Incidence and Prevalence of Intrasubtype HIV-1 Dual Infection in At-Risk Men in the United States

• Published in: The Journal of infectious diseases 2014-04, Vol.209 (7), p.1032-1038
• Main Authors: Wagner, Gabriel A., Pacold, Mary E., Pond, Sergei L. Kosakovsky, Caballero, Gemma, Chaillon, Antoine, Rudolph, Abby E., Morris, Sheldon R., Little, Susan J., Richman, Douglas D., Smith, Davey M.
• Format: Article
• Language: English
• Subjects: Adult; Biological and medical sciences; Blood plasma; Coinfection; Coinfection - epidemiology; Coinfection - virology; Complementary DNA; Design analysis; Female; Fundamental and applied biological sciences. Psychology; Genotype; High-Throughput Nucleotide Sequencing; HIV; HIV 1; HIV infections; HIV Infections - epidemiology; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; HIV/AIDS; Homosexuality, Male; Human immunodeficiency virus 1; Human viral diseases; Humans; Incidence; Infectious diseases; Major and Brief Reports; Male; Medical sciences; Microbiology; Miscellaneous; Phylogeny; Polymerase chain reaction; Prevalence; RNA, Viral - genetics; Superinfection; T lymphocytes; United States - epidemiology; Viral diseases; Viral diseases of the lymphoid tissue and the blood. Aids; Virology
• ISSN: 0022-1899; 1537-6613
• DOI: 10.1093/infdis/jit633

Background. Human immunodeficiency virus type 1 (HIV-1) dual infection (DI) has been associated with decreased CD4 T-cell counts and increased viral loads; however, the frequency of intrasubtype DI is poorly understood. We used ultradeep sequencing (UDS) to estimate the frequency of DI in a primary infection cohort of predominantly men who have sex with men (MSM). Methods. HIV-1 genomes from longitudinal blood samples of recently infected, therapy-naive participants were interrogated with UDS. DI was confirmed when maximum sequence divergence was excessive and supported by phylogenetic analysis. Coinfection was defined as DI at baseline; superinfection was monoinfection at baseline and DI at a later time point. Results. Of 118 participants, 7 were coinfected and 10 acquired superinfection. Superinfection incidence rate was 4.96 per 100 person-years (95% confidence interval [CI], 2.67-9.22); 6 occurred in the first year and 4 in the second. Overall cumulative prevalence of intrasubtype DI was 14.4% (95% CI, 8.6%-22.1%). Primary HIV-1 incidence was 4.37 per 100 person-years (95% CI, 3.56-5.36). Conclusions. Intrasubtype DI was frequent and comparable to primary infection rates among MSM in San Diego; however, superinfection rates declined over time. DI is likely an important component of the HIV epidemic dynamics, and development of stronger immune responses to the initial infection may protect from superinfection.