South Africa Spike Deletion In Florida

[niman]

Recent reports of a variant from South Africa suggests it transmits more easily than the UK variant.  Both usually have 3 amino acids deleted from the Spike protein as well as RBD mutation N501Y and G clade mutation D614G.  The Spike deletion in South Africa (L242 A243 L244) is also in a recently deposited (at GISAID and Genbank) isolate collected on July 3 in Florida, USA/FL-BPHL-2075.  This isolate only has one additional Spike non-synonymous change, D614G

[niman]

LOCUS       MW286605               29806 bp    RNA     linear   VRL 23-NOV-2020
DEFINITION  Severe acute respiratory syndrome coronavirus 2 isolate
            SARS-CoV-2/human/USA/FL-BPHL-2075/2020, complete genome.
ACCESSION   MW286605
VERSION     MW286605.1
KEYWORDS    .
SOURCE      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  ORGANISM  Severe acute respiratory syndrome coronavirus 2
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;
            Betacoronavirus; Sarbecovirus.
REFERENCE   1  (bases 1 to 29806)
  AUTHORS   Schmedes,S. and Blanton,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-NOV-2020) BPHL, FLDOH, 1217 N Pearl St, Jacksonville,
            FL 32202, USA
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: bwa v. 0.7.17; ivar v. 1.2.2
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..29806
                     /organism="Severe acute respiratory syndrome coronavirus
                     2"
                     /mol_type="genomic RNA"
                     /isolate="SARS-CoV-2/human/USA/FL-BPHL-2075/2020"
                     /host="Homo sapiens"
                     /db_xref="taxon:2697049"
                     /country="USA: FL"
                     /collection_date="2020-07-03"