Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples

Melissa Laird Smith, Ben Murrell, Kemal Eren, Caroline Ignacio, Elise Landais, Steven Weaver, Pham Phung, Colleen Ludka, Lance Hepler, Gemma Caballero, Tristan Pollner, Yan Guo, Douglas Richman, The IAVI Protocol C Investigators & The IAVI African HIV Research Network, Pascal Poignard, Ellen E. Paxinos, Sergei L. Kosakovsky Pond, Davey M. Smith

Abstract

The ability to study rapidly evolving viral populations has been constrained by the read length of next-generation sequencing approaches and the sampling depth of single-genome amplification methods. Here, we develop and characterize a method using Pacific Biosciences’ Single Molecule, Real-Time (SMRT®) sequencing technology to sequence multiple, intact full-length human immunodeficiency virus-1 env genes amplified from viral RNA populations circulating in blood, and provide computational tools for analyzing and visualizing these data.