TABLE 1.

Determination of SGA-direct sequencing error rates using in vitro-synthesized HIV-1 RNA templates

StrainNo. (%) of:Total no. of errorsb (%)Number of recombinants (%)
Genomes sequencedGenomes with no errorsNucleotides sequencedTransitionsTransversionsInsertionsaDeletionsa
BORId9.4F12c291271,34015 (0.0210)7 (0.0098)2 (0.0028)3 (0.0042)27 (0.038)0 (<1)
BORId9.4F8c30974,25021 (0.0283)7 (0.0094)7 (0.0094)2 (0.0027)37 (0.050)0 (<1)
Total for both strains5921145,59036 (0.0247)14 (0.0096)9 (0.0062)5 (0.0034)64 (0.044)0 (<1)
YU2d272471,5082 (0.0028)01 (0.0014)03 (0.0042)0 (<1)
SG3d231661,3317 (0.0114)001 (0.0016)8 (0.013)0 (<1)
Total for both strains5040132,8399 (0.0068)01 (0.0008)1 (0.0008)11 (0.0083)0 (<1)
  • a Insertion or deletion of 1 or 2 A or T nucleotides to a preexisting run of A or T residues.

  • b Total errors including transitions, transversions, insertions, and deletions.

  • c T7-generated HIV-1 RNA transcripts were mixed 1:1 and subjected to SGA analysis as described in the text.

  • d HIV-1 vRNA from transfected human 293T cell culture supernatants was mixed 1:1 and subjected to SGA analysis as described in the text.