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. 2003 Nov;69(11):6541–6549. doi: 10.1128/AEM.69.11.6541-6549.2003

TABLE 6.

Sequence analysis of the presumptive positive PCR fragments

Water brand Sequence analysisa
Statusb
Result Homology
GI
    E Valetta-like virus Control identical CC
    E Valetta-like virus Control identical CC
    E-2 Valetta-like virus Control identical CC
    S Bacterial sequence Similar to AE004929c AA
    S Southampton-like virus Control identical CC
    S-4 Southampton-like virus Control identical CC
    S-5 Bacterial sequence Similar to AE004929c AA
    S-6 Southampton-like virus Control identical CC
    S-6 Southampton-like virus Control identical CC
    S-9 Southampton-like virus Control identical CC
    S-11 Southampton-like virus Control identical CC
    X Valetta-like virus Control identical CC
    X Valetta-like virus Control identical CC
    X-2 Valetta-like virus Control identical CC
    AA Bacterial sequence Similar to AE004929c AA
GII
    E Camberwell-like virus Control identical CC
    E-3 Camberwell-like virus Control identical CC
    S-2 Camberwell-like virus Control identical CC
    S-3 Camberwell-like virus Control identical CC
    S-4 Camberwell-like virus Control identical CC
    S-5 Camberwell-like virus Control identical CC
    S-5 Camberwell-like virus Control identical CC
    S-6 Sequence of unknown origin Unknown AA
    S-6 Camberwell-like virus Control identical CC
    X Camberwell-like virus Control identical CC
    X Sequence of unknown origin Unknown AA
    X-4 Bacterial sequence Similar to X75567d AA
    X-4 Bacterial sequence Similar to AE004929c AA
    AF Camberwell-like virus Control identical CC
    AF Sequence of unknown origin Unknown AA
    AF-3 Bacterial sequence Similar to X87286d AA
    AF-3 Camberwell-like virus Control identical CC
    AF-3 Sequence of unknown origin Unknown AA
Both genogroups
    S-5 Southampton-like virus Control identical CC
Sequence of unknown origin Unknown AA
a

Sequence homology is given as the closest match after comparison with GenBank database entries by using the BLAST program. Sequences of unknown origin had no similarity to any entry in the database. “Control Identical” means that the sequence found was identical to the positive control used in that experimental series.

b

A PCR fragment was classified either as cross-contamination (CC) when its nucleotide sequence was found 100% identical to the nucleotide sequence of the positive control used in the given experiment or as nonspecific amplification (AA) when the sequence was not of viral origin.

c

Bacterial sequence similar to that of putative C4-dicarboxylate transporter from Pseudomonas spp.

d

Bacterial sequence similar to that of 23S rRNA gene of Thiomonas cuprina or Nannocystis exedens.