Table 3. Genetic diversity of DENV-1 at different levels and at different times of viral evolutionary divergence based on a 1,759 nt fragment including the E-gene.
| Dataseta | No. of variable nt sites/No. of nt analysed | No. of variable aa sites/No. of aa analysed | π ntb | |
| % | % | mean | range | |
| Serotype 1 | 537/1759 | 92/586 | ||
| 59 sequences | 30.5% | 15.7% | 6.5% | 0–10% |
| Genotype IV | 338/1759 | 47/586 | ||
| 26 sequences | 19.2% | 8.0% | 4.3% | 0–9.1% |
| FP 2001–2006 | 128/1759 | 47/586 | ||
| 181 sequences | 7.3% | 8.0% | 0.4% | 0–1% |
| FP 2001 epidemic period | 34/1759 | 13/586 | ||
| 42 sequencesc | 1.9% | 2.2% | 0.1% | 0–0.3% |
| FP 2002–2005 endemic period d | 78/1759 | 27/586 | ||
| 93 sequences | 4.4% | 4.6% | 0.3% | 0–0.9% |
| FP 2006 epidemic period | 28/1759 | 10/586 | ||
| 41 sequences | 1.6% | 1.7% | 0.2% | 0–0.5% |
a
Sequences in datasets “Serotype 1”, “Genotype IV” and “FP 2001–2006” were also used for phylogenetic reconstructions (Figures 2, 3, S1, S2).
b
The pairwise distances were calculated among the nucleotide sequences in each dataset (π nt).
c
Five samples collected in February 2001 before the beginning of the 2001 outbreak were excluded from the comparative analysis of DENV-1 evolution during the endemic and epidemic periods (a total of 176 samples collected between March 2001 and December 2006 was analyzed).
d
Results were significantly different between endemic and epidemic periods (see Methods for details of statistical analysis).