaatgg
     6841 caatcatcat catggtagca gtaggtcttc tgggcttgat caccgccaat gaactcggat
     6901 ggttggagag aacaaagagt gacctaagcc atctaatggg aaggagagag gagggagcaa
     6961 ccataggatt ctcaatggac attgacctgc ggccagcctc agcttgggcc atctatgctg
     7021 ccttgacaac tttcatcacc ccagccgtcc aacatgcagt gaccacttca tacaacaact
     7081 actccttaat ggcgatggcc acgcaagctg gagtgttgtt tggtatgggc aaagggatgc
     7141 cattctacgc atgggacttt ggagtcccgc tgctaatgat aggttgctac tcacaattaa
     7201 cacccctgac cctaatagtg gccatcattt tgctcgtggc gcactacatg tacttgatcc
     7261 cagggctgca ggcagcagct gcgcgtgctg cccagaagag aacggcagct ggcatcatga
     7321 agaaccctgt tgtggatgga atagtggtga ctgacattga cacaatgaca attgaccccc
     7381 aagtggagaa aaagatggga caggtgctac tcatagcagt agccgtctcc agcgccatac
     7441 tgtcgcggac cgcctggggg tggggggagg ctggggccct gatcacagcc gcaacttcca
     7501 ctttgtggga aggctctccg aacaagtact ggaactcctc tacagccact tcactgtgta
     7561 acatttttag gggaagttac ttggctggag cttctctaat ctacacagta acaagaaacg
     7621 ctggcttggt caagagacgt gggggtggaa caggagagac cctgggagag aaatggaagg
     7681 cccgcttgaa ccagatgtcg gccctggagt tctactccta caaaaagtca ggcatcaccg
     7741 aggtgtgcag agaagaggcc cgccgcgccc tcaaggacgg tgtggcaacg ggaggccatg
     7801 ctgtgtcccg aggaagtgca aagctgagat ggttggtgga gcggggatac ctgcagccct
     7861 atggaaaggt cattgatctt ggatgtggca gagggggctg gagttactac gccgccacca
     7921 tccgcaaagt tcaagaagtg aaaggataca caaaaggagg ccctggtcat gaagaacccg
     7981 tgttggtgca aagctatggg tggaacatag tccgtctcaa gagtggggtg gacgtctttc
     8041 atatggcggc tgagccgtgt gacacgttgc tgtgtgacat aggcgagtca tcatctagtc
     8101 ctgaagtcga agaagcacgg acgctcagag tcctctccat ggtgggggat tggcttgaaa
     8161 aaagaccagg agccttttgt ataaaagtgt tgtgcccata caccagcact atgatggaaa
     8221 ccctggagcg actgcagcgt aggtatgggg gaggactggt cagagtgcca ctctcccgca
     8281 actctacaca tgagatgtac tgggtttctg gagcgaaaag caacaccata aaaagtgtgt
     8341 ccaccacgag ccagctcctc ttggggcgca tggacgggcc taggaggcca gtgaaatatg
     8401 aggaggatgt gaatctcggc tctggcacgc gggctgtggt aagctgcgct gaagctccca
     8461 acatgaagat cattggtaac cgcattgaaa ggatccgcag tgagcacgcg gaaacgtggt
     8521 tctttgacga gaaccaccca tataggacat gggcttacca tggaagctat gaggccccca
     8581 cacaagggtc agcatcctct ctagtaaacg gggttgtcag gctcctgtca aaaccctggg
     8641 atgtggtgac tggagtcaca ggaatagcca tgaccgacac cacaccgtat ggtcagcaaa
     8701 gagttttcaa ggaaaaagtg gacactaggg tgccagaccc ccaagaaggc actcgtcagg
     8761 ttatgagcat ggtctcttcc tggttgtgga aagagctagg caaacacaaa cggccacgag
     8821 tctgtaccaa agaagagttc atcaacaagg ttcgtagcaa tgcagcatta ggggcaatat
     8881 ttgaagagga aaaagagtgg aagactgcag tggaagctgt gaacgatcca aggttctggg
     8941 ctctagtgga caaggaaaga gagcaccacc tgagaggaga gtgccagagt tgtgtgtaca
     9001 acatgatggg aaaaagagaa aagaaacaag gggaatttgg aaaggccaag ggcagccgcg
     9061 ccatctggta tatgtggcta ggggctagat ttctagagtt cgaagccctt ggattcttga
     9121 acgaggatca ctggatgggg agagagaact caggaggtgg tgttgaaggg ctgggattac
     9181 aaagactcgg atatgtccta gaagagatga gtcgcatacc aggaggaagg atgtatgcag
     9241 atgacactgc tggctgggat acccgcatca gcaggtttga tctagagaat gaagctctaa
     9301 tcaccaacca aatggagaaa gggcacaggg ccttggcatt ggccataatc aagtacacat
     9361 accaaaacaa agtggtaaag gtccttagac cagctgaaaa agggaaaaca gttatggaca
     9421 ttatttcgag acaagaccaa agggggagcg gacaagtcgt cacttacgct cttaacacat
     9481 ttaccaacct agtggtgcaa ctcattcgga atatggaggc tgaggaagtt ctagagatgc
     9541 aagacttgtg gctgctgcgg aggtcagaga aagtgaccaa ctggttgcag agcaacggat
     9601 gggataggct caaacgaatg gcagtcagtg gagatgattg cgttgtgaag ccaattgatg
     9661 ataggtttgc acatgccctc aggttcttga atgatatggg aaaagttagg aaggacacac
     9721 aagagtggaa accctcaact ggatgggaca actgggaaga agttccgttt tgctcccacc
     9781 acttcaacaa gctccatctc aaggacggga ggtccattgt ggttccctgc cgccaccaag
     9841 atgaactgat tggccgggcc cgcgtctctc caggggcggg atggagcatc cgggagactg
     9901 cttgcctagc aaaatcatat gcgcaaatgt ggcagctcct ttatttccac agaagggacc
     9961 tccgactgat ggccaatgcc atttgttcat ctgtgccagt tgactgggtt ccaactggga
    10021 gaactacctg gtcaatccat ggaaagggag aatggatgac cactgaagac atgcttgtgg
    10081 tgtggaacag agtgtggatt gaggagaacg accacatgga agacaagacc ccagttacga
    10141 aatggacaga cattccctat ttgggaaaaa gggaagactt gtggtgtgga tctctcatag
    10201 ggcacagacc gcgcaccacc tgggctgaga acattaaaaa cacagtcaac atggtgcgca
    10261 ggatcatagg tgaggaagaa aagtacatgg actacctatc cacccaagtt cgctacttgg
    10321 gtgaagaagg gtctacacct ggagtgctgt aagcaccaat cttaatgttg tcaggcctgc
    10381 tagtcagcca cagcttgggg aaagctgtgc agcctgtgac ccccccagga gaagctggga
    10441 aaccaagcct atagtcaggc cgagaacgcc atggcacgga agaagccatg ctgcctgtga
    10501 gcccctcaga ggacactgag tcaaaaaacc ccacgcgctt ggaggcgcag gatgggaaaa
    10561 gaaggtggcg accttcccca cccttcaatc tggggcctga actggagat
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niman Grand Master

niman

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Sequences producing significant alignments:

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Sequences producing significant alignments:
Select for downloading or viewing reports Description Max score Total score Query cover E value Ident Accession
Zika virus isolate Dominican Republic/2016/PD2, complete genome
18465 18465 100% 0.0 99% KU853013.1
Zika virus isolate Dominican Republic/2016/PD1, complete genome
18465 18465 100% 0.0 99% KU853012.1
Zika virus isolate ZIKV/Human/USA/2016/ZF10.UR-010 polyprotein gene, complete cds
18429 18429 100% 0.0 99% KX842449.1
Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM2-7719 polyprotein gene, complete cds
18426 18426 100% 0.0 99% KX838905.1
Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM1-7501 polyprotein gene, complete cds
18420 18420 100% 0.0 99% KX838904.1
Zika virus isolate ZIKV/Human/USA/2016/ZL2.SA-Hu0015 polyprotein gene, complete cds
18420 18420 100% 0.0 99% KX832731.1
Zika virus isolate PHE_semen_Guadeloupe, complete genome
18417 18417 100% 0.0 99% KX673530.1
Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM3-7729 polyprotein gene, complete cds
18408 18408 100% 0.0 99% KX838906.1
Zika virus isolate 1_0049_PF polyprotein gene, complete cds
18357 18357 100% 0.0 99% KX447510.1
Zika virus isolate Paraiba_01, complete genome
18354 18354 100% 0.0 99% KX280026.1
Zika virus isolate 1_0181_PF polyprotein gene, complete cds
18348 18348 100% 0.0 99% KX447512.1
Zika virus strain PF13/251013-18, complete genome
18348 18348 100% 0.0 99% KX369547.1
Zika virus strain Haiti/1225/2014, complete genome
18348 18348 100% 0.0 99% KU509998.3
Zika virus strain H/PF/2013, complete genome
18345 18345 100% 0.0 99% KJ776791.2
Zika virus isolate 1_0087_PF polyprotein gene, complete cds
18345 18345 100% 0.0 99% KX447509.1
Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds
18345 18345 100% 0.0 99% KU991811.1
Zika virus isolate BeH823339 polyprotein gene, complete cds
18345 18345 100% 0.0 99% KU729217.2
Zika virus isolate 1_0134_PF polyprotein gene, complete cds
18339 18339 100% 0.0 99% KX447513.1
Zika virus isolate Brazil_2015_MG, complete genome
18336 18336 100% 0.0 99% KX811222.1
Zika virus isolate 9, complete genome
18336 18336 100% 0.0 99% KX197205.1
Zika virus isolate 1_0030_PF polyprotein gene, complete cds
18336 18336 100% 0.0 99% KX447515.1
Zika virus isolate 1_0015_PF polyprotein gene, complete cds
18336 18336 100% 0.0 99% KX447511.1
Zika virus strain ZikaSPH2015, complete genome
18336 18336 100% 0.0 99% KU321639.1
Zika virus isolate SN089, complete genome
18330 18330 100% 0.0 99% KX879604.1
Zika virus isolate 1_0035_PF polyprotein gene, complete cds
18330 18330 100% 0.0 99% KX447514.1
Zika virus isolate Haiti/1/2016, complete genome
18330 18330 100% 0.0 99% KX051563.1
Zika virus isolate 1_0111_PF polyprotein gene, complete cds
18327 18327 100% 0.0 99% KX447516.1
Zika virus isolate BeH828305 polyprotein gene, complete cds
18327 18327 100% 0.0 99% KU729218.1
Zika virus isolate SSABR1, complete genome
18327 18327 100% 0.0 99% KU707826.1
Zika virus strain Natal RGN, complete genome
18327 18327 100% 0.0 99% KU527068.1
Zika virus strain BeH819966 polyprotein gene, complete cds
18327 18327 100% 0.0 99% KU365779.1
Zika virus isolate SN062, complete genome
18321 18321 100% 0.0 99% KX879603.1
Zika virus isolate 103451, complete genome
18321 18321 100% 0.0 99% KX262887.1
Zika virus isolate ZIKV/H.sapiens/Brazil/PE243/2015, complete genome
18321 18321 100% 0.0 99% KX197192.1
Zika virus isolate Rio-S1, complete genome
18321 18321 100% 0.0 99% KU926310.1
Zika virus isolate Rio-U1, complete genome
18321 18321 100% 0.0 99% KU926309.1
Zika virus strain 8375 polyprotein gene, complete cds
18321 18321 100% 0.0 99% KU501217.1
Zika virus isolate Bahia07, partial genome
18318 18318 100% 0.0 99% KU940228.1
Zika virus strain 103344 polyprotein gene, complete cds
18318 18318 100% 0.0 99% KU501216.1
Zika virus strain ZIKV/Homo sapiens/HND/R103451/2015, complete genome
18312 18312 100% 0.0 99% KX694534.1
Zika virus strain ZIKV/Homo sapiens/PAN/BEI-259634_V4/2016, complete genome
18312 18312 100% 0.0 99% KX198135.1
Zika virus strain BeH815744 polyprotein gene, complete cds
18312 18312 100% 0.0 99% KU365780.1
Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds
18309 18309 100% 0.0 99% KU647676.1
Zika virus strain BeH818995 polyprotein gene, complete cds
18309 18309 100% 0.0 99% KU365777.1
Zika virus isolate 1_0038_PF polyprotein gene, complete cds
18303 18303 100% 0.0 99% KX447517.1
Zika virus isolate 17271 polyprotein gene, complete cds
18303 18303 100% 0.0 99% KU758877.1
Zika virus isolate Zika virus/Homo sapiens/COL/UF-1/2016, complete genome
18303 18303 100% 0.0 99% KX247646.1
Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259364_V1-V2/2015, complete genome
18303 18303 100% 0.0 99% KX156776.1
Zika virus isolate HS-2015-BA-01 polyprotein gene, complete cds
18300 18300 100% 0.0 99% KX520666.1
Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259359_V1-V3/2015, complete genome
18300 18300 100% 0.0 99% KX156774.1
Zika virus isolate Brazil-ZKV2015, complete genome
18300 18300 99% 0.0 99% KU497555.1
Zika virus isolate FLR polyprotein gene, complete cds
18294 18294 100% 0.0 99% KU820897.5
Zika virus isolate MEX_I_7 polyprotein gene, complete cds
18294 18294 100% 0.0 99% KX247632.1
Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259249_V1-V3/2015, complete genome
18294 18294 100% 0.0 99% KX156775.1
Zika virus strain ZIKV/Homo sapiens/COL/FLR/2015, complete genome
18294 18294 100% 0.0 99% KX087102.1
Zika virus strain BeH819015 polyprotein gene, complete cds
18294 18294 100% 0.0 99% KU365778.1
Zika virus isolate Z1106033 polyprotein gene, complete cds
18294 18294 100% 0.0 99% KU312312.1
Zika virus isolate MEX/InDRE/Sm/2016, complete genome
18291 18291 100% 0.0 99% KU922960.1
Zika virus strain ZIKV/Aedes sp./MEX_I-44/2016, complete genome
18285 18285 100% 0.0 99% KX856011.1
Zika virus isolate TS17-2016, complete genome
18285 18285 100% 0.0 99% KX806557.1
Zika virus isolate ZIKV/COL/FCC00093/2015 polyprotein gene, complete cds
18285 18285 100% 0.0 99% KX548902.1
Zika virus strain ZIKV/Aedes.sp/MEX/MEX_I-7/2016, complete genome
18285 18285 100% 0.0 99% KX446951.1
Zika virus isolate ZIKVNL00013 polyprotein gene, complete cds
18285 18285 100% 0.0 99% KU937936.1
Zika virus isolate MEX/InDRE/Lm/2016, complete genome
18285 18285 100% 0.0 99% KU922923.1
Zika virus strain PRVABC59, complete genome
18285 18285 100% 0.0 99% KU501215.1
Zika virus strain ZIKV/Homo Sapiens/PRI/PRVABC59/2015, complete genome
18282 18282 100% 0.0 99% KX601168.1
Zika virus strain ZIKV/Aedes.sp/MEX/MEX_2-81/2016, complete genome
18282 18282 100% 0.0 99% KX446950.1
Zika virus strain ZIKV/Homo sapiens/PRI/PRVABC59/2015, complete genome
18282 18282 100% 0.0 99% KX087101.2
Zika virus isolate FB-GWUH-2016, complete genome
18282 18282 100% 0.0 99% KU870645.1
Zika virus strain Zika virus/Homo sapiens/VEN/UF-1/2016, complete genome
18276 18276 100% 0.0 99% KX702400.1
Zika virus strain PRVABC-59, complete genome
18276 18276 100% 0.0 99% KX377337.1
Zika virus isolate R116265, complete genome
18267 18267 100% 0.0 99% KX766029.1
Zika virus isolate GZ01 polyprotein gene, complete cds
18267 18267 100% 0.0 99% KU820898.1
Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds
18264 18264 100% 0.0 99% KX056898.1
Zika virus isolate Z16019 polyprotein gene, complete cds
18264 18264 100% 0.0 99% KU955590.1
Zika virus isolate R114916, complete genome
18260 18260 100% 0.0 99% KX766028.1
Zika virus isolate GD01 polyprotein gene, complete cds
18258 18258 100% 0.0 99% KU740184.2
Zika virus isolate GDZ16001 polyprotein gene, complete cds
18258 18258 100% 0.0 99% KU761564.1
Zika virus isolate Zhejiang04, complete genome
18254 18254 100% 0.0 99% KX117076.1
Zika virus isolate Zika virus/CN/SZ02/2016 polyprotein gene, complete cds
18245 18245 100% 0.0 99% KX185891.1
Zika virus isolate SZ-WIV01 polyprotein gene, complete cds
18245 18245 100% 0.0 99% KU963796.1
Zika virus isolate ZKC2/2016, complete genome
18240 18240 100% 0.0 99% KX253996.1
Zika virus isolate Z16006 polyprotein gene, complete cds
18240 18240 100% 0.0 99% KU955589.1
Zika virus isolate ZJ03, complete genome
18240 18240 100% 0.0 99% KU820899.2
Zika virus isolate ZIKV_SMGC-1, complete genome
18236 18236 100% 0.0 99% KX266255.1
Zika virus isolate Zika virus/SZ01/2016/China polyprotein gene, complete cds
18236 18236 100% 0.0 99% KU866423.2
Zika virus isolate Bahia09, partial genome
18222 18222 99% 0.0 99% KU940224.1
Zika virus isolate VE_Ganxian, complete genome
18101 18101 100% 0.0 99% KU744693.1
Zika virus isolate ZKA-16-291 polyprotein gene, complete cds
18078 18078 100% 0.0 99% KX827309.1
Zika virus isolate ZKA-16-097 polyprotein gene, complete cds
18065 18065 100% 0.0 99% KX813683.1
Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome
18011 18011 100% 0.0 99% KU681081.3
Zika virus strain ZIKV/Homo sapiens/THA/PLCal_ZV/2013, complete genome
17897 17897 100% 0.0 99% KX694532.1
Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome
17704 17704 100% 0.0 98% KU955593.1
Zika virus isolate FSS13025 polyprotein gene, partial cds
17703 17703 99% 0.0 98% JN860885.1
Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds
17667 17667 98% 0.0 99% KF993678.1
Zika virus polyprotein gene, complete cds
17558 17558 100% 0.0 98% EU545988.1
Zika virus isolate Zika virus/H.sapiens-tc/PHL/2012/CPC-0740, complete genome
17411 17411 100% 0.0 98% KU681082.3
Zika virus strain ZIKV/Aedes sp./MYS/P6-740/1966, complete genome
16401 16401 100% 0.0 95% KX601167.1
Zika virus isolate P6-740 polyprotein gene, partial cds
16393 16393 99% 0.0 95% HQ234499.1
Zika virus strain ZIKV/Aedes aegypti/MYS/P6-740/1966, complete genome
16392 16392 100% 0.0 95% KX694533.1
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