Viral quasispecies reconstruction via tensor factorization with successive read removal

Abstract

Motivation: As RNA viruses mutate and adapt to environmental changes, often developing resistance to anti-viral vaccines and drugs, they form an ensemble of viral strains--a viral quasispecies. While high-throughput sequencing (HTS) has enabled in-depth studies of viral quasispecies, sequencing errors and limited read lengths render the problem of reconstructing the strains and estimating their spectrum challenging. Inference of viral quasispecies is difficult due to generally non-uniform frequencies of the strains, and is further exacerbated when the genetic distances between the strains are small.

Results: This paper presents TenSQR, an algorithm that utilizes tensor factorization framework to analyze HTS data and reconstruct viral quasispecies characterized by highly uneven frequencies of its components. Fundamentally, TenSQR performs clustering with successive data removal to infer strains in a quasispecies in order from the most to the least abundant one; every time a strain is inferred, sequencing reads generated from that strain are removed from the dataset. The proposed successive strain reconstruction and data removal enables discovery of rare strains in a population and facilitates detection of deletions in such strains. Results on simulated datasets demonstrate that TenSQR can reconstruct full-length strains having widely different abundances, generally outperforming state-of-the-art methods at diversities 1-10% and detecting long deletions even in rare strains. A study on a real HIV-1 dataset demonstrates that TenSQR outperforms competing methods in experimental settings as well. Finally, we apply TenSQR to analyze a Zika virus sample and reconstruct the full-length strains it contains.

Availability and implementation: TenSQR is available at https://github.com/SoYeonA/TenSQR.

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

An illustration of the tensor factorization representation of the viral quasispecies assembly problem

Fig. 2.

Performance comparison of TenSQR, aBayesQR, ShoRAH, ViQuaS and PredictHaplo in terms of Recall, Precision, Predicted Proportion (PredProp), Reconstruction Rate (ReconRate) and JSD on the simulated data with $\epsilon =2\times {10}^{-3}$ for a mixture of (a) 5 viral strains and (b) 10 viral strains. (For the plots that include error bars, please see the corresponding Supplementary Fig. S2 in Supplementary Material B)

Fig. 3.

Performance comparison of TenSQR, aBayesQR, ShoRAH, ViQuaS and PredictHaplo in terms of Recall, Precision, Predicted Proportion (PredProp), Reconstruction Rate (ReconRate) and JSD on the simulated data with $\epsilon =7\times {10}^{-3}$ for a mixture of (a) 5 viral strains and (b) 10 viral strains. (For the plots that include error bars, please see the corresponding Supplementary Fig. S3 in Supplementary Material B)