Department of Computer Science, University of Colorado Boulder, Boulder, CO, USA.
BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
Sci Adv. 2024 Jun 14;10(24):eadk5108. doi: 10.1126/sciadv.adk5108.
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus but delayed by up to two days to control omicron-era severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, while rapid tests are superior to reverse transcription quantitative polymerase chain reaction (RT-qPCR) to control founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Last, we illustrate the model's flexibility by quantifying trade-offs in the use of post-diagnosis testing to shorten isolation times.
任何专注于传染病检测和及时诊断的项目的一个基本问题是其在减少传播方面的有效性。在这里，我们引入了检测有效性（TE）——通过检测和诊断后隔离在人群层面上减少传播的比例——以及一个模型，该模型将检测规范和使用、体内病原体动力学和人类行为纳入其中，以估计 TE。我们使用 TE 来指导建议，表明今天的快速诊断应该在症状出现后立即使用，以控制甲型流感和呼吸道合胞病毒，但可以延迟最多两天，以控制奥密克戎时代的严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）。此外，虽然快速检测在控制原始株 SARS-CoV-2 方面优于逆转录定量聚合酶链反应（RT-qPCR），但奥密克戎时代病毒动力学和快速检测敏感性的变化导致了逆转，尽管 RT-qPCR 的周转时间更长，但 TE 更高。最后，我们通过量化使用诊断后检测来缩短隔离时间的权衡来展示模型的灵活性。
