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使用Ion AmpliSeq技术进行SARS-CoV-2的替代基因组测序方法
Md Shazid Hasan1, M Shaminur Rahman1, Prosanto Kumar Das1
1Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh.
MethodsX
|March 25, 2024
概括
这项研究提出了一种具有成本效益的替代方法,用于测序整个SARS-CoV-2基因组,这对于跟踪大流行至关重要. 经过验证的方法使用易于获得的试剂进行高通量测序,有利于资源有限的设置.
科学领域:
- 病毒学 病毒学
- 基因组学就是基因组学.
- 分子生物学分子生物学
背景情况:
- 准确追踪SARS-CoV-2大流行需要了解其全球遗传特征.
- 费舍尔科学公司开发了Ion AmpliSeq SARS-CoV-2研究小组,用于针对性全基因组测序.
研究的目的:
- 为了验证一种替代的,具有成本效益的方法来完成SARS-CoV-2基因组测序.
- 评估使用不同的商业测序套件和试剂的可行性.
主要方法:
- 使用两个不同的主混合 (EM和PM) 的初始池进行SARS-CoV-2cDNA放大.
- 使用了NEBNext®快速DNA图书馆准备套件用于Ion TorrentTM,作为标准Ion AmpliSeq图书馆套件Plus的替代品.
- 使用Ion Torrent技术进行的测序.
主要成果:
- 成功测序了SARS-CoV-2全基因组,平均深度为2351.
- 98.1%的总读数与参考序列 (武汉-胡-1) 保持一致.
- 使用两种测试试剂组检索完整的基因组,尽管覆盖范围不同,但成本较低.
结论:
- 针对SARS-CoV-2全基因组的一种替代性,高通量测序程序已经成功验证.
- 这种方法提供了一个低成本的协议,适合发展中国家,其测序设施有限.
- 经过验证的技术有助于全球跟踪SARS-CoV-2大流行,特别是在孟加拉国等资源有限的地区.
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