Research Article: Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study

Date Published: December 27, 2017

Publisher: Public Library of Science

Author(s): Christine Johnston, Amalia Magaret, Pavitra Roychoudhury, Alexander L. Greninger, Daniel Reeves, Joshua Schiffer, Keith R. Jerome, Cassandra Sather, Kurt Diem, Jairam R. Lingappa, Connie Celum, David M. Koelle, Anna Wald, Nicola Low

Abstract: BackgroundQuantitative estimation of the extent to which the immune system’s protective effect against one herpes simplex virus type 2 (HSV-2) infection protects against infection with additional HSV-2 strains is important for understanding the potential for HSV-2 vaccine development. Using viral genotyping, we estimated the prevalence of HSV-2 dual-strain infection and identified risk factors.Methods and findingsPeople with and without HIV infection participating in HSV-2 natural history studies (University of Washington Virology Research Clinic) and HIV prevention trials (HIV Prevention Trials Network 039 and Partners in Prevention HSV/HIV Transmission Study) in the US, Africa, and Peru with 2 genital specimens each containing ≥105 copies herpes simplex virus DNA/ml collected a median of 5 months apart (IQR: 2–11 months) were included. It is unlikely that 2 strains would be detected in the same sample simultaneously; therefore, 2 samples were required to detect dual-strain infection. We identified 85 HSV-2 SNPs that, in aggregate, could determine whether paired HSV-2 strains were the same or different with >90% probability. These SNPs were then used to create a customized high-throughput array-based genotyping assay. Participants were considered to be infected with more than 1 strain of HSV-2 if their samples differed by ≥5 SNPs between the paired samples, and dual-strain infection was confirmed using high-throughput sequencing (HTS). We genotyped pairs of genital specimens from 459 people; 213 (46%) were men, the median age was 34 years (IQR: 27–44), and 130 (28%) were HIV seropositive. Overall, 272 (59%) people were from the US, 59 (13%) were from Peru, and 128 (28%) were from 8 countries in Africa. Of the 459 people, 18 (3.9%) met the criteria for dual-strain infection. HTS and phylogenetic analysis of paired specimens confirmed shedding of 2 distinct HSV-2 strains collected at different times in 17 pairs, giving an estimated dual-strain infection prevalence of 3.7% (95% CI = 2.0%–5.4%). Paired samples with dual-strain infection differed by a median of 274 SNPs in the UL_US region (range 129–413). Matching our observed dual-strain infection frequency to simulated data of varying prevalences and allowing only 2 samples per person, we inferred the true prevalence of dual-strain infection to be 7%. In multivariable analysis, controlling for HIV status and continent of origin, people from Africa had a higher risk for dual-strain infection (risk ratio [RR] = 9.20, 95% CI = 2.05–41.32), as did people who were HIV seropositive (RR = 4.06, 95% CI = 1.42–11.56).ConclusionsHSV-2 dual-strain infection was detected in 3.7% of paired samples from individual participants, and was more frequent among people with HIV infection. Simulations suggest that the true prevalence of dual-strain infection is 7%. Our data indicate that naturally occurring immunity to HSV-2 may be protective against infection with a second strain. This study is limited by the inability to determine the timing of acquisition of the second strain.

Partial Text: Development of an effective herpes simplex virus type 2 (HSV-2) prophylactic vaccine is a global priority to improve sexual health [1,2]. Although several HSV-2 subunit vaccine candidates appeared effective in animal models, these vaccines have failed to prevent HSV-2 disease in humans in Phase III clinical trials, despite eliciting high levels of neutralizing antibody [3,4]. Knowledge of HSV-2 immunology has advanced with identification of B cell and T cell epitopes as well as identification of tissue-resident memory T cells; however, correlates of HSV-2 immunity in immunocompetent people have not been identified [5–9].

In this report, we systematically studied the prevalence of HSV-2 dual-strain infection using paired genital swab samples collected at 2 different time points from 459 people in 3 continents. Among 18 pairs of samples that appeared to have different strains at the 2 time points by genotyping, we definitively confirmed that 2 different strains were shed at different time points in 13 people using whole genome sequencing, and were unable to perform confirmatory sequencing in 4 pairs. These results revealed that the prevalence of HSV-2 dual-strain infection was 3.7%, with sampling-adjusted estimates indicating that the true prevalence may be 7%. In multivariable analysis, dual-strain infection was associated with people who were from Africa and people with HIV infection. The finding that HSV-2 dual-strain infection was relatively rare in this sample may indicate that the natural immune response is usually sufficient to protect against infection with a second strain of HSV-2. These data suggest that a vaccine format that elicits a breadth and level of specific immunity that meets, or exceeds, that achieved by natural genital HSV-2 infection may be efficacious in preventing infection with wild-type virus.



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