期刊文献

Geographical Variability Affects CCHFV Detection by RT–PCR: A Tool for In-Silico Evaluation of Molecular Assays 收藏

地理变异性通过RT-PCR影响CCHFV检测：用于分子测定的硅硅酸中的工具

原文求助发布源

作者

Cesare E. M. Gruber[ 1]; Barbara Bartolini[ 1;[*]; Concetta Castilletti[ 1]; Ali Mirazimi[ 2;3;4]; Roger Hewson[ 5]; Iva Christova[ 6]; Tatjana Avšič[ 7]; Roland Grunow[ 8]; Anna Papa[ 9]; María P. Sánchez-Seco[ 10]; Marion Koopmans[ 11]; Giuseppe Ippolito[ 1]; Maria R. Capobianchi[ 1]; Chantal B. E. M. Reusken[ 11;12];Antonino Di Caro[ 1]

作者单位

[1] National Institute for Infectious Diseases (INMI) “L. Spallanzani” IRCCS, WHO Collaborating Center for clinical care, diagnosis, response and training on Highly Infectious Diseases, 00149 Rome, Italy [2] Public Health agency of Sweden, 17182 Solna, Sweden [3] National veterinary Institute, 75189 Uppsala, Sweden [4] Department of laboratory Medicine, Clinical Microbiology, Karolinska Institute and Karolinska, 17177 Stockholm, Sweden [5] Public Health England, National Infection Service WHO Collaborating Centre for Virus Reference and Research (Special Pathogens) Porton Down, Salisbury SP40JG, UK [6] National Reference Laboratory on Vector-Borne Pathogens, Leptospira and Listeria, Microbiology Department, National Center of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria [7] Faculty of Medicine, Institute of Microbiology and Immunology, 1000 Ljubljana, Slovenia [8] Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany [9] Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece [10] National Centre of Microbiology, Institute of Health “Carlos III”, Majadahonda, 28220 Madrid, Spain [11] Erasmus MC, Department of Viroscience, WHO Collaborating Centre for arbovirus and viral hemorrhagic fever reference and research, 3015 CN Rotterdam, The Netherlands [12] Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands [*] Author to whom correspondence should be addressed. Viruses 2019, 11(10), 953; https://doi.org/10.3390/v11100953

关键词

CCHFV; molecular detection; Crimean–Congo hemorrhagic fever virus; arthropod-borne virus; laboratory preparedness; emerging diseases

关键词译文

CCHFV;分子检测;克里米亚刚果出血热病毒;节肢动物传播病毒;实验室准备;新兴疾病

发布日期

2019-10-16

页码

953

DOI

10.3390/v11100953

来源信息

Viruses ISSN：1999-4915, 2019年, 11卷, 10期, 953页

摘要

The Crimean–Congo hemorrhagic fever virus (CCHFV) is considered to be a major emerging infectious threat, according to the WHO R&D blueprint. A wide range of CCHFV molecular assays have been developed, employing varied primer/probe combinations. The high genetic variability of CCHFV often hampers the efficacy of available molecular tests and can affect their diagnostic potential. Recently, increasing numbers of complete CCHFV genomic sequences have become available, allowing a better appreciation of the genomic evolution of this virus. We summarized the current knowledge on molecular methods and developed a new bioinformatics tool to evaluate the existing assays for CCHFV detection, with a special focus on strains circulating in different geographical areas. Twenty-two molecular methods and 181 sequences of CCHFV were collected, respectively, from PubMed and GenBank databases. Up to 28 mismatches between primers and probes of each assay and CCHFV strains were detected through in-silico PCR analysis. Combinations of up to three molecular methods markedly decreased the number of mismatches within most geographic areas. These results supported the good practice of CCHFV detection of performing more than one assay, aimed for different sequence targets. The choice of the most appropriate tests must take into account patient’s travel history and geographic distribution of the different CCHFV strains.

摘要译文

根据世界卫生组织的研发蓝图，克里米亚刚果出血热病毒（CCHFV）被认为是一个主要的新兴传染性威胁。已经开发出广泛的CCHFV分子测定，采用不同的引物/探针组合。 CCHFV的高遗传变异通常妨碍了可用分子试验的功效，并会影响其诊断潜力。最近，越来越多的完整CCHFV基因组序列已经可用，从而更好地欣赏该病毒的基因组进化。我们总结了目前关于分子方法的知识，并开发了一种新的生物信息学工具，以评估CCHFV检测的现有测定，特别关注在不同地理区域循环的菌株。分别由PubMed和Genbank数据库收集二十二个分子方法和181个CCHFV序列。通过硅PCR分析检测每种测定和CCHFV菌株的引物和探针之间的28个错配。最多三种分子方法的组合显着降低了大多数地理区域内的不匹配数量。这些结果支持CCHFV检测的良好做法，用于执行多个测定的旨在针对不同的序列靶标。选择最合适的测试必须考虑到患者的旅行历史和不同CCHFV菌株的地理分布。