Current thinking states that these virus populations are mutant spectrums of genetic variants that arise through errors during genome replication that generate new genotypes. Intra-individual RNA virus infections exist as a population of closely related virus genotypes. Importantly, concordance between the 454 and Illumina sequencing allowed unambiguous minority-variant detection and accurate determination of virus population turnover in vitro.

Using QUASR, we have determined influenza virus genome dynamics in sequential samples from an in vitro evolution of 2009 pandemic H1N1 (A/H1N1/09) influenza from samples sequenced on both the Roche 454 GSFLX and Illumina GAIIx platforms.

QUASR significantly reduces the error-related noise in deep-sequencing datasets, resulting in increased mapping accuracy and reduction of erroneous mutations. Here, we report the development and assessment of the Quality Assessment of Short Read (QUASR) Pipeline ( ) specific for virus genome short read analysis that minimizes sequencing errors from multiple deep-sequencing platforms, and enables post-mapping analysis of the minority variants within the viral population. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency.

Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. RNA viruses within infected individuals exist as a population of evolutionary-related variants.

Qcs 2.38