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 B 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.