Genomic and spatial epidemiology: lessons learned from SARS-CoV-2 pandemic.

Current opinion in HIV and AIDS Pub Date : 2025-05-01 Epub Date: 2025-04-01 DOI:10.1097/COH.0000000000000936
Yangji Choi, David De Ridder, Gilbert Greub
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Abstract

Purpose of review: The SARS-CoV-2 pandemic presented unprecedented challenges, particularly in understanding its complex spatial transmission patterns. The high transmissibility of the virus led to frequent super-spreading events. These events demonstrated clear spatial clustering patterns, often tied to specific events that facilitated transmission. The uneven geographic distribution of medical resources and varying access to care amplified the impact of SARS-CoV-2. Asymptomatic cases further complicated the situation, as infected individuals could silently spread the virus before being identified.Thus, this review examines how genomic and spatial epidemiology approaches can be integrated to answer some of the above-mentioned challenges. We first describe the methodological foundations of genomics and spatial epidemiology, detailing opportunities of their applications during the SARS-CoV-2 pandemic. We then present a novel interdisciplinary framework that combines these approaches to better guide public health interventions.

Recent findings: During the pandemic, the genomic and spatial approaches were used to address key questions, including "how does the pathogen evolve and diversify?" and "how does the pathogen spread geographically?". Genomic epidemiology allows researchers to identify viral lineages and new variants. Conversely, spatial epidemiology focused on geographic distribution of infections, analyzing how the virus spread. However, despite their complementary nature, these approaches were largely applied independently during the pandemic. This separation limited our collective ability to fully understand the complex relationships between viral evolution and geographic spread.

Summary: While phylogeography has traditionally combined phylogenetic and geographic data to understand long-term evolutionary patterns across large areas, events such as the recent SARS-CoV-2 pandemic demand frameworks that can inform public health interventions through joint analysis of genomic and local-scale spatial data.

基因组和空间流行病学:从SARS-CoV-2大流行中吸取的教训。
审查目的:SARS-CoV-2大流行带来了前所未有的挑战,特别是在了解其复杂的空间传播模式方面。该病毒的高传播性导致了频繁的超级传播事件。这些事件显示出明确的空间聚集模式,通常与促进传播的特定事件有关。医疗资源的地理分布不均和获得护理的机会不同,加剧了SARS-CoV-2的影响。无症状病例使情况进一步复杂化,因为感染者可能在被发现之前悄无声息地传播病毒。因此,本综述探讨了基因组学和空间流行病学方法如何整合以应对上述一些挑战。我们首先描述了基因组学和空间流行病学的方法学基础,详细介绍了它们在SARS-CoV-2大流行期间的应用机会。然后,我们提出了一个新的跨学科框架,结合这些方法,以更好地指导公共卫生干预。最近的发现:在大流行期间,使用了基因组和空间方法来解决关键问题,包括“病原体如何进化和多样化?”和“病原体如何在地理上传播?”。基因组流行病学使研究人员能够识别病毒谱系和新的变种。相反,空间流行病学侧重于感染的地理分布,分析病毒如何传播。然而,尽管这些方法具有互补性,但在大流行期间基本上是独立应用的。这种分离限制了我们充分理解病毒进化和地理传播之间复杂关系的集体能力。摘要:虽然系统地理学传统上是将系统发育和地理数据结合起来,以了解大范围内的长期进化模式,但像最近的SARS-CoV-2大流行这样的事件需要框架,可以通过联合分析基因组和局部尺度的空间数据,为公共卫生干预提供信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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