NeoChip for specific and rapid identification of congenital CMV and neonatal HSV infections on minimal sample volume

NeoChip 用于以最少的样本量特异性快速识别先天性 CMV 和新生儿 HSV 感染

• 批准号: 10701864
• 负责人: Shelley M Lawrence
• 金额: $ 51.57万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10701864
• 关键词: Address; Advocate; Antibiotics; Antibodies; Antimicrobial Resistance; Antiviral Agents; Antiviral resistance; Base Sequence; Biological; Biological Assay; Birth; Blinded; Blood; Blood Volume; Blood specimen; California; Child; Clinical; Clinical Research; Collaborations; Congenital herpes simplex; Consumption; Culture Techniques; Cytomegalovirus; DNA; Data; Databases; Detection; Diagnosis; Diagnostic; Disabled Persons; Disease; Dryness; Dyes; Early Intervention; Early identification; Enrollment; Epidemiology; Etiology; Evaluation; Failure; Fingerprint; Fluorescence; Funding; Genome; Genomic Segment; Genotype; Goals; Health; Herpes Simplex Infections; Hour; Immunoglobulin G; Immunoglobulin M; Individual; Infant; Infection; Investigation; Laboratories; Life; Machine Learning; Measures; Microbe; Modality; Modernization; Molecular; Mothers; Neonatal; Neonatal Screening; Newborn Infant; Nucleic Acid Amplification Tests; Nucleotides; Outcome; Pathogen detection; Pathogenicity; Patients; Perinatal; Polymerase Chain Reaction; Predictive Value; Pregnant Women; Prevalence; RNA; Reaction; Reporting; Research; Research Personnel; Resistance; Resolution; Risk; Saliva; Sampling; Simplexvirus; Specificity; Spottings; Symptoms; Techniques; Technology; Testing; Therapeutic; Therapeutic Intervention; Time; Tissues; Training; Translating; Tube; United States; Universities; Update; Urine; Variant; Viral; Viral Load result; accurate diagnosis; antimicrobial; artificial intelligence algorithm; biobank; clinical database; clinical outcome measures; clinically relevant; congenital cytomegalovirus; cost; detection limit; detection method; diagnosis standard; diagnostic biomarker; diagnostic tool; digital; disease prognosis; falls; intercalation; interdisciplinary approach; intervention program; machine learning algorithm; melting; microbial; multidisciplinary; neonatal infection; neonate; next generation sequencing; offspring; pathogen; pathogen genomics; pathogenic virus; point of care; postnatal; prevent; prospective; rapid diagnosis; reactivation from latency; resistance gene; screening program; single molecule; technology validation; timeline; transmission process

Project Summary Congenital cytomegalovirus (cCMV) and neonatal herpes simplex virus (nHSV) impose major health threats on neonates. Although CMV and HSV are lifelong infections with periods of latency and reactivation, most maternal infections remain undiagnosed due to nonspecific or absent clinical symptoms. In the United States, a child is permanently disabled by cCMV infection every hour, even though 9 of 10 infants are asymptomatic after birth and remain undiagnosed. Invasive nHSV, on the other hand, is a rare neonatal infection that presents with a broad range of clinical symptoms, including those that may be life-threatening. Viral culture and DNA detection by polymerase chain reaction (PCR) have become the “Gold Standard” for the diagnosis of cCMV and nHSV infection, despite poor sensitivity of PCR assays in neonates and time consuming culture techniques (up to 5-7 days). Universal genotyping of pathogen genomic sequences using High Resolution Melt (U-HRM) provides a simple, low cost, rapid, and modern alternative to viral cultures and PCR techniques. By measuring the fluorescence of an intercalating dye as PCR-amplified pathogen DNA or RNA fragments are heated and disassociate, sequence defined melt curves, or “fingerprints”, are generated with single-nucleotide resolution in a closed-tube reaction. These unique microbial “fingerprints” are then automatically identified and quantified using machine learning technology, with an accuracy of 99-100% on minimal blood volume (1 mL), in a platform called NeoChip. Presently, we have established unique signature melt curves for 40 bacterial species and antimicrobial resistance genes that commonly infect neonates. Additionally, NeoChip has been expanded to distinguish individually amplified melt curve signatures for multiple pathogen identification and quantification, as required for polymicrobial infection. In this proposal, we will build out NeoChip’s comprehensive database by incorporating clinical strains of CMV and HSV with actionable antiviral resistance genes. Because NeoChip identifies variances in nucleic acid sequences, individual differentiation and quantification of CMV and HSV strains are possible. We will also translate the NeoChip for specific and rapid diagnosis of cCMV and nHSV infection in a large prospective clinical study of pregnant women and their offspring(s), as well as directly compare the platform to standard quantitative nucleic acid test (QNAT) assays, IgG/IgM antibody testing, and clinical outcome measures for statistical concordance (predictive value). Finally, we will validate and translate NeoChip for cCMV detection and clinical correlation using dried blood spot (DBS) samples for incorporation into standard universal newborn screening programs. NeoChip’s goal is to provide an accurate and valid test for the timely diagnosis of pathogen etiology (viral, bacterial, and fungal) in a single test with efficacy on broad tissue matrices and capacity to inform microbial resistance, thereby facilitating early administration of targeted antimicrobials and therapeutics. This proposal directly addresses the funding call by applying a multidisciplinary approach to address the biomedical challenges of rapidly and accurately diagnosing cCMV and nHSV to facilitate disease prognostication and early therapeutic or intervention programs.

项目摘要 先天性巨细胞病毒（CCMV）和新生儿疱疹单纯病毒（NHSV）对 尽管CMV和HSV是终身感染，具有潜伏期和重新激活的周期，但大多数母体 由于非特异性或没有临床症状，感染仍未诊断。在美国，一个孩子是 每小时会因CCMV感染而永久残疾，即使10个婴儿中有9例出生后不对称 保持未诊断。另一方面，侵入性NHSV是一种罕见的新生儿感染，表现为宽阔 临床症状范围，包括可能威胁生命的症状。病毒培养和DNA检测 聚合酶链反应（PCR）已成为诊断CCMV和NHSV感染的“黄金标准”， 尽管PCR测定在新生儿和耗时的文化技术（最多5-7天）中，尽管PCR测定不良。 使用高分辨率熔体（U-HRM）对病原体基因组序列的通用基因分型提供了一个简单的， 低成本，快速和现代的病毒培养和PCR技术替代品。通过测量 作为PCR扩增的病原体DNA或RNA片段的插入染料被加热并分离，序列 定义的熔体曲线或“指纹”是在闭管反应中以单核苷酸分辨率产生的。 然后使用机器学习自动识别和量化这些独特的微生物“指纹” 在一个名为neochip的平台中，技术的精度为99-100％（1毫升）。目前， 我们已经为40种细菌物种和抗菌抗性基因建立了独特的特征熔融曲线，这些曲线是 通常感染的新生儿。此外，Neochip已扩展以区分单独放大的熔体 曲线特征是多种病原体鉴定和定量的曲线特征，如多数菌感染所需。 在此提案中，我们将通过结合CMV的临床菌株来构建Neochip的综合数据库 HSV具有可操作的抗病毒抗性基因。因为Neochip鉴定了核酸的方差 CMV和HSV菌株的序列，个体分化和定量是可能的。我们也会翻译 在大量的前瞻性临床研究中，用于CCMV和NHSV感染的特异性和快速诊断 孕妇及其后代，并将平台直接比较标准定量核 酸测试（QNAT）测定，IgG/IgM抗体测试和统计一致性的临床结果指标 （预测值）。最后，我们将验证和翻译Neochip使用CCMV检测和使用临床相关性 公司的干血点（DBS）样本用于标准的通用新生儿筛查计划。 Neochip的 目标是为病原体病因（病毒，细菌和细菌及时诊断）提供准确有效的测试 真菌）在一次测试中具有效率的广泛组织物质和能力来告知微生物抗性的能力，从而 促进靶向抗菌药物和治疗的早期给药。该建议直接解决了 通过采用多学科的方法来筹集资金，以应对快速，准确的生物医学挑战 诊断CCMV和NHSV以促进疾病提示和早期治疗或干预计划。