Implementing genomic surveillance to support SARS-CoV-2 control and mitigation strategies in the Philippines

随着科学家和公共卫生从业人员努力了解和控制新冠肺炎大流行，基因组监测的应用，即跟踪病毒基因足迹的变化，已经成为一个宝贵的工具。基因组序列为病毒如何进化和传播以及如何更有效地控制提供了独特的见解。这些信息加强了传统的监测方法，如接触者追踪，以解决传播情景，例如提供证据，以确定受感染的医院工作人员是否有过多个患者和社区接触的最可能的传播途径，指导改进的感染控制。它同时提供了一种手段，通过跟踪病毒谱系的局部灭绝或重新引入，监测诸如封锁等控制努力的影响。我们建议在菲律宾建立基因组监测和反应能力，在那里它可以为当地和区域规模的感染控制提供信息，例如在医疗保健环境中以及不同岛屿或省份之间。我们将部署最新的测序和分析技术，以确定存档样本中病毒传播的特征，并能够快速解释来自新病例调查的基因组数据，以直接告知反应。这一方法将对整个岛屿群岛和全球的SARS-CoV-2动态提供关键和可转移的见解。此外，该项目将建设监测和应对能力，以应对未来的病毒威胁以及控制和消除继续构成主要负担的疾病。

As scientists and public health practitioners battle to understand and control the COVID-19 pandemic, the application of genomic surveillance i.e. tracking changes in the virus' genetic footprint, has become an invaluable tool. Genome sequences provide unique insights into how the virus is evolving and spreading and how it can be more effectively controlled. This information enhances traditional surveillance methods like contact tracing to resolve transmission scenarios e.g. providing evidence to determine the most likely route of transmission if an infected hospital worker has had multiple patient and community contacts, guiding improved infection control. It simultaneously provides a means to monitor the impact of control efforts, such as lockdown, by tracking the local extinction or re-introduction of virus lineages. We propose to build genomic surveillance and response capacity in the Philippines, where it can inform infection control at local and regional scales, e.g within healthcare settings and between different islands or provinces. We will deploy the latest sequencing and analytical technologies to characterize virus circulation from archived samples and enable rapid interpretation of genomic data from new case investigations to directly inform responses. This approach will provide crucial and transferrable insights into SARS-CoV-2 dynamics across the island archipelago and globally. Moreover, this project will build surveillance and response capacity against future viral threats and for the control and elimination of diseases that continue to pose a major burden.