title: High-throughput profiling of point mutations across the HIV-1 genome.
abstract: BACKGROUND
  The HIV-1 pandemic is not the result of a static pathogen but a large genetically diverse and dynamic viral population. The virus is characterized by a highly mutable genome rendering efforts to design a universal vaccine a significant challenge and drives the emergence of drug resistant variants upon antiviral pressure. Gaining a comprehensive understanding of the mutational tolerance of each HIV-1 genomic position is therefore of critical importance.
  
  
  RESULTS
  Here we combine high-density mutagenesis with the power of next-generation sequencing to gauge the replication capacity and therefore mutational tolerability of single point mutations across the entire HIV-1 genome. We were able to achieve the evaluation of point mutational effects on viral replicative capacity for 5,553 individual HIV-1 nucleotide positions - representing 57% of the viral genome. Replicative capacity was assessed at 3,943 nucleotide positions for a single alternate base change, 1,459 nucleotide positions for two alternate base changes, and 151 nucleotide positions for all three possible alternate base changes. This resulted in the study of how a total of 7,314 individual point mutations impact HIV-1 replication on a single experimental platform. We further utilize the dataset for a focused structural analysis on a capsid inhibitor binding pocket.
  
  
  CONCLUSIONS
  The approach presented here can be applied to any pathogen that can be genetically manipulated in a laboratory setting. Furthermore, the methodology can be utilized under externally applied selection conditions, such as drug or immune pressure, to identify genetic elements that contribute to drug or host interactions, and therefore mutational routes of pathogen resistance and escape.
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. almawsawi@gmail.com.|AIDS Institute, University of California, Los Angeles, CA, 90095, USA. almawsawi@gmail.com.
authors.forename: Laith Q
authors.initials: LQ
authors.lastname: Al-Mawsawi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. WCHNicholas@mednet.ucla.edu.|Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA. WCHNicholas@mednet.ucla.edu.
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. aolson@mednet.ucla.edu.
authors.forename: C Anders
authors.initials: CA
authors.lastname: Olson
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. viviancshi@gmail.com.
authors.forename: Vivian Cai
authors.initials: VC
authors.lastname: Shi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. qhf.zju@gmail.com.
authors.forename: Hangfei
authors.initials: H
authors.lastname: Qi
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. XiaojuanZheng@mednet.ucla.edu.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. TWu@mednet.ucla.edu.
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Wu
authors.affiliation: Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA. rsun@mednet.ucla.edu.|AIDS Institute, University of California, Los Angeles, CA, 90095, USA. rsun@mednet.ucla.edu.|Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA. rsun@mednet.ucla.edu.
authors.forename: Ren
authors.initials: R
authors.lastname: Sun
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008967:Molecular Biology / Q000379:methods; D016296:Mutagenesis; D017354:Point Mutation; D014773:Virology / Q000379:methods; D014779:Virus Replication