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SARS-CoV2 BA.2.86 Derivative Sequences Map

Likely Local Zika Transmission In June In Miami Beach Florida

niman

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niman Grand Master

niman

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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.

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niman Grand Master

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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). 

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niman Grand Master

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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  JOURNAL   Unpublished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"
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niman Grand Master

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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"
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niman Grand Master

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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"
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niman Grand Master

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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"
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niman Grand Master

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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"
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niman Grand Master

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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
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