Analyzing Viral Quasispecies Diversity

The viral quasi-species inferred from the NGS runs were used to analyze the distribution and evolution of the intrahost diversity. Among the individuals sampled, two consecutive quasi-species were available for five of them. For every viral quasi-species, the nucleotide frequencies per position obtained in the fourth step of the NGS procedure described in section 2.3 were summarized. The analyses focused on positions with high diversity, arbitrarily defined as those where the frequencies of the mutations present were larger than 10%. Finally, the positions identified were located within the genome.