TABLE 4.

SNP sites for identification of serotypes and serotype III subtypesa based on partial cps sequencing, between the 3′ end of cpsE-cpsF and the 5′ end of cpsGb

Molecular serotypeNucleotide at positionb:
149515001501151215181527159516111620162716291655183218561866187118921971202620882134
IXcTcCc
Ia/III-3dT
IbGTCCTCA
II/III-4dT
III-1TCAC
III-2TCC
IVTTA
VTCCG
VIATCCA
VIITTTA
ConsensusCACCTATCCGGCCTGTAGGGT
  • a Please see the text and previous publications (26, 43) for an explanation of the methods.

  • b The numbering start point 1 refers to start point 1 of the sequence with GenBank accession number AF332908 (for serotype reference strain 3139). Please also refer to Fig. 1 of a previous publication (26). Only the sequences between 1451 and 2164 were analyzed.

  • c The two sites at 1627 and 1832 were not entirely specific for the proposed serotype IX, but the combination can effectively identify the proposed serotype IX. Further, the specific sites for the cpsH region (see Fig. 3) make the design of serotype IX-specific PCR easier and more specific.

  • d Ia and III-3, as well as II and III-4, share the same sequences as described previously (26).