Chaudron Sandra E, Leemann Christine, Kusejko Katharina, Nguyen Huyen, Tschumi Nadine, Marzel Alex, Huber Michael, Böni Jürg, Perreau Matthieu, Klimkait Thomas, Yerly Sabine, Ramette Alban, Hirsch Hans H, Rauch Andri, Calmy Alexandra, Vernazza Pietro, Bernasconi Enos, Cavassini Matthias, Metzner Karin J, Kouyos Roger D, Günthard Huldrych F
Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
J Infect Dis. 2022 Sep 28;226(7):1256-1266. doi: 10.1093/infdis/jiac166.
Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and insufficient longitudinal samples.
Using the Swiss HIV Cohort Study (SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22 243 HIV-1 partial polymerase sequences was used to identify potential superinfections among 4575 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.
This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1%-7%, superinfections are not negligible events.
研究人类免疫缺陷病毒1型（HIV-1）的重复感染对于理解病毒传播、疾病进展和疫苗设计具有重要意义。但由于采样频率低和纵向样本不足，检测仍然具有挑战性。
利用瑞士HIV队列研究（SHCS），我们开发了一种用于重复感染的分子流行病学筛查方法。由22243个HIV-1部分聚合酶序列构建的系统发育树，用于在4575名有纵向序列的SHCS参与者中识别潜在的重复感染。通过对生物样本库中的血浆样本进行近全长病毒基因组测序（NFVGS），对一部分潜在的重复感染进行检测。
基于系统发育和距离标准，识别出325例潜在的HIV-1重复感染，并根据因样本误识别而被检测为重复感染的可能性进行分类。对128例潜在的重复感染进行了NFVGS检测；其中，52例被NFVGS证实，15例未被证实，61例由于测序样本未包括在原始筛查中导致重复感染信号的相关时间点，无法通过采样来确认或排除重复感染。因此，NFVGS能够支持67例采样充分的潜在重复感染中的52例。
据我们所知，这种基于队列的分子方法识别出了最大的已确认重复感染人群，表明虽然重复感染罕见，患病率为1%-7%，但并非可以忽略不计的事件。
