Broad Detection of Infectious Agents in Blood by Microarrays and Deep Sequencing

描述（由申请人提供）：血源性感染因子，包括新的/新出现的关注病原体，对我们的血液供应和美国每年进行的500万次输血的安全性构成持续威胁。在这里，我们建议应用两种最先进的诊断技术，一种称为Virochip的泛病毒微阵列和大规模并行深度测序，以全面识别血液中的感染因子。Virochip将扩展到包括血液传播的非病毒和病毒病原体，我们将严格评估分析测试特性（例如灵敏度、特异性、检测限、准确性），以检测与最常见的血液传播感染相关的病原体，包括疟疾、恰加斯病、艾滋病毒、B/C型肝炎和登革热病毒。扩展后的病毒芯片和深度测序随后将用于启动针对血源性传染因子的广谱监测计划。我们最初将重点分析来自非甲-戊型临床肝炎患者和献血后急性疾病（如发热）的递延献血者的血清样本-这些样本携带已知/新型传染性病原体的先验概率很高。我们将分析来自年龄、性别和地理位置相匹配的献血者的随机个体或合并血清样本，以检测我们血液供应中循环的传染性病原体。我们将通过血清学和PCR对输血中发现的任何新型病毒进行全基因组测序和流行病学筛查。本研究的一个主要目标是评估病毒芯片和深度测序作为确保输血安全的全面病原体筛查工具的实用性。在血液中发现新的传染性病原体也将促使对其流行病学和致病性进行进一步的详细调查。 公共卫生相关性：已知的新型/新兴传染病原不断威胁着美国每年进行的500万次输血的安全，但缺乏能够全面检测血源性病原体或识别新型/不同菌株的诊断工具阻碍了监测工作。本研究旨在研究Virochip（一种泛病毒微阵列）和大规模并行深度测序作为互补策略的实用性，用于（1）广泛检测血源性病原体，以及（2）识别新型/新兴传染性病原体。这项研究的结果有可能推动这些技术最终获得FDA批准，作为基础广泛的筛查工具，以确保输血安全，具有重大的临床和公共卫生意义。在血液中发现新的传染性病原体也将为研究其流行病学及其对我们血液供应的威胁开辟新的途径。

DESCRIPTION (provided by applicant): Bloodborne infectious agents, including novel / emerging pathogens of concern, pose a continual threat to our blood supply and the safety of the 5 million transfusions performed annually in the United States. Here we propose to apply two state-of-the-art diagnostic technologies, a pan-viral microarray called the Virochip and massively parallel deep sequencing, to comprehensively identify infectious agents in blood. The Virochip will be expanded to cover bloodborne nonviral as well as viral pathogens, and we will rigorously assess analytical test characteristics (e.g. sensitivity, specificity, limits of detection, accuracy) for detection of pathogens associated with the most common bloodborne infections, including malaria, Chagas disease, HIV, hepatitis B/C, and dengue virus. The expanded Virochip and deep sequencing will then be used to launch a broad- spectrum surveillance program for bloodborne infectious agents. We will initially focus on analyzing serum samples from patients with nonA-E clinical hepatitis and deferred blood donors with post-donation acute illness such as fever - samples which carry a high a priori probability of harboring known / novel infectious agents. We will analyze random individual or pooled serum samples from donors matched by age, sex, and geographic location for infectious agents circulating in our blood supply. We will perform whole-genome sequencing and epidemiological screening by serology and PCR for any novel viruses identified in transfused blood. A major goal of this research is to assess the utility of Virochip and deep sequencing as comprehensive pathogen screening tools for ensuring transfusion safety. Identification of novel infectious agents in blood will also spur further detailed investigations into their epidemiology and pathogenicity. PUBLIC HEALTH RELEVANCE: Known as well as novel / emerging infectious agents continually threaten the safety of the 5 million transfusions performed annually in the United States, yet the lack of diagnostic tools able to comprehensively test for bloodborne pathogens or to identify novel / divergent strains has hindered surveillance efforts. This study proposes to investigate the utility of the Virochip, a pan-viral microarray, and massively parallel deep sequencing as complementary strategies for (1) broad-based detection of bloodborne pathogens, and (2) identification of novel / emerging infectious agents. The results from this study have the potential to advance these technologies for eventual FDA approval as broad-based screening tools to ensure transfusion safety, with significant clinical and public health implications. Identification of novel infectious agents in blood will also open up new avenues of research into their epidemiology and the threat that they pose to our blood supply.