title: Intra-host evolutionary rates in HIV-1C env and gag during primary infection.
abstract: BACKGROUND
  HIV-1 nucleotide substitution rates are central for understanding the evolution of HIV-1. Their accurate estimation is critical for analysis of viral dynamics, identification of divergence time of HIV variants, inference of HIV transmission clusters, and modeling of viral evolution.
  
  
  METHODS
  Intra-patient nucleotide substitution rates in HIV-1C gag and env gp120 V1C5 were analyzed in a longitudinal cohort of 32 individuals infected with a single viral variant. Viral quasispecies were derived by single genome amplification/sequencing from serially sampled blood specimens collected at median (IQR) of 5 (4-6) times per subject from enrollment (during Fiebig stages II to V) over a median (IQR) of 417 (351-471) days post-seroconversion (p/s). HIV-1C evolutionary rates were estimated by BEAST v.1.7 using a relaxed lognormal molecular clock model. The effect of antiretroviral therapy (ART) on substitution rates in gag and env was assessed in a subset of six individuals who started ARV therapy during the follow-up period.
  
  
  RESULTS
  During primary HIV-1C infection, the intra-patient substitution rates were estimated at a median (IQR) of 5.22E-03 (3.28E-03-7.55E-03) substitutions per site per year of infection within gag, and 1.58E-02 (9.99E-03-2.04E-02) substitutions per site per year within env gp120 V1C5. The substitution rates in env gp120 V1C5 were higher than in gag (p<0.001, Wilcoxon signed rank test). The median (IQR) relative rates of evolution at codon positions 1, 2, and 3 were 0.73 (0.48-0.84), 0.67 (0.52-0.86), and 1.54 (1.21-1.71) in gag, and 1.01 (0.86-1.15), 1.05 (0.99-1.21), and 0.86 (0.67-0.94) in env gp120 V1C5, respectively. A first to the third position codon rate ratio >1.0 within env was found in 25 (78.1%) cases, but only in 4 (12.5%) cases in gag, while a second to the third position codon rate ratio >1.0 in env was observed in 26 (81.3%) cases, but in gag only in 2 (6.3%) cases (p<0.001 for both comparisons, Fisher's exact test). No ART effect on substitution rates in gag and env was found, at least within the first 3-4 months after ART initiation. Individuals with early viral set point ⩾4.0 log10 copies/ml had higher substitution rates in env gp120 V1C5 (median (IQR) 1.88E-02 (1.54E-02-2.46E-02) vs. 1.04E (7.24E-03-1.55E-02) substitutions per site per year; p=0.017, Mann-Whitney sum rank test), while individuals with early viral set point ⩾3.0 log10 copies/ml had higher substitution rates in gag (median (IQR) 5.66E-03 (3.45E-03-7.94E-03) vs. 1.78E-03 (4.57E-04-5.15E-03); p=0.028; Mann-Whitney sum rank test).
  
  
  CONCLUSIONS
  The results suggest that in primary HIV-1C infection, (1) intra-host evolutionary rates in env gp120 V1C5 are about 3-fold higher than in gag; (2) selection pressure in env is more frequent than in gag; (3) initiation of ART does not change substitution rates in HIV-1C env or gag, at least within the first 3-4 months after starting ART; and (4) intra-host evolutionary rates in gag and env gp120 V1C5 are higher in individuals with elevated levels of early viral set point.
authors.affiliation: Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, 651 Huntington Avenue, Boston 02115, MA, USA; Botswana-Harvard AIDS Institute, P/Bag BO 320, Gaborone, Botswana. Electronic address: vnovi@hsph.harvard.edu.
authors.forename: Vlad
authors.initials: V
authors.lastname: Novitsky
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: Raabya
authors.initials: R
authors.lastname: Rossenkhan
authors.forename: Sikhulile
authors.initials: S
authors.lastname: Moyo
authors.forename: M
authors.initials: M
authors.lastname: Essex
mesh_terms: D000328:Adult; D044966:Anti-Retroviral Agents / Q000494:pharmacology / Q000627:therapeutic use; D003062:Codon; D015331:Cohort Studies; D019143:Evolution, Molecular; D005260:Female; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D018709:Statistics, Nonparametric; D019562:Viral Load; D055815:Young Adult; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D044966:Anti-Retroviral Agents; D003062:Codon; D015699:HIV Envelope Protein gp120; D054301:gag Gene Products, Human Immunodeficiency Virus
keywords: Evolutionary rates; HIV-1; Primary infection; Substitution rates; Subtype C