aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Soyeon Ahn, Haris Vikalo

Abstract

RNA viruses replicate with high mutation rates, creating closely related viral populations. The heterogeneous virus populations, referred to as viral quasispecies, rapidly adapt to environmental changes thus adversely affecting efficiency of antiviral drugs and vaccines. Therefore, studying the underlying genetic heterogeneity of viral populations plays a significant role in the development of effective therapeutic treatments. Recent high-throughput sequencing technologies have provided invaluable opportunity for uncovering the structure of quasispecies populations. However, accurate reconstruction of viral quasispecies remains difficult due to limited read lengths and presence of sequencing errors. The problem is particularly challenging when the strains in a population are highly similar, that is, the sequences are characterized by low mutual genetic distances, and further exacerbated if some of those strains are relatively rare; this is the setting where state-of-the-art methods struggle. In this article, we present a novel viral quasispecies reconstruction algorithm, aBayesQR, that uses a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. The search for the most lik...Continue Reading

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Citations

Jun 23, 2020·Briefings in Bioinformatics·Sergey KnyazevAlexander Zelikovsky
May 31, 2019·Bioinformatics·Jasmijn A BaaijensAlexander Schönhuth
Mar 29, 2019·Genome Biology and Evolution·Rubén GonzálezSantiago F Elena
Sep 15, 2020·Bioinformatics·Borja FreireLeena Salmela
Mar 11, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Anton EliseevKeith A Crandall
Oct 27, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Andrew MelnykMurray Patterson
Dec 4, 2021·Frontiers in Cellular and Infection Microbiology·Yingping WuXiaoping Xia

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Software Mentioned

HaploClique assembler VGA )
ViQuaS
DeclareMathSizes
MiSeq Benchtop Sequencer
QuRe
ShoRAH
ViSpA
QuasiRecomb
aBayesQR
InferQuasi

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