Martínez-Puchol Sandra, Tarradas-Alemany Maria, Mejías-Molina Cristina, Itarte Marta, Rusiñol Marta, Baliellas Jordi, Abasolo Nerea, Canela Núria, Monastiri Abir, López-Roig Marc, Serra-Cobo Jordi, Abril Josep F, Bofill-Mas Sílvia
Laboratory of Viruses Contaminants of Water and Food, Departament de Genètica. Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Catalonia, Spain.
Vicerectorat de Recerca. Universitat de Barcelona, Barcelona, Catalonia, Spain.
Heliyon. 2024 May 19;10(11):e31556. doi: 10.1016/j.heliyon.2024.e31556. eCollection 2024 Jun 15.
The COVID-19 pandemic has underscored the importance of understanding the role of animals in the transmission of coronaviruses (CoVs) and their impact on human health. A One Health approach, integrating human, animal, and environmental health, is essential for effective CoVs control. Next-generation sequencing has played a pivotal role in identifying and monitoring the evolution of novel CoVs strains, like SARS-CoV-2. However, viral occurrence and diversity studies in environmental and animal samples are challenging because of the complexity of viral communities and low abundance of viruses in these samples. Target enrichment sequencing (TES) has emerged as a valuable tool for investigating viral families in challenging samples. This approach involves the specific capture and enrichment of viral genomes using sequence-specific probes, thereby enhancing the efficiency of detection and characterization. In this study, we aimed to develop and validate a TES panel to study CoVs in various complex environmental and animal derived samples. The results demonstrated the panel's effectiveness in capturing and sequencing a wide diversity of CoVs providing valuable insights into their abundance and host diversity in urban wastewater, farm animal corpses lixiviates and bat guano samples. In sewage samples, CoVs were detected solely when TES was employed while in guano samples, sequencing of CoVs species was achieved in 2 out of 4 samples showing an almost three-logarithmic increase in the number of reads obtained in comparison with the untargeted approach. For animal lixiviates, only the TES application enabled the acquisition of CoVs reads. The information obtained can significantly contribute to early detection, surveillance, and control measures for CoVs, including viral discovery and potential spillover events. Additionally, this sequencing panel shows potential for studying other significant viral families and monitoring viral diversity in different animal populations.
新冠疫情凸显了了解动物在冠状病毒传播中的作用及其对人类健康影响的重要性。采用整合人类、动物和环境卫生的“同一健康”方法对于有效控制冠状病毒至关重要。新一代测序技术在识别和监测新型冠状病毒毒株（如严重急性呼吸综合征冠状病毒2）的演变过程中发挥了关键作用。然而，由于病毒群落的复杂性以及环境和动物样本中病毒丰度较低，对环境和动物样本中的病毒发生情况及多样性进行研究具有挑战性。靶向富集测序（TES）已成为研究具有挑战性样本中病毒科的一种有价值的工具。这种方法涉及使用序列特异性探针特异性捕获和富集病毒基因组，从而提高检测和表征效率。在本研究中，我们旨在开发并验证一种TES检测板，用于研究各种复杂环境和动物源样本中的冠状病毒。结果表明，该检测板在捕获和测序多种冠状病毒方面具有有效性，为了解城市污水、农场动物尸体浸出液和蝙蝠粪便样本中冠状病毒的丰度及其宿主多样性提供了有价值的见解。在污水样本中，仅采用TES时才能检测到冠状病毒；而在粪便样本中，4个样本中有2个实现了冠状病毒物种的测序，与非靶向方法相比，获得的读数数量增加了近三个对数级。对于动物浸出液，只有应用TES才能获得冠状病毒读数。所获得的信息可显著有助于冠状病毒的早期检测、监测和控制措施，包括病毒发现和潜在的溢出事件。此外，该测序检测板在研究其他重要病毒科以及监测不同动物群体中的病毒多样性方面显示出潜力。
