title: Improved prediction of HIV‐1 coreceptor usage with sequence information from the second hypervariable loop of gp120.
abstract: BACKGROUND
  Human immunodeficiency virus type 1 (HIV‐1) uses the CD4 receptor and a coreceptor to gain cell entry. Coreceptor usage is mainly determined by the V3 loop of gp120. Therefore, coreceptor usage is currently inferred from the genotype on the basis of V3 alone. However, several mutations outside V3 have been repeatedly reported to influence coreceptor usage. In this study, the impact of the V2 loop on coreceptor usage prediction was analyzed.
  
  
  METHODS
  Sequences were analyzed for differences at specific positions and position‐independent features with the Fisher exact and Student t tests. Prediction models were trained with support vector machines and evaluated in cross‐validation on clonal data. Models trained on the clonal data set were validated on 2 clinical data sets.
  
  
  RESULTS
  Several mutations and position‐independent features within V2 were statistically significantly different between R5 and X4 viruses. Cross‐validation on the clonal data set revealed a statistically significantly higher area under the receiver operating characteristic curve if features of both loops were used, compared with those using only V2 or V3 alone. Similar results were found with clinically derived data sets.
  
  
  CONCLUSIONS
  The ability of the V2 loop to improve coreceptor usage prediction has been shown in a large data set. Utilization of this information can lead to considerable improvements in the prediction of coreceptor use both on clonal data sets and on clinically derived data sets.
authors.affiliation: Max Planck Institute for Informatics, Saarbrücken, Canada. athielen@mpi‐inf.mpg.de
authors.forename: Alexander
authors.initials: A
authors.lastname: Thielen
authors.forename: Nadine
authors.initials: N
authors.lastname: Sichtig
authors.forename: Rolf
authors.initials: R
authors.lastname: Kaiser
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Lam
authors.forename: P Richard
authors.initials: PR
authors.lastname: Harrigan
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D000595:Amino Acid Sequence; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D006801:Humans; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation; D015728:Receptors, HIV / Q000032:analysis*; D016415:Sequence Alignment; D053586:Virus Internalization
chemical_list: D015699:HIV Envelope Protein gp120; D015728:Receptors, HIV; C514793:gp120 protein, Human immunodeficiency virus 1