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
References
May 11, 2002·Briefings in Bioinformatics·Ross LippertSorin Istrail
Feb 13, 2009·The Journal of Infectious Diseases·Birgitte B SimenUNKNOWN Terry Beirn Community Programs for Clinical Research on AIDS
Jun 30, 2009·PloS One·Thuy LeMichael J Kozal
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Osvaldo ZagordiNiko Beerenwinkel
Jul 28, 2010·PLoS Pathogens·Adam S Lauring, Raul Andino
Jul 31, 2010·Nucleic Acids Research·Osvaldo ZagordiNiko Beerenwinkel
Jan 7, 2011·BMC Bioinformatics·Mattia C F ProsperiGiovanni Ulivi
Apr 28, 2011·BMC Bioinformatics·Osvaldo ZagordiNiko Beerenwinkel
Oct 26, 2011·BMC Bioinformatics·Irina AstrovskayaAlex Zelikovsky
Nov 18, 2011·Bioinformatics·Mattia C F Prosperi, Marco Salemi
Mar 27, 2012·BMC Bioinformatics·John ArcherDavid L Robertson
Feb 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Armin TöpferNiko Beerenwinkel
Jun 17, 2014·Bioinformatics·Serghei MangulEleazar Eskin
Jun 29, 2014·Nucleic Acids Research·Francesca Di GiallonardoKarin J Metzner
Jan 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Sandhya PrabhakaranVolker Roth
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
Feb 4, 2021·Bioinformatics·Chen CaoQuan Long
Mar 11, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Anton EliseevKeith A Crandall
Feb 7, 2021·Molecular Biology and Evolution·Chen CaoQuan Long
Jul 3, 2021·Nucleic Acids Research·Sergey KnyazevAlex Zelikovsky
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