Y Chromosome DNA in Women's Vaginal Samples as a Biomarker of Recent Vaginal Sex and Condom Use With Male Partners in the HPV Infection and Transmission Among Couples Through Heterosexual Activity Cohort Study

Sex Transm Dis. 2018 Jan;45(1):28-34. doi: 10.1097/OLQ.0000000000000688.


Background: Y chromosome DNA from male epithelial and sperm cells was detected in vaginal samples after unprotected sex in experimental studies. We assessed the strength of this association in an observational setting to examine the utility of Y chromosome DNA as a biomarker of recent sexual behaviors in epidemiological studies.

Methods: The HPV (human papillomavirus) Infection and Transmission Among Couples Through Heterosexual Activity cohort study enrolled 502 women attending a university or college in Montréal, Canada, and their male partners from 2005 to 2010. Participants completed self-administered questionnaires. We used real-time polymerase chain reaction to test women's baseline vaginal samples for Y chromosome DNA and assessed which sexual behaviors were independent predictors of Y chromosome DNA positivity and quantity with logistic and negative binomial regression.

Results: Y chromosome DNA positivity decreased from 77% in women in partnerships reporting vaginal sex 0 to 1 day ago to 13% in women in partnerships reporting last vaginal sex of 15 or more days ago (adjusted odds ratio, 0.09; 95% confidence interval, 0.02-0.36). The mean proportion of exfoliated vaginal sample cells with Y chromosome DNA was much lower for women who reported always using condoms (0.01%) than for women who reported never using condoms (2.07%) (adjusted ratio, 26.8; 95% confidence interval, 8.9-80.5). No association was found with reported oral/digital sex frequency or concurrency of partnerships.

Conclusions: Y chromosome DNA quantity is strongly associated with days since last vaginal sex and lack of condom use in observational settings. Y chromosome DNA quantity may prove useful as a correlate of recent vaginal sex in observational studies lacking data on sexual behavior, such as surveillance studies of human papillomavirus infection prevalence.

Publication types

  • Observational Study

MeSH terms

  • Biomarkers / analysis
  • Canada
  • Chromosomes, Human, Y / genetics*
  • Coitus*
  • Condoms / statistics & numerical data*
  • DNA / analysis*
  • Female
  • Heterosexuality*
  • Human papillomavirus 16 / isolation & purification
  • Humans
  • Male
  • Odds Ratio
  • Papillomavirus Infections / transmission*
  • Papillomavirus Infections / virology
  • Polymerase Chain Reaction
  • Population Surveillance
  • Predictive Value of Tests
  • Prevalence
  • Risk Factors
  • Sexual Partners*
  • Surveys and Questionnaires
  • Vagina / metabolism*
  • Vagina / virology
  • Young Adult


  • Biomarkers
  • DNA