ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.
BACKGROUND
The combined effect of a high replication rate and the low fidelity of the viral polymerase in most RNA viruses and some DNA viruses results in the formation of a viral quasispecies. Uncovering information about quasispecies populations significantly benefits the study of disease progression, antiviral drug design, vaccine design and viral pathogenesis. We present a new analysis pipeline called ViQuaS for viral quasispecies spectrum reconstruction using short next-generation sequencing reads. ViQuaS is based on a novel reference-assisted de novo assembly algorithm for constructing local haplotypes. A significantly extended version of an existing global strain reconstruction algorithm is also used.


RESULTS
Benchmarking results showed that ViQuaS outperformed three other previously published methods named ShoRAH, QuRe and PredictHaplo, with improvements of at least 3.1-53.9% in recall, 0-12.1% in precision and 0-38.2% in F-score in terms of strain sequence assembly and improvements of at least 0.006-0.143 in KL-divergence and 0.001-0.035 in root mean-squared error in terms of strain frequency estimation, over the next-best algorithm under various simulation settings. We also applied ViQuaS on a real read set derived from an in vitro human immunodeficiency virus (HIV)-1 population, two independent datasets of foot-and-mouth-disease virus derived from the same biological sample and a real HIV-1 dataset and demonstrated better results than other methods available.
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
Duleepa
D
Jayasundara
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
I
I
Saeed
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
Suhinthan
S
Maheswararajah
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
B C
BC
Chang
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
S-L
SL
Tang
Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC 3010, Portland House Research and Advisors Ltd., Melbourne, VIC 3000, Australia, Yourgene Bioscience, No. 376-5, Fuxing Rd., Shu-Lin District, New Taipei City, Taiwan and Biodiversity Research Center, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan.
Saman K
SK
Halgamuge
D000465:Algorithms; D029544:Foot-and-Mouth Disease Virus / Q000145:classification / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans