Table 4. Intra-host genetic diversity analysis of DENV-1 populations from 17 sera of patients infected in FP between 2001 and 2006.
| DENV-1 samples characteristics serum number clinical presentationa, sex/age patient, geographical origin, sample date (month/year) | No. of clones | % of mutant clones | % of variable nt sites | % of nt mutations | π nt | π aa | dN | dS | dN/dS |
| serum 2.2001 | 41 | 61% | 6% | 0.17% | 0.3% | 0.7% | 0.003 | 0.005 | 0.600 |
| DF. F/7 years | |||||||||
| Bora Bora 02/2001 | |||||||||
| serum 7.2001 | 53 | 77% | 8% | 0.18% | 0.4% | 0.7% | 0.003 | 0.005 | 0.600 |
| DHF. M/30 years | |||||||||
| Tahiti 03/2001 | |||||||||
| serum 14.2001 | 39 | 56% | 4% | 0.10% | 0.2% | 0.4% | 0.002 | 0.002 | 1.000 |
| DHF. F/55 years | |||||||||
| Raiatea 04/2001 | |||||||||
| serum 26.2001 | 50 | 62% | 8% | 0.16% | 0.3% | 0.7% | 0.003 | 0.003 | 1.000 |
| DSS. F/12 years | |||||||||
| Tahiti 06/2001 | |||||||||
| serum 35.2001 | 48 | 77% | 8% | 0.20% | 0.4% | 0.8% | 0.004 | 0.005 | 0.800 |
| DSS. M/6 years | |||||||||
| Tahiti 08/2001 | |||||||||
| serum 37.2001 | 39 | 49% | 4% | 0.11% | 0.2% | 0.3% | 0.001 | 0.005 | 0.200 |
| DSS. M/6 years | |||||||||
| Tahiti 08/2001 | |||||||||
| serum 47.2001 | 24 | 88% | 2% | 0.19% | 0.3% | 0.5% | 0.002 | 0.008 | 0.250 |
| DHF. F/11 years | |||||||||
| Tuamotu 10/2001 | |||||||||
| serum 41.2002 | 31 | 48% | 9% | 0.33% | 0.7% | 1.4% | 0.006 | 0.008 | 0.750 |
| DF. F/13 years | |||||||||
| Marquesas 08/2002 | |||||||||
| serum 42.2002 | 36 | 75% | 10% | 0.37% | 0.8% | 1.5% | 0.007 | 0.010 | 0.700 |
| DF. F/13 years | |||||||||
| Tahiti 08/2002 | |||||||||
| serum 47.2002 | 34 | 82% | 8% | 0.34% | 0.7% | 1.2% | 0.005 | 0.011 | 0.455 |
| DF. M/6 years | |||||||||
| Moorea 12/2002 day 1b | |||||||||
| serum 49.2002 | 38 | 76% | 9% | 0.29% | 0.6% | 1.1% | 0.005 | 0.009 | 0.556 |
| DF. M/6 years | |||||||||
| Moorea 12/2002 day 4b | |||||||||
| serum 10.2003 | 35 | 77% | 11% | 0.57% | 1.1% | 2.6% | 0.011 | 0.009 | 1.222 |
| DF. F/43 years | |||||||||
| Tahiti 06/2003 | |||||||||
| serum 10.2004 | 34 | 88% | 10% | 0.44% | 0.8% | 1.5% | 0.007 | 0.012 | 0.583 |
| DF. M/51 years | |||||||||
| Tahiti 09/2004 | |||||||||
| serum 3.2005 | 44 | 59% | 4% | 0.15% | 0.3% | 0.4% | 0.002 | 0.005 | 0.400 |
| DF. M/38 years | |||||||||
| Tahiti 05/2005 | |||||||||
| serum 14.2006 | 49 | 92% | 8% | 0.26% | 0.4% | 0.8% | 0.003 | 0.007 | 0.429 |
| DHF. F/43 years | |||||||||
| Tahiti 03/2006 | |||||||||
| serum 32.2006 | 28 | 54% | 4% | 0.19% | 0.4% | 0.7% | 0.003 | 0.006 | 0.500 |
| DF. M/14 years | |||||||||
| Austral 08/2006 | |||||||||
| serum 51.2006 | 39 | 54% | 5% | 0.15% | 0.3% | 0.6% | 0.002 | 0.004 | 0.500 |
| DHF. M/14 years | |||||||||
| Raiatea 11/2006 | |||||||||
| total 17 sera | 662 | ||||||||
| average | 39 | 69% | 7% | 0.25% | 0.5% | 0.9% | 0.004 | 0.007 | 0.620 |
| 9 DF sera | 321 | ||||||||
| average | 36 | 69% | 8% | 0.32% c | 0.6% c | 1.2%c | 0.005c | 0.008c | 0.641 |
| 8 DHF/DSS sera | 341 | ||||||||
| average | 43 | 69% | 6% | 0.17% c | 0.3% c | 0.6%c | 0.003c | 0.005c | 0.597 |
Each clone sequence was compared to other clone sequences for each serum sample.
The percentage of variable nucleotide (nt) sites was the number of variable nt sites ×100 divided by the number of nt analysed (758 nt).
The percentage of nucleotide (nt) mutations was the number of nt mutations ×100 divided by the number of nt sequenced for each serum sample.
The average pairwise distance was calculated among the nucleotide (π nt) and amino acid (π aa) sequences in each serum.
The mean ratio of non-synonymous (dN) and synonymous (dS) substitutions per site were estimated using the pairwise method of Nei and Gojobori.
DF = dengue fever, DHF = dengue haemorraghic fever, DSS = dengue shock syndrome.
Strains 47.2002 and 49.2002 corresponded to sequential samples from the same patient (day 1 and day 4 of the symptoms).
Overall, the time of serum collection relative to infection that do not appear to be a critical parameter for the study of DENV intra-host genetic diversity [42],[43] ranged from one to six days in documented cases.
Differences between DF and DHF sera were statistically significant (p<0.05, see Methods for details of statistical analysis).