These questions were addressed in a total of 453 non-redundant sequences using a population model approach based on recent studies of the amplification of Alu sequences among human and chimpanzee lineages [ 16, 17].
Additionally, the user is able to simulate an "evolved" population of a single genome sequence, using a population simulator.
Using a population genetic data set of 217 sequence fragments from C. remanei and 130 orthologous fragments from C. sp. 23, we identified 2,033 SNPs and 292 indels across the 39.5 kb of sequence in C. remanei.
Loss of detectable NVP-R mutations using standard population sequencing was observed at a median of 12 months of age in infants who received SWEN (60% of 5) or SD-NVP (80% of 5) (Table 4).
Using standard population sequencing, 15% of 13 infants who received SWEN and 15% of 20 infants who received SD-NVP had drug resistance (p = 1.00; Figure 2).
The proportion of in utero infected infants who received SWEN or SD-NVP and who possessed NVP-R were 88% of 8 vs. 50% of 14, respectively (p = 0.17) using standard population sequencing, and 88% of 8 vs. 64% of 14, respectively (p = 0.35) by low frequency clonal analysis.
We inferred divergence for each of five lineage-pairs by comparing across nucleotide divergence, previously estimated using population sequencing, and the coalescent model implemented in 3s that samples a single chromosome per locus.
Viral susceptibility was inferred before salvage therapy initiation and at virological failure using deep and population sequencing genotypes interpreted with the HIVdb, Rega and ANRS algorithms.
Since intrasample variability in the V3 region using population sequencing has been reported [ 11], two distinct PCR products were analyzed for each of the cases selected for the WB4 vs. WB20 comparison.
Thus, having only chronically infected children may actually underestimate the prevalence of transmitted drug resistance as the wild type virus with increased fitness may predominate and minor viral populations with drug resistant mutations may be too low to detect using population sequencing.
