完善在废水中发现新出现的SARS-CoV-2突变的检测方法:关于Omicron变种的案例研究
Xiaoqing Xu1, Yu Deng1, Jiahui Ding1
1Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
The Science of the total environment
|August 17, 2023
概括
修改RT-qPCR试验可以改善对SARS-CoV-2 Omicron变种的废水监测. 精细的原料/探针序列提高了检测灵敏度和特异性,用于公共卫生监测.
科学领域:
- 环境微生物学环境微生物学
- 分子诊断学 分子诊断学
- 公共卫生病毒学.
背景情况:
- 污水监测对于跟踪导致COVID-19的病毒SARS-CoV-2至关重要.
- 新兴的SARS-CoV-2变种,如Omicron,由于累积的突变,对现有的诊断试验提出了挑战.
- 优化RT-qPCR原料/探针设计对于在废水中准确检测变体至关重要.
研究的目的:
- 开发和验证一种改进的RT-qPCR检测方法,用于废水中的SARS-CoV-2 Omicron变体.
- 评估原始和修改后的原料/探针组对Omicron变异突变的性能.
- 突出调整诊断工具以应对不断变化的病毒威胁的必要性.
主要方法:
- 来自香港的882个Omicron变体序列的in silico分析,以确定原始/探针不匹配.
- 基于in silico发现的三种常用的RT-qPCR试验的修改.
- 评估使用废水样本进行的七项原始和三项修改试验.
- 对六个废水样本进行测序,以确认初级/探头结合点的不匹配.
主要成果:
- 七个原始测定中的五个显示出对Omicron变体 (LoD 1.532.76副本/μL) 的良好的敏感性.
- UCDC-N1和Charité-E测定表现不佳,负载量高 (>10副本/μL) 和错误的结果.
- 经过修改的测试表明,在检测81个废水样本中的Omicron时,提高了灵敏度,特异性和可重复性.
结论:
- 初始剂/探针序列不匹配对检测SARS-CoV-2变种的RT-qPCR测定性能产生重大影响.
- 重新配置和完善起料/探头组件对于保持废水监测的诊断效率至关重要.
- 这项研究强调了分子诊断方法的持续适应对于有效的流行病控制的重要性.
更多相关视频
09:26Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
1.2K
10:53Concentration of Virus Particles from Environmental Water and Wastewater Samples Using Skimmed Milk Flocculation and Ultrafiltration
Published on: March 17, 2023
1.6K
相关概念视频
Viral Mutations
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Coronavirus
Coronaviruses, including the severe acute respiratory syndrome coronavirus (SARS-CoV), are enveloped viruses characterized by their single-stranded, positive-sense RNA genome and helical nucleocapsid structure. The hallmark of these viruses is their club-shaped spike (S) glycoproteins that protrude from the viral envelope, facilitating attachment to host cells. Typically, coronaviruses infect the upper respiratory tract, often causing mild or asymptomatic disease. However, certain strains like...
