Wertheim Joel O, Kosakovsky Pond Sergei L, Forgione Lisa A, Mehta Sanjay R, Murrell Ben, Shah Sharmila, Smith Davey M, Scheffler Konrad, Torian Lucia V
Department of Medicine, University of California San Diego, San Diego, California, United States of America.
New York City Department of Health and Mental Hygiene, New York, New York, United States of America.
PLoS Pathog. 2017 Jan 9;13(1):e1006000. doi: 10.1371/journal.ppat.1006000. eCollection 2017 Jan.
Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these contact networks. For HIV-1, a rapidly evolving pathogen with low per-contact transmission rates, viral genetic sequences are an additional source of data that can be used to infer or refine transmission networks.
The New York City Department of Health and Mental Hygiene interviews individuals newly diagnosed with HIV and elicits names of sexual and injection drug using partners. By law, the Department of Health also receives HIV sequences when these individuals enter healthcare and their physicians order resistance testing. Our study used both HIV sequence and partner naming data from 1342 HIV-infected persons in New York City between 2006 and 2012 to infer and compare sexual/drug-use named partner and genetic transmission networks. Using these networks, we determined a range of genetic distance thresholds suitable for identifying potential transmission partners. In 48% of cases, named partners were infected with genetically closely related viruses, compatible with but not necessarily representing or implying, direct transmission. Partner pairs linked through the genetic similarity of their HIV sequences were also linked by naming in 53% of cases. Persons who reported high-risk heterosexual contact were more likely to name at least one partner with a genetically similar virus than those reporting their risk as injection drug use or men who have sex with men.
We analyzed an unprecedentedly large and detailed partner tracing and HIV sequence dataset and determined an empirically justified range of genetic distance thresholds for identifying potential transmission partners. We conclude that genetic linkage provides more reliable evidence for identifying potential transmission partners than partner naming, highlighting the importance and complementarity of both epidemiological and molecular genetic surveillance for characterizing regional HIV-1 epidemics.
性传播感染通过接触网络传播。性伴询问和通知是常用的公共卫生工具，用于识别、通知和为这些接触网络中的相关人员提供检测。对于人类免疫缺陷病毒1型（HIV-1）这种传播率低且快速演变的病原体，病毒基因序列是可用于推断或完善传播网络的额外数据来源。
纽约市卫生和精神卫生部门对新诊断出感染HIV的个体进行访谈，并询问其性伴和注射吸毒同伴的姓名。根据法律，当这些个体接受医疗保健且其医生开具耐药性检测医嘱时，卫生部门也会收到HIV序列。我们的研究使用了2006年至2012年纽约市1342名HIV感染者的HIV序列和性伴姓名数据，以推断和比较性/吸毒相关的指名性伴和基因传播网络。利用这些网络，我们确定了一系列适合识别潜在传播性伴的基因距离阈值。在48%的案例中，指名性伴感染了基因密切相关的病毒，这与直接传播相符，但不一定代表或意味着直接传播。通过HIV序列的基因相似性联系起来的性伴对，在53%的案例中也通过指名联系起来。报告有高危异性接触的人比报告其风险为注射吸毒或男男性行为的人更有可能指名至少一名感染基因相似病毒的性伴。
我们分析了一个规模空前且详细的性伴追踪和HIV序列数据集，并确定了用于识别潜在传播性伴的基于经验的合理基因距离阈值范围。我们得出结论，基因联系为识别潜在传播性伴提供了比性伴指名更可靠的证据，凸显了流行病学和分子基因监测在描述区域HIV-1流行特征方面的重要性和互补性。
