Abstract
BackgroundA virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. However automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet.ResultsWe developed Quasispecies Analysis Package (QAP), an integrated software platform to address the problems associated with making biological interpretations from massive viral population sequencing data. QAP provides quantitative insight into virus ecology by first introducing the definition “virus OTU” and supports a wide range of viral community analyses and results visualizations. Various forms of QAP were developed in consideration of broader users, including a command line, a graphical user interface and a web server. Utilities of QAP were thoroughly evaluated with high-throughput sequencing data from hepatitis B virus, hepatitis C virus, influenza virus and human immunodeficiency virus, and the results showed highly accurate viral quasispecies characteristics related to biological phenotypes.ConclusionsQAP provides a complete solution for virus community high throughput sequencing data analysis, and it would facilitate the easy analysis of virus quasispecies in clinical applications.
Highlights
A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases
Comprehensive evaluation using HBV quasispecies sequencing data To assess the advantages of integrated analysis tools in Quasispecies Analysis Package (QAP), comprehensive data sets of HBV QS were used, including clone-based sequencing (CBS), next-generation sequencing (NGS) and third-generation sequencing (TGS) data
Datasets details were described in Additional file 1, and amplification details for HBV NGS data were illustrated in Additional file 2: Table S3, and Additional file 3: Fig. S6
Summary
A virus community is the spectrum of viral strains populating an infected host, which plays a key role in pathogenesis and therapy response in viral infectious diseases. Automatic and dedicated pipeline for interpreting virus community sequencing data has not been developed yet. Due to the high genomic variability of RNA viruses and some DNA viruses, a massive, complex and dynamic distribution of variants, termed a viral quasispecies (QS), is generated during replication in viral infections [1]. There are no existing tools providing a complete pipeline for quasispecies HTS data analysis and quasispecies population characteristics. An integrated and automatic software for the characterization of viral quasispecies could be of great interest for time-effective, full exploitation of quasispecies HTS data
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