title: Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.
abstract: BACKGROUND
  Aiming to answer the broad question "When does mutation occur?" this study examined the time of appearance, dominance, and completeness of in vivo Gag mutations in primary HIV-1 subtype C infection.
  
  
  METHODS
  A primary HIV-1C infection cohort comprised of 8 acutely and 34 recently infected subjects were followed frequently up to 500 days post-seroconversion (p/s). Gag mutations were analyzed by employing single-genome amplification and direct sequencing. Gag mutations were determined in relation to the estimated time of seroconversion. Time of appearance, dominance, and completeness was compared for different types of in vivo Gag mutations.
  
  
  RESULTS
  Reverse mutations to the wild type appeared at a median (IQR) of 62 (44;139) days p/s, while escape mutations from the wild type appeared at 234 (169;326) days p/s (p<0.001). Within the subset of mutations that became dominant, reverse and escape mutations appeared at 54 (30;78) days p/s and 104 (47;198) days p/s, respectively (p<0.001). Among the mutations that reached completeness, reverse and escape mutations appeared at 54 (30;78) days p/s and 90 (44;196) days p/s, respectively (p=0.006). Time of dominance for reverse mutations to and escape mutations from the wild type was 58 (44;105) days p/s and 219 (90;326) days p/s, respectively (p<0.001). Time of completeness for reverse and escape mutations was 152 (100;176) days p/s and 243 (101;370) days p/s, respectively (p=0.001). Fitting a Cox proportional hazards model with frailties confirmed a significantly earlier time of appearance (hazard ratio (HR): 2.6; 95% CI: 2.3-3.0), dominance (4.8 (3.4-6.8)), and completeness (3.6 (2.3-5.5)) of reverse mutations to the wild type Gag than escape mutations from the wild type. Some complex mutational pathways in Gag included sequential series of reversions and escapes.
  
  
  CONCLUSIONS
  The study identified the timing of different types of in vivo Gag mutations in primary HIV-1 subtype C infection in relation to the estimated time of seroconversion. Overall, the in vivo reverse mutations to the wild type occurred significantly earlier than escape mutations from the wild type. This shorter time to incidence of reverse mutations remained in the subsets of in vivo Gag mutations that reached dominance or completeness.
authors.affiliation: Harvard School of Public Health AIDS Initiative, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Novitsky
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: Lauren
authors.initials: L
authors.lastname: Margolin
authors.forename: Jeannie
authors.initials: J
authors.lastname: Baca
authors.forename: Lemme
authors.initials: L
authors.lastname: Kebaabetswe
authors.forename: Raabya
authors.initials: R
authors.lastname: Rossenkhan
authors.forename: Caitlin
authors.initials: C
authors.lastname: Bonney
authors.forename: Michaela
authors.initials: M
authors.lastname: Herzig
authors.forename: David
authors.initials: D
authors.lastname: Nkwe
authors.forename: Sikhulile
authors.initials: S
authors.lastname: Moyo
authors.forename: Rosemary
authors.initials: R
authors.lastname: Musonda
authors.forename: Elias
authors.initials: E
authors.lastname: Woldegabriel
authors.forename: Erik
authors.initials: E
authors.lastname: van Widenfelt
authors.forename: Joseph
authors.initials: J
authors.lastname: Makhema
authors.forename: Stephen
authors.initials: S
authors.lastname: Lagakos
authors.forename: M
authors.initials: M
authors.lastname: Essex
mesh_terms: D000208:Acute Disease; D000328:Adult; D015331:Cohort Studies; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000235:genetics* / Q000821:virology*; D006679:HIV Seropositivity; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D017422:Sequence Analysis, DNA; D013997:Time Factors; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D054301:gag Gene Products, Human Immunodeficiency Virus