Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum

Abstract

Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations.Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies.Availability and implementation: Freely available on the web at http://www.vivanbioinfo.orgContact: nshomron@post.tau.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages

“…High-throughput or deep sequencing approaches drastically reduced time and cost requirements for genomic sequencing. Additional advantages of this methodology are the significant increase in sequence coverage and depth that permit to study co-infection, recombination, and quasispecies diversity (Isakov et al, 2015;Pérez et al, 2014).…”

Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase

“…Alignments were processed using SAMTools to obtain a pileup of the called bases at each position. The ViVan pipeline was used to identify statistically significant variants above the background noise due to sequencing error in every sufficiently covered site (Ͼ1,000ϫ) (29). Briefly, for each position throughout the viral genome, base identity and their quality scores were gathered.…”

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum

“…Because spontaneous mutations necessarily enter the population at a frequency of 1/N, where N is the number of the chromosomes in the population, identifying a cohort of extremely rare polymorphisms will enrich for very young mutations [39]. Mutational spectra from rare variants through deep population sequencing has already been employed in viral systems such as HIV [40], where the main challenge lies in accurately calling extremely rare variants from a heterogeneous viral population [41–43]. Rare variants have also been applied to characterizing context dependent mutational patterns in 202 human genes [44], although in species where single individual sequencing is accessible and populations are not homogeneous, population structure must be accounted for [45].…”