一个黄金标准的数据集和评估从废水中估计血统丰度的方法
Jannatul Ferdous1, Samuel Kunkleman1, William Taylor1
1Department of Bioinformatics and Genomics, UNC Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.
The Science of the total environment
|July 6, 2024
概括
废水监测有效地通过基因组测序追踪SARS-CoV-2变种. 弗雷亚和VaQuERo软件在从复杂的废水样本中识别病毒系的精度更高.
科学领域:
- 环境微生物学环境微生物学
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
背景情况:
- 基于基因组的废水监测对于监测SARS-CoV-2变种至关重要.
- 废水的复杂基因复杂化了病毒解和变种识别.
- 需要标准化的数据集来评估解卷工具的性能.
研究的目的:
- 为评估SARS-CoV-2废水解工具创建一个黄金标准数据集.
- 为了比较八个常见的解卷软件包的性能.
- 评估原料计划和废水矩阵对序列化和解卷化的影响.
主要方法:
- 创建了一个合成病毒控制混合物,其成分已知.
- 混合物被入废水RNA矩阵中,并使用牛津纳米孔技术进行了测序.
- 八个解卷工具 (Freyja, kallisto, Kraken 2/Bracken, LCS, Lollipop, lineagespot, Alcov, VaQuERo) 进行了评估. 这些工具包括:
主要成果:
- 弗雷亚和VaQuERo在识别SARS-CoV-2血统方面显示出最高的准确性.
- 弗雷耶超越了CDC废水监测协议中的其他工具.
- 在Freyja和VaQuERo之间,在处理虚假阴性和虚假阳性方面观察到微小的差异.
结论:
- 弗雷亚和VaQuERo是SARS-CoV-2变种在废水中脱的高度准确的工具.
- 该研究强调了初级选择和样本矩阵对测序结果的影响.
- 这项工作为基于废水的病毒监测工具开发提供了基准.
更多相关视频
08:03Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.1K
06:54Author Spotlight: Understanding and Detecting Environmental Antimicrobial Resistance by Combining Culture-Based Techniques and Genomics
Published on: July 19, 2024
1.0K
相关概念视频
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
01:30Methods to Assess Microbial Populations
Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...