niman Posted September 17, 2016 Report Posted September 17, 2016 Scripps Clinic has recently released 5 Zika sequences from Miami Beach. Three were from the first 3 batches of mosquitoes from Miami Beach and the characterization sheets give collection dates and number of mosquitoes in each batch. The other two sequences were from cases, one local case and the other a travel case from Cuba. The two human sequences and two of the mosquito sequences are closely related, indicating the travel case was infected in Miami Beach and not Cuba (which is also supported by the 21 day gap between onset of symptoms and return from Cuba). The collection date for the sample for this case was June 22. In addition, the sequence from the earlier mosquito batch suggests it was from an independent introduction.
niman Posted September 17, 2016 Author Report Posted September 17, 2016 (edited) The two closely related Aedes aegypti mosquito batches, ZM1 (containing 39 mosquitoes collected August 22) and ZM2 (containing 25 mosquitoes collected August 23) are closely related to the human cases, Hu15 (local case collected August 24) and ZF10 (traveler from Cuba collected June 22). The distinct mosquito sequence was ZM3 (containing 15 mosquitoes collected August 15). Edited September 17, 2016 by niman
niman Posted September 17, 2016 Author Report Posted September 17, 2016 ZM1: LOCUS KX838904 10524 bp RNA linear VRL 14-SEP-2016 DEFINITION Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM1-7501 polyprotein gene, complete cds. ACCESSION KX838904 VERSION KX838904.1 GI:1063797021 DBLINK BioProject: PRJNA342539 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10524) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Zika virus sequences from Florida, USA, 2016 JOURNAL Unpublished REFERENCE 2 (bases 1 to 10524) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Direct Submission JOURNAL Submitted (12-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 Coverage :: 160,000 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10524 /organism="Zika virus" /mol_type="genomic RNA" /isolate="ZIKV/Aedes_aegypti/USA/2016/ZM1-7501" /isolation_source="pool of 39 adult mosquitoes" /host="Aedes aegypti" /db_xref="taxon:64320" /country="USA: Miami, Florida" /collection_date="22-Aug-2016"
niman Posted September 17, 2016 Author Report Posted September 17, 2016 ZM2: LOCUS KX838905 10475 bp RNA linear VRL 14-SEP-2016 DEFINITION Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM2-7719 polyprotein gene, complete cds. ACCESSION KX838905 VERSION KX838905.1 GI:1063797023 DBLINK BioProject: PRJNA342539 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10475) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Zika virus sequences from Florida, USA, 2016 JOURNAL Unpublished REFERENCE 2 (bases 1 to 10475) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Direct Submission JOURNAL Submitted (12-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 Coverage :: 160,000 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10475 /organism="Zika virus" /mol_type="genomic RNA" /isolate="ZIKV/Aedes_aegypti/USA/2016/ZM2-7719" /isolation_source="pool of 25 adult mosquitoes" /host="Aedes aegypti" /db_xref="taxon:64320" /country="USA: Miami, Florida" /collection_date="23-Aug-2016"
niman Posted September 17, 2016 Author Report Posted September 17, 2016 Hu15: LOCUS KX832731 10467 bp RNA linear VRL 14-SEP-2016 DEFINITION Zika virus isolate ZIKV/Human/USA/2016/ZL2.SA-Hu0015 polyprotein gene, complete cds. ACCESSION KX832731 VERSION KX832731.1 GI:1063797019 DBLINK BioProject: PRJNA342539 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10467) AUTHORS Grubaugh,N., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Watkins,D., Lichtenberger,P., Ricciardi,M., Bailey,V., Magnani,D. and Andersen,K. TITLE Zika virus sequences from Florida, USA, 2016 JOURNAL Unpublished REFERENCE 2 (bases 1 to 10467) AUTHORS Grubaugh,N., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Watkins,D., Lichtenberger,P., Ricciardi,M., Bailey,V., Magnani,D. and Andersen,K. TITLE Direct Submission JOURNAL Submitted (11-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. V2 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10467 /organism="Zika virus" /mol_type="genomic RNA" /isolate="ZIKV/Human/USA/2016/ZL2.SA-Hu0015" /isolation_source="saliva" /host="Homo sapiens" /db_xref="taxon:64320" /country="USA: Miami, Florida" /collection_date="24-Aug-2016"
niman Posted September 17, 2016 Author Report Posted September 17, 2016 ZF10: LOCUS KX842449 10388 bp RNA linear VRL 14-SEP-2016 DEFINITION Zika virus isolate ZIKV/Human/USA/2016/ZF10.UR-010 polyprotein gene, complete cds. ACCESSION KX842449 VERSION KX842449.1 GI:1063906997 DBLINK BioProject: PRJNA342539 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10388) 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 10388) 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 (13-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 Coverage :: 80,000 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10388 /organism="Zika virus" /mol_type="genomic RNA" /isolate="ZIKV/Human/USA/2016/ZF10.UR-010" /isolation_source="urine" /host="Homo sapiens" /db_xref="taxon:64320" /country="USA: Miami, Florida" /collection_date="22-Jun-2016" /note="direct clinical sequencing; person returned from Cuba 21 days prior to sample collection, but infection may have occurred in Miami"
niman Posted September 17, 2016 Author Report Posted September 17, 2016 ZM3: LOCUS KX838906 10610 bp RNA linear VRL 14-SEP-2016 DEFINITION Zika virus isolate ZIKV/Aedes_aegypti/USA/2016/ZM3-7729 polyprotein gene, complete cds. ACCESSION KX838906 VERSION KX838906.1 GI:1063797025 DBLINK BioProject: PRJNA342539 KEYWORDS . SOURCE Zika virus ORGANISM Zika virus Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA stage; Flaviviridae; Flavivirus. REFERENCE 1 (bases 1 to 10610) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Zika virus sequences from Florida, USA, 2016 JOURNAL Unpublished REFERENCE 2 (bases 1 to 10610) AUTHORS Grubaugh,N., Paul,L., Gangavarupu,K., Oliveira,G., Robles-Sikisaka,R., Michael,S., Isern,S. and Andersen,K. TITLE Direct Submission JOURNAL Submitted (12-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 Coverage :: 160,000 Sequencing Technology :: Illumina ##Assembly-Data-END## FEATURES Location/Qualifiers source 1..10610 /organism="Zika virus" /mol_type="genomic RNA" /isolate="ZIKV/Aedes_aegypti/USA/2016/ZM3-7729" /isolation_source="pool of 15 adult mosquitoes" /host="Aedes aegypti" /db_xref="taxon:64320" /country="USA: Miami, Florida" /collection_date="23-Aug-2016"
niman Posted October 14, 2016 Author Report Posted October 14, 2016 Updated table at Andersen lab website puts location of infection for Florida ex-Cuba case (FL010U) in Florida Samples Scripps ID Patient ID Sample type Quality score % Coverage Location of infection FL001Sa 001 Saliva *** 99.71 Martinique FL008U 008 Urine *** 90.07 Puerto Rico FL010U 010 Urine **** 97.69 USA: Florida FL016U 016 Urine *** 99.88 Puerto Rico FL021U 021 Urine *** 97.45 USA: Florida FL022U 022 Urine *** 97.77 USA: Florida FL030U 030 Urine *** 99.75 USA: Florida FL032U 032 Urine *** 99.75 USA: Florida FL036Se 036 Serum *** 99.73 USA: Florida FL038U 038 Urine *** 99.76 USA: Florida FL039U 039 Urine **** 99.75 USA: Florida Hu0015Sa Hu0015 Saliva *** 99.75 USA: Florida FL01M 7501 Mosquito **** 99.75 USA: Florida FL02M 7719 Mosquito **** 99.74 USA: Florida FL03M 7727 Mosquito **** 99.83 USA: Florida FL04M 16-10416 Mosquito **** 99.72 USA: Florida FL05M 16-3125 Mosquito **** 99.74 USA: Florida FL06M Mosquito **** 99.71 USA: Florida ZC188Se 423568715 Serum **** 98.26 Columbia ZC192Se 423401315 Serum **** 98.36 Columbia ZC204Se 424439915 Serum **** 99.74 Columbia ZC207Se 423217515 Serum **** 96.68 Columbia 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
niman Posted October 14, 2016 Author Report Posted October 14, 2016 Last night's audio update http://recombinomics.co/thedrnimanshow/2016/10/100716.mp3
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