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使用呼吸道病原体小组对乌拉圭的基因组废水病毒流行病学进行有针对性的丰富测序

Florencia Cancela¹, Andrés Lizasoain², Yanina Panzera³

¹Laboratorio de Ecología Viral y Virus Zoonóticos, Unidad Académica de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, 11600, Montevideo, Uruguay.

Food and environmental virology

|January 9, 2025

概括

一个有针对性的测序小组有效地识别了废水中的各种呼吸道和肠道病毒,帮助基因组流行病学. 这种方法提高了用于公共卫生监测的复杂环境样本中的病毒检测灵敏度.

科学领域:

环境病毒学环境病毒学
基因组流行病学基因组流行病学
下一代测序的测序方法

背景情况:

人类呼吸道和肠道病毒导致全球显著的发病率和死亡率.
基于废水的流行病学 (WBE) 使用下一代测序 (NGS) 监测社区病毒动态.
在WBE中复杂的环境样本可能由于抑制剂和宿主材料而具有较低的病毒检测灵敏度.

研究的目的:

评估一个有针对性的丰富测序面板,用于检测废水中排泄的42种呼吸道病毒.
评估呼吸道病原体ID/AMR丰富面板 (RPIP) 与病毒监测的生物信息学分析相结合的实用性.

主要方法:

使用RPIP小组分析乌拉圭的3个污水样本.
针对性丰富测序针对皮科纳病毒,亚登病毒,冠病毒,帕拉米克索病毒,奥斯托米克索病毒,奥斯托赫尔佩斯病毒,肺病毒和帕尔沃病毒家族.
使用Explify软件进行生物信息学分析,用于病毒识别和表征.

主要成果:

RPIP小组成功识别了频繁传播的和以前未经记录的病毒.
检测到的病毒包括肠道病毒 (Coxsackievirus A1,A19),流感A-H1N1和全长的SARS-CoV-2.
由于覆盖范围较低,其他检测到的病原体如人类博卡病毒,人类帕雷科病毒,肠道病毒A71和肠道病毒D68的分析有限.

结论:

针对性丰富测序,就像RPIP小组一样,是一种可行的基因组流行病学工具,用于废水中的呼吸道和肠道病毒监测.
该方法提高了病毒检测的灵敏度,但需要大量的测序深度,可能会对主要菌株产生偏见.
这种方法可以更全面地了解社区层面的病毒循环动态.

关键词:

肠道和呼吸道病毒.有针对性的丰富测序.乌拉圭乌拉圭乌拉圭乌拉圭乌拉圭基于废水的流行病学.

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