niman Posted October 2, 2016 Report Share Posted October 2, 2016 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. Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 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 Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 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 Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 ENV Phylo Tree Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 Annotated full tree Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 mp3 describing above http://recombinomics.co/thedrnimanshow/2016/10/100216.mp3 Link to comment Share on other sites More sharing options...
niman Posted October 2, 2016 Author Report Share Posted October 2, 2016 ENV Tree Link to comment Share on other sites More sharing options...
niman Posted October 4, 2016 Author Report Share Posted October 4, 2016 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 | Link to comment Share on other sites More sharing options...
niman Posted October 7, 2016 Author Report Share Posted October 7, 2016 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" Link to comment Share on other sites More sharing options...
niman Posted October 7, 2016 Author Report Share Posted October 7, 2016 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 Link to comment Share on other sites More sharing options...
niman Posted October 7, 2016 Author Report Share Posted October 7, 2016 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|KU853013.1| Zika virus isolate Dominican Republic/2016/PD2, complete genome 18465 18465 100% 0.0 99% KU853013.1 Select seq gb|KU853012.1| Zika virus isolate Dominican Republic/2016/PD1, complete genome 18465 18465 100% 0.0 99% KU853012.1 Select seq gb|KX842449.1| Zika virus isolate ZIKV/Human/USA/2016/ZF10.UR-010 polyprotein gene, complete cds 18429 18429 100% 0.0 99% KX842449.1 Select seq gb|KX838905.1| Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM2-7719 polyprotein gene, complete cds 18426 18426 100% 0.0 99% KX838905.1 Select seq gb|KX838904.1| Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM1-7501 polyprotein gene, complete cds 18420 18420 100% 0.0 99% KX838904.1 Select seq gb|KX832731.1| Zika virus isolate ZIKV/Human/USA/2016/ZL2.SA-Hu0015 polyprotein gene, complete cds 18420 18420 100% 0.0 99% KX832731.1 Select seq gb|KX673530.1| Zika virus isolate PHE_semen_Guadeloupe, complete genome 18417 18417 100% 0.0 99% KX673530.1 Select seq gb|KX838906.1| Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM3-7729 polyprotein gene, complete cds 18408 18408 100% 0.0 99% KX838906.1 Select seq gb|KX447510.1| Zika virus isolate 1_0049_PF polyprotein gene, complete cds 18357 18357 100% 0.0 99% KX447510.1 Select seq gb|KX280026.1| Zika virus isolate Paraiba_01, complete genome 18354 18354 100% 0.0 99% KX280026.1 Select seq gb|KX447512.1| Zika virus isolate 1_0181_PF polyprotein gene, complete cds 18348 18348 100% 0.0 99% KX447512.1 Select seq gb|KX369547.1| Zika virus strain PF13/251013-18, complete genome 18348 18348 100% 0.0 99% KX369547.1 Select seq gb|KU509998.3| Zika virus strain Haiti/1225/2014, complete genome 18348 18348 100% 0.0 99% KU509998.3 Select seq gb|KJ776791.2| Zika virus strain H/PF/2013, complete genome 18345 18345 100% 0.0 99% KJ776791.2 Select seq gb|KX447509.1| Zika virus isolate 1_0087_PF polyprotein gene, complete cds 18345 18345 100% 0.0 99% KX447509.1 Select seq gb|KU991811.1| Zika virus isolate Brazil/2016/INMI1 polyprotein gene, complete cds 18345 18345 100% 0.0 99% KU991811.1 Select seq gb|KU729217.2| Zika virus isolate BeH823339 polyprotein gene, complete cds 18345 18345 100% 0.0 99% KU729217.2 Select seq gb|KX447513.1| Zika virus isolate 1_0134_PF polyprotein gene, complete cds 18339 18339 100% 0.0 99% KX447513.1 Select seq gb|KX811222.1| Zika virus isolate Brazil_2015_MG, complete genome 18336 18336 100% 0.0 99% KX811222.1 Select seq gb|KX197205.1| Zika virus isolate 9, complete genome 18336 18336 100% 0.0 99% KX197205.1 Select seq gb|KX447515.1| Zika virus isolate 1_0030_PF polyprotein gene, complete cds 18336 18336 100% 0.0 99% KX447515.1 Select seq gb|KX447511.1| Zika virus isolate 1_0015_PF polyprotein gene, complete cds 18336 18336 100% 0.0 99% KX447511.1 Select seq gb|KU321639.1| Zika virus strain ZikaSPH2015, complete genome 18336 18336 100% 0.0 99% KU321639.1 Select seq gb|KX879604.1| Zika virus isolate SN089, complete genome 18330 18330 100% 0.0 99% KX879604.1 Select seq gb|KX447514.1| Zika virus isolate 1_0035_PF polyprotein gene, complete cds 18330 18330 100% 0.0 99% KX447514.1 Select seq gb|KX051563.1| Zika virus isolate Haiti/1/2016, complete genome 18330 18330 100% 0.0 99% KX051563.1 Select seq gb|KX447516.1| Zika virus isolate 1_0111_PF polyprotein gene, complete cds 18327 18327 100% 0.0 99% KX447516.1 Select seq gb|KU729218.1| Zika virus isolate BeH828305 polyprotein gene, complete cds 18327 18327 100% 0.0 99% KU729218.1 Select seq gb|KU707826.1| Zika virus isolate SSABR1, complete genome 18327 18327 100% 0.0 99% KU707826.1 Select seq gb|KU527068.1| Zika virus strain Natal RGN, complete genome 18327 18327 100% 0.0 99% KU527068.1 Select seq gb|KU365779.1| Zika virus strain BeH819966 polyprotein gene, complete cds 18327 18327 100% 0.0 99% KU365779.1 Select seq gb|KX879603.1| Zika virus isolate SN062, complete genome 18321 18321 100% 0.0 99% KX879603.1 Select seq gb|KX262887.1| Zika virus isolate 103451, complete genome 18321 18321 100% 0.0 99% KX262887.1 Select seq gb|KX197192.1| Zika virus isolate ZIKV/H.sapiens/Brazil/PE243/2015, complete genome 18321 18321 100% 0.0 99% KX197192.1 Select seq gb|KU926310.1| Zika virus isolate Rio-S1, complete genome 18321 18321 100% 0.0 99% KU926310.1 Select seq gb|KU926309.1| Zika virus isolate Rio-U1, complete genome 18321 18321 100% 0.0 99% KU926309.1 Select seq gb|KU501217.1| Zika virus strain 8375 polyprotein gene, complete cds 18321 18321 100% 0.0 99% KU501217.1 Select seq gb|KU940228.1| Zika virus isolate Bahia07, partial genome 18318 18318 100% 0.0 99% KU940228.1 Select seq gb|KU501216.1| Zika virus strain 103344 polyprotein gene, complete cds 18318 18318 100% 0.0 99% KU501216.1 Select seq gb|KX694534.1| Zika virus strain ZIKV/Homo sapiens/HND/R103451/2015, complete genome 18312 18312 100% 0.0 99% KX694534.1 Select seq gb|KX198135.1| Zika virus strain ZIKV/Homo sapiens/PAN/BEI-259634_V4/2016, complete genome 18312 18312 100% 0.0 99% KX198135.1 Select seq gb|KU365780.1| Zika virus strain BeH815744 polyprotein gene, complete cds 18312 18312 100% 0.0 99% KU365780.1 Select seq gb|KU647676.1| Zika virus strain MRS_OPY_Martinique_PaRi_2015 polyprotein gene, complete cds 18309 18309 100% 0.0 99% KU647676.1 Select seq gb|KU365777.1| Zika virus strain BeH818995 polyprotein gene, complete cds 18309 18309 100% 0.0 99% KU365777.1 Select seq gb|KX447517.1| Zika virus isolate 1_0038_PF polyprotein gene, complete cds 18303 18303 100% 0.0 99% KX447517.1 Select seq gb|KU758877.1| Zika virus isolate 17271 polyprotein gene, complete cds 18303 18303 100% 0.0 99% KU758877.1 Select seq gb|KX247646.1| Zika virus isolate Zika virus/Homo sapiens/COL/UF-1/2016, complete genome 18303 18303 100% 0.0 99% KX247646.1 Select seq gb|KX156776.1| Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259364_V1-V2/2015, complete genome 18303 18303 100% 0.0 99% KX156776.1 Select seq gb|KX520666.1| Zika virus isolate HS-2015-BA-01 polyprotein gene, complete cds 18300 18300 100% 0.0 99% KX520666.1 Select seq gb|KX156774.1| Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259359_V1-V3/2015, complete genome 18300 18300 100% 0.0 99% KX156774.1 Select seq gb|KU497555.1| Zika virus isolate Brazil-ZKV2015, complete genome 18300 18300 99% 0.0 99% KU497555.1 Select seq gb|KU820897.5| Zika virus isolate FLR polyprotein gene, complete cds 18294 18294 100% 0.0 99% KU820897.5 Select seq gb|KX247632.1| Zika virus isolate MEX_I_7 polyprotein gene, complete cds 18294 18294 100% 0.0 99% KX247632.1 Select seq gb|KX156775.1| Zika virus strain ZIKV/Homo sapiens/PAN/CDC-259249_V1-V3/2015, complete genome 18294 18294 100% 0.0 99% KX156775.1 Select seq gb|KX087102.1| Zika virus strain ZIKV/Homo sapiens/COL/FLR/2015, complete genome 18294 18294 100% 0.0 99% KX087102.1 Select seq gb|KU365778.1| Zika virus strain BeH819015 polyprotein gene, complete cds 18294 18294 100% 0.0 99% KU365778.1 Select seq gb|KU312312.1| Zika virus isolate Z1106033 polyprotein gene, complete cds 18294 18294 100% 0.0 99% KU312312.1 Select seq gb|KU922960.1| Zika virus isolate MEX/InDRE/Sm/2016, complete genome 18291 18291 100% 0.0 99% KU922960.1 Select seq gb|KX856011.1| Zika virus strain ZIKV/Aedes sp./MEX_I-44/2016, complete genome 18285 18285 100% 0.0 99% KX856011.1 Select seq gb|KX806557.1| Zika virus isolate TS17-2016, complete genome 18285 18285 100% 0.0 99% KX806557.1 Select seq gb|KX548902.1| Zika virus isolate ZIKV/COL/FCC00093/2015 polyprotein gene, complete cds 18285 18285 100% 0.0 99% KX548902.1 Select seq gb|KX446951.1| Zika virus strain ZIKV/Aedes.sp/MEX/MEX_I-7/2016, complete genome 18285 18285 100% 0.0 99% KX446951.1 Select seq gb|KU937936.1| Zika virus isolate ZIKVNL00013 polyprotein gene, complete cds 18285 18285 100% 0.0 99% KU937936.1 Select seq gb|KU922923.1| Zika virus isolate MEX/InDRE/Lm/2016, complete genome 18285 18285 100% 0.0 99% KU922923.1 Select seq gb|KU501215.1| Zika virus strain PRVABC59, complete genome 18285 18285 100% 0.0 99% KU501215.1 Select seq gb|KX601168.1| Zika virus strain ZIKV/Homo Sapiens/PRI/PRVABC59/2015, complete genome 18282 18282 100% 0.0 99% KX601168.1 Select seq gb|KX446950.1| Zika virus strain ZIKV/Aedes.sp/MEX/MEX_2-81/2016, complete genome 18282 18282 100% 0.0 99% KX446950.1 Select seq gb|KX087101.2| Zika virus strain ZIKV/Homo sapiens/PRI/PRVABC59/2015, complete genome 18282 18282 100% 0.0 99% KX087101.2 Select seq gb|KU870645.1| Zika virus isolate FB-GWUH-2016, complete genome 18282 18282 100% 0.0 99% KU870645.1 Select seq gb|KX702400.1| Zika virus strain Zika virus/Homo sapiens/VEN/UF-1/2016, complete genome 18276 18276 100% 0.0 99% KX702400.1 Select seq gb|KX377337.1| Zika virus strain PRVABC-59, complete genome 18276 18276 100% 0.0 99% KX377337.1 Select seq gb|KX766029.1| Zika virus isolate R116265, complete genome 18267 18267 100% 0.0 99% KX766029.1 Select seq gb|KU820898.1| Zika virus isolate GZ01 polyprotein gene, complete cds 18267 18267 100% 0.0 99% KU820898.1 Select seq gb|KX056898.1| Zika virus isolate Zika virus/GZ02/2016 polyprotein gene, complete cds 18264 18264 100% 0.0 99% KX056898.1 Select seq gb|KU955590.1| Zika virus isolate Z16019 polyprotein gene, complete cds 18264 18264 100% 0.0 99% KU955590.1 Select seq gb|KX766028.1| Zika virus isolate R114916, complete genome 18260 18260 100% 0.0 99% KX766028.1 Select seq gb|KU740184.2| Zika virus isolate GD01 polyprotein gene, complete cds 18258 18258 100% 0.0 99% KU740184.2 Select seq gb|KU761564.1| Zika virus isolate GDZ16001 polyprotein gene, complete cds 18258 18258 100% 0.0 99% KU761564.1 Select seq gb|KX117076.1| Zika virus isolate Zhejiang04, complete genome 18254 18254 100% 0.0 99% KX117076.1 Select seq gb|KX185891.1| Zika virus isolate Zika virus/CN/SZ02/2016 polyprotein gene, complete cds 18245 18245 100% 0.0 99% KX185891.1 Select seq gb|KU963796.1| Zika virus isolate SZ-WIV01 polyprotein gene, complete cds 18245 18245 100% 0.0 99% KU963796.1 Select seq gb|KX253996.1| Zika virus isolate ZKC2/2016, complete genome 18240 18240 100% 0.0 99% KX253996.1 Select seq gb|KU955589.1| Zika virus isolate Z16006 polyprotein gene, complete cds 18240 18240 100% 0.0 99% KU955589.1 Select seq gb|KU820899.2| Zika virus isolate ZJ03, complete genome 18240 18240 100% 0.0 99% KU820899.2 Select seq gb|KX266255.1| Zika virus isolate ZIKV_SMGC-1, complete genome 18236 18236 100% 0.0 99% KX266255.1 Select seq gb|KU866423.2| Zika virus isolate Zika virus/SZ01/2016/China polyprotein gene, complete cds 18236 18236 100% 0.0 99% KU866423.2 Select seq gb|KU940224.1| Zika virus isolate Bahia09, partial genome 18222 18222 99% 0.0 99% KU940224.1 Select seq gb|KU744693.1| Zika virus isolate VE_Ganxian, complete genome 18101 18101 100% 0.0 99% KU744693.1 Select seq gb|KX827309.1| Zika virus isolate ZKA-16-291 polyprotein gene, complete cds 18078 18078 100% 0.0 99% KX827309.1 Select seq gb|KX813683.1| Zika virus isolate ZKA-16-097 polyprotein gene, complete cds 18065 18065 100% 0.0 99% KX813683.1 Select seq gb|KU681081.3| Zika virus isolate Zika virus/H.sapiens-tc/THA/2014/SV0127- 14, complete genome 18011 18011 100% 0.0 99% KU681081.3 Select seq gb|KX694532.1| Zika virus strain ZIKV/Homo sapiens/THA/PLCal_ZV/2013, complete genome 17897 17897 100% 0.0 99% KX694532.1 Select seq gb|KU955593.1| Zika virus isolate Zika virus/H.sapiens-tc/KHM/2010/FSS13025, complete genome 17704 17704 100% 0.0 98% KU955593.1 Select seq gb|JN860885.1| Zika virus isolate FSS13025 polyprotein gene, partial cds 17703 17703 99% 0.0 98% JN860885.1 Select seq gb|KF993678.1| Zika virus strain PLCal_ZV from Canada polyprotein gene, partial cds 17667 17667 98% 0.0 99% KF993678.1 Select seq gb|EU545988.1| Zika virus polyprotein gene, complete cds 17558 17558 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 17411 17411 100% 0.0 98% KU681082.3 Select seq gb|KX601167.1| Zika virus strain ZIKV/Aedes sp./MYS/P6-740/1966, complete genome 16401 16401 100% 0.0 95% KX601167.1 Select seq gb|HQ234499.1| Zika virus isolate P6-740 polyprotein gene, partial cds 16393 16393 99% 0.0 95% HQ234499.1 Select seq gb|KX694533.1| Zika virus strain ZIKV/Aedes aegypti/MYS/P6-740/1966, complete genome 16392 16392 100% 0.0 95% KX694533.1 Link to comment Share on other sites More sharing options...
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