A systematic molecular epidemiology screen reveals numerous HIV-1 superinfections in the Swiss HIV Cohort Study. Journal of Infectious Diseases
Chaudron et al. aimed to study immunodeficiency virus type 1 (HIV-1) superinfection in the Swiss HIV Cohort Study (SHCS). Superinfection is the acquisition of another HIV-1 strain among individuals with an already established HIV-1 infection.
The authors used a phylogeny built from 22’243 HIV-1 partial polymerase sequences to identify potential superinfections among 4’575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples.
Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52 of 67 adequately sampled potential superinfections.
In conclusion, the study confirms that superinfections are rare but not negligible events, with an estimated prevalence of 1% to 7%, most likely an underestimation since detection is challenging. Nevertheless, this work paves the way for follow-up studies to benefit from the sample size and the NGS data generated to molecularly characterize HIV-1 superinfection and investigate other risk factors associated. Better molecular characterization and risk factors understanding could provide further insights into HIV transmission and pathogenesis, benefit HIV vaccine research, and enable preventive measures to raise awareness on HIV-1 superinfection in the community.