Recently released D68 enterovirus sequences from 2014 New York collections include the novel acute flaccid paralysis (AFP) sub-clade.

LOCUS       KT099085                 443 bp    RNA     linear   VRL 29-JUN-2015
DEFINITION  Enterovirus D68 isolate NY09 capsid VP1 gene, partial cds.
ACCESSION   KT099085
VERSION     KT099085.1  GI:848237409
KEYWORDS    .
SOURCE      Enterovirus D68 (EV-D68)
  ORGANISM  Enterovirus D68
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Picornavirales; Picornaviridae; Enterovirus; Enterovirus D.
REFERENCE   1  (bases 1 to 443)
  AUTHORS   Zhen,W., Duong,S., Chandrasekaran,A., Zhang,F., Joseph,A., Damle,A.
            and Juretschko,S.
  TITLE     A rapid one-step, real time RT-PCR assay for Enterovirus
            D68-specific Detection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 443)
  AUTHORS   Zhen,W. and Juretschko,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUN-2015) Molecular Diagnostics, North Shore LIJ
            Health System Laboratories, 10 Nevada Drive, Lake Success, NY
            11375, USA
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..443
                     /organism="Enterovirus D68"
                     /mol_type="genomic RNA"
                     /isolate="NY09"
                     /isolation_source="nasopharyngeal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:42789"
                     /country="USA: NY"
                     /collection_date="18-Sep-2014"
     CDS             <1..>443
                     /codon_start=1
                     /product="capsid VP1"
                     /protein_id="AKN24918.1"
                     /db_xref="GI:848237410"
                     /translation="ESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQT
                     RTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQL
                     RRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMLVP"
ORIGIN      
        1 gagagcatca tcaaaacagc aaccgacact gtgaaaagtg agattaatgc tgaacttggt
       61 gtggtcccta gcttaaatgc agttgaaaca ggtgcaactt ctaacactga accagaagaa
      121 gccatacaaa ctcgcacagt gataaatcag cacggtgtat ccgagactct agtggagaat
      181 tttctcagta gagcagcttt ggtatcaaag agaagttttg aatacaaaga tcatacttcg
      241 tctgcagcac aagcagacaa gaactttttc aaatggacaa ttaacaccag atcctttgta
      301 cagttaagaa gaaaattaga attattcaca taccttagat ttgatgctga gatcactata
      361 ctcacaactg tagcagtgaa tggtagtagt aataatacat acgtgggtct tcctgacttg
      421 acacttcaag caatgttagt acc

LOCUS       KP742372                 340 bp    RNA     linear   VRL 02-JUN-2015
DEFINITION  Enterovirus D68 isolate NY56/288 capsid VP1 gene, partial cds.
ACCESSION   KP742372
VERSION     KP742372.1  GI:754294958
KEYWORDS    .
SOURCE      Enterovirus D68 (EV-D68)
  ORGANISM  Enterovirus D68
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Picornavirales; Picornaviridae; Enterovirus; Enterovirus D.
REFERENCE   1  (bases 1 to 340)
  AUTHORS   Zhuge,J., Vail,E., Bush,J.L., Singelakis,L., Huang,W., Nolan,S.M.,
            Haas,J.P., Engel,H., Della Posta,M., Yoon,E.C., Fallon,J.T. and
            Wang,G.
  TITLE     Evaluation of a Real-Time Reverse Transcription-PCR Assay for
            Detection of Enterovirus D68 in Clinical Samples from an Outbreak
            in New York State in 2014
  JOURNAL   J. Clin. Microbiol. 53 (6), 1915-1920 (2015)
   PUBMED   25854481
REFERENCE   2  (bases 1 to 340)
  AUTHORS   Zhuge,J., Vail,E., Bush,J.L., Singelakis,L., Huang,W., Nolan,S.M.,
            Haas,J., Fallon,J.T. and Wang,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-FEB-2015) Pathology and Clinical Laboratories,
            Westchester Medical Center, 100 Woods Road, Valhalla, NY 10595, USA
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..340
                     /organism="Enterovirus D68"
                     /mol_type="genomic RNA"
                     /isolate="NY56/288"
                     /isolation_source="nasopharyngeal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:42789"
                     /country="USA: NY"
                     /collection_date="17-Sep-2014"
     CDS             <1..>340
                     /codon_start=2
                     /product="capsid VP1"
                     /protein_id="AJI76526.1"
                     /db_xref="GI:754294959"
                     /translation="ATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEY
                     KDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNT
                     YVGLPDLTLQA"
ORIGIN      
        1 tgcaacttct aacactgaac cagaagaagc catacaaact cgcacagtga taaatcagca
       61 cggtgtatcc gagactctag tggagaattt tctcagtaga gcagctttgg tatcaaagag
      121 aagttttgaa tacaaagatc atacttcgtc tgcagcacaa gcagacaaga actttttcaa
      181 atggacaatt aacaccagat cctttgtaca gttaagaaga aaattagaat tattcacata
      241 ccttagattt gatgctgaga tcactatact cacaactgta gcagtgaatg gtagtagtaa
      301 taatacatac gtgggtcttc ctgacttgac acttcaagca

D68 AFP including 2014 sequences from New York