Characterization of plasma virome in people who inject drugs to identify early transmission networks of HIV and other bloodborne infections

迫切需要采用创新的方法来抗击艾滋病毒和艾滋病的死灰复燃。 注射吸毒者中的丙型肝炎病毒感染(PWID)。阿片类药物在美国的流行 各州威胁要破坏2030年消除这两种病毒的国家目标。而三级预防 战略在一定程度上促进了健康结果的改善，但一直难以阻止 传染病的传播。此外，艾滋病毒和丙型肝炎病毒等血液传播感染没有任何症状 初始感染，因此流行病的开始可能早于第一个诊断病例的确认 在社区里。此外，监督也因以下原因而受到阻碍：“自我报告” 污名化和刑事化。我们建议使用受试者之间共享的血浆病毒组分 静脉注射非法药物，以早期识别PWID的传播网络。 传播研究表明，在PWID中，丙型肝炎病毒先于艾滋病毒感染，因此出现了新的丙型肝炎病毒 感染是艾滋病毒感染风险社区的有力预测因素。我们现在问是否有病毒存在 在丙型肝炎病毒传播之前在PWID中共享的组件。我们的假设是未知的病毒 在感染艾滋病毒或丙型肝炎病毒之前，致病性会在血液中积累，并通过注射传播 药物使用，以便它们的序列揭示了这些流行病学联系。我们将首先确认我们的初步计划 在我们的巴尔的摩队列中使用分子和血清学评估在另一个PWID队列中进行的观察 从旧金山来的。与巴尔的摩的队列一样，旧金山的队列允许获取血浆样本 在感染丙型肝炎病毒之前、期间和之后。我们将比较年龄和年龄之间的血浆病毒体 性别匹配20例丙型肝炎病毒阳性(丙型肝炎病毒+PWID)和20例丙型肝炎病毒阴性(丙型肝炎病毒-PWID)。电浆 从两个时间点开始，对两组之间相同持续时间的随访进行测试。这个 丙型肝炎病毒+PWID将在感染丙型肝炎病毒之前和期间进行检测。差异将由以下因素决定 列举两组在两个时间点的病毒感染情况。然后血浆病毒体就会被 在病毒靶标浓缩后，使用牛津纳米孔进一步表征NGS。长时间的读取允许 适合系统发育研究的病毒株(单倍型)的鉴定。我们将确定等离子体的特征 来自巴尔的摩队列(n=10)的已知共享(连锁)丙型肝炎病毒序列的受试者中的病毒。此外，我们 将在获取丙型肝炎病毒之前对相同的受试者进行测序，以识别共享的(链接的)病毒序列 丙型肝炎病毒收购。来自旧金山队列的血浆样本的相似序列特征(n=10) 也将在两个时间点完成。对两个队列进行排序进一步验证了该方法，因为没有 应在两个队列之间观察到病毒组分的序列共享(连锁)。 通过使用常规收集的样本，这项工作可以改变药物使用网络的研究，并 改变对艾滋病毒、丙型肝炎病毒的公共卫生监测，揭露再感染和重复感染的隐秘动态。

There is an urgent need for implementing innovative methods to combat the resurgence of HIV and hepatitis C virus (HCV) infection among people who inject drugs (PWID). The opioid epidemic in the United States threatens to undermine national 2030 elimination goals for both viruses. While tertiary prevention strategies have facilitated to a certain extent in improving health outcomes it has been difficult to interdict transmission of infectious diseases. Moreover, bloodborne infections like HIV and HCV have no symptoms on initial infection, and thus the beginning of an epidemic can predate the recognition of the first diagnosed case in the community. In addition, surveillance is also hindered by disincentives for “self-report” caused by stigmatization and criminalization. We propose using plasma virome components shared between subjects due to intravenous injection of illicit drugs for early identification of transmission networks in PWID. Transmission studies have shown that HCV precedes HIV infection in PWID, and hence new HCV infections serve as strong predictors of communities at risk for HIV. We now ask if there are virome components that are shared before HCV transmission in PWID. Our hypothesis is that viruses of unknown pathogenicity will accumulate in blood before HIV or HCV infection and that they will be transmitted by injection drug use such that their sequences reveal those epidemiological linkages. We will first confirm our preliminary observations made in our Baltimore cohort using molecular and serology assessments in another PWID cohort from San Francisco. Like the Baltimore cohort, the San Francisco cohort allows access to plasma samples before, during, and after acquisition of HCV infection. We will compare plasma virome between age and gender matched twenty HCV positive (HCV+PWID) and twenty HCV negative (HCV-PWID) PWID. Plasma from two time points covering the same duration of follow up between the two groups will be tested. The HCV+PWID will be tested before and during acquisition of HCV. Differences will be determined by enumerating viral infections between the groups at both time points. The plasma virome will then be characterized further by NGS using Oxford Nanopore after viral target enrichment. The long reads allow identification of viral strains (haplotype) suitable for phylogenetic studies. We will characterize the plasma virome in subjects from the Baltimore cohort (n=10) known to share (linked) HCV sequences. In addition, we will sequence the same subjects before HCV acquisition to identify shared (linked) virome sequences before HCV acquisition. Similar sequence characterization of plasma samples from the San Francisco cohort (n=10) will also be done at two time points. Sequencing both cohorts further validates the approach since no sequence sharing (linkage) of the virome components should be observed between the two cohorts. By using routinely collected samples, this work could transform the research of drug use networks and change public health surveillance of HIV, HCV, and expose occult dynamics of reinfection and superinfection.