BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads
2014
Hong, Lewis Z | Hong, Shuzhen | Wong, Han Teng | Aw, Pauline PK | Cheng, Yan | Wilm, Andreas | de Sessions, Paola F | Lim, Seng Gee | Nagarajan, Niranjan | Hibberd, Martin L | Quake, Stephen R | Burkholder, William F
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.
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