一个实时监测SARS-CoV-2遗传学的程序
Hayden N Brochu1, Kuncheng Song1, Qimin Zhang1
1Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA.
Scientific reports
|August 30, 2024
概括
全国范围的基础设施迅速测序了超过594,000个SARS-CoV-2基因组,使得美国的COVID-19变种能够实时进行基因组监测. 该系统支持公共卫生和流行病准备.
科学领域:
- 基因组监测是指基因组的监测.
- 病毒学 病毒学
- 公共卫生基础设施公共卫生基础设施
背景情况:
- COVID-19大流行凸显了对SARS-CoV-2变种的快速基因组监测的迫切需要.
- 现有的基础设施不足以及时检测和监测新出现的病毒系.
- 需要一个强大的系统来处理样本,测序和向公共卫生当局传播数据.
研究的目的:
- 描述美国针对SARS-CoV-2基因组监测的全国性基础设施的开发和部署.
- 详细介绍"Virseq"协议,用于高覆盖率,抗突变的全基因组测序.
- 建立一个快速应对新出现的传染病威胁的模型.
主要方法:
- 开发一个模块化基础设施,用于样本封存,整合和表征.
- 实施"Virseq"协议,用于SARS-CoV-2分离体的全基因组测序.
- 对594,832个SARS-CoV-2基因组的分析和379个共感染的特征.
主要成果:
- 从2020年3月到2023年7月,成功测序了594,832个高覆盖率的SARS-CoV-2基因组.
- "Virseq"协议显示出突变耐药性,并捕获了所有主要的SARS-CoV-2血统.
- 鉴定和表征了379种临床相关的多菌株共同感染.
- 开发了模拟方法,以可靠地检测新兴血统.
结论:
- 开发的基础设施有效地支持国家基因组监测计划,包括美国疾病控制和预防中心的努力.
- 描述的系统提供了一个可扩展的模型,用于国家一级快速应对新出现的流行病.
- 持续的基因组监测对于监测病毒演变和为公共卫生战略提供信息至关重要.
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