Abstract
Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼0.005% to ∼0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population.
Highlights
Many viruses have such high replication and mutation rates that they exist as a quasispecies in vivo [1]
The methodology consists of three key steps: 1) Assigning unique tags to individual viral sequences to distinguish each variant within the viral quasispecies, 2) Controlling the complexity of the library during amplification to ensure sufficient coverage for sampled viral sequences, and 3) Using a tag linkage strategy to deduce the fulllength templates from non-overlapping amplicons
Library Preparation for Sequencing The underlying rationale is to assign a unique tag to individual viral sequences within the quasispecies and to distribute the tag to every sequencing read originated from the same viral sequence (Figure 1A)
Summary
Many viruses have such high replication and mutation rates that they exist as a quasispecies in vivo [1]. A viral quasispecies population contains a variety of genotypic variants that are related by similar mutations and exist in varying abundance depending on their relative fitness within the host environment. Viral sequence variation in the quasispecies population can be rapidly generated by point mutation and/or recombination [1,2]. Mutation rates can be as high as in the order of one per replication cycle, in which the progeny virus is unlikely to be identical to its parental template. This diverse array of viral sequences permits robust adaptation and evolution
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