Background

Quantitative 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 findings

People 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 U_L_U_S 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).

Conclusions

HSV-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.

中文翻译：

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美国，秘鲁和撒哈拉以南非洲的8个国家的双株2型生殖器单纯疱疹病毒2型（HSV-2）感染：巢式截面病毒基因分型研究

背景

定量估计免疫系统对一种2型单纯疱疹病毒（HSV-2）感染的保护作用可防止其他HSV-2株感染的程度，对于理解HSV-2疫苗开发的潜力很重要。使用病毒基因分型，我们估计了HSV-2双株感染的患病率，并确定了危险因素。

方法和发现

患有或未感染HIV的人参加了美国，非洲和秘鲁的HSV-2自然史研究（华盛顿大学病毒学研究诊所）和HIV预防试验（HIV预防试验网络039和预防HSV / HIV传播合作伙伴）。 2个生殖器标本，每个样本均≥10 ⁵包括平均间隔5个月（IQR：2-11个月）收集的单纯疱疹病毒DNA / ml拷贝数。在同一样品中不可能同时检测到2个菌株。因此，需要2个样本来检测双株感染。我们确定了85个HSV-2 SNP，这些SNP合计可以确定配对的HSV-2菌株是相同还是不同，可能性> 90％。然后将这些SNP用于创建定制的基于高通量阵列的基因分型分析。如果参与者的样品在配对样品之间的差异大于或等于5个SNP，则认为参与者感染了1株以上的HSV-2，并且使用高通量测序（HTS）确认了双株感染。我们对459人的生殖器标本进行了基因分型。213名（46％）是男性，中位年龄为34岁（IQR：27-44），130例（28％）为HIV血清反应阳性。总体而言，有272人（59％）来自美国，有59人（13％）来自秘鲁，有128人（28％）来自非洲的8个国家。在459人中，有18人（3.9％）达到了双株感染的标准。HTS和配对标本的系统发育分析证实，在17个对中，在不同时间收集了2个不同的HSV-2株脱落，估计双株感染率为3.7％（95％CI = 2.0％–5.4％）。带有双毒株感染的配对样本在U中的中位数为274个SNP HTS和配对标本的系统发育分析证实，在17个对中，在不同时间收集了2个不同的HSV-2株脱落，估计双株感染率为3.7％（95％CI = 2.0％–5.4％）。带有双毒株感染的配对样本在U中的中位数为274个SNP HTS和配对标本的系统发育分析证实，在17个对中，在不同时间收集了2个不同的HSV-2株脱落，估计双株感染率为3.7％（95％CI = 2.0％–5.4％）。带有双毒株感染的配对样本在U中的中位数为274个SNP_L _U _S区域（范围129–413）。将我们观察到的双株感染频率与不同患病率的模拟数据进行匹配，并且每人仅允许2个样本，我们推断双株感染的真实患病率为7％。在多变量分析中，控制艾滋病毒状况和原产国，非洲人与双株感染的风险较高（风险比[RR] = 9.20，95％CI = 2.05–41.32），HIV阳性的人也是如此。 （RR = 4.06，95％CI = 1.42-11.56）。

结论

在个人参与者的配对样本中，有3.7％的人检测到HSV-2双株感染，并且在HIV感染者中更为常见。模拟表明，双株感染的真实患病率为7％。我们的数据表明，天然存在的对HSV-2的免疫力可能对第二种菌株的感染具有保护作用。这项研究受到无法确定第二个菌株获取时间的限制。