July 7, 2019  |  

Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants

Authors: Artyomenko, Alexander and Wu, Nicholas C. and Mangul, Serghei and Eskin, Eleazar and Sun, Ren and Zelikovsky, Alex

As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous “swarm” of mutant variants. The long read length offered by single-molecule sequencing technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this paper, we present 2SNV, a method able to tolerate the high error-rate of the single-molecule protocol and reconstruct mutant variants. 2SNV uses linkage between single nucleotide variations to efficiently distinguish them from read errors. To benchmark the sensitivity of 2SNV, we performed a single-molecule sequencing experiment on a sample containing a titrated level of known viral mutant variants. Our method is able to accurately reconstruct clone with frequency of 0.2 % and distinguish clones that differed in only two nucleotides distantly located on the genome. 2SNV outperforms existing methods for full-length viral mutant reconstruction. The open source implementation of 2SNV is freely available for download at http://?alan.?cs.?gsu.?edu/?NGS/???q=?content/?2snv.

DOI: 10.1007/978-3-319-31957-5_12
Year: 2016

Read Publication

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.