Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, South Dakota.
Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands.
S D Med. 2023 Jun;76(6):248-256.
During the coronavirus disease 2019 (COVID-19) pandemic, real-time reverse transcription polymerase chain reaction (RT-PCR) became an essential tool for laboratories to provide high-sensitivity qualitative diagnostic testing for patients and real-time data to public health officials. Here we explore the predictive value of quantitative data from RT-PCR cycle threshold (Ct) values in epidemiological measures, symptom presentation, and variant transition.
To examine the association with hospitalizations and deaths, data from 74,479 patients referred to the Avera Institute for Human Genetics (AIHG) for COVID-19 testing in 2020 were matched by calendar week to epidemiological data reported by the South Dakota Department of Health. We explored the association between symptom data, patient age, and Ct values for 101 patients. We also explored changes in Ct values during variant transition detected by genomic surveillance sequencing of the AIHG testing population during 2021.
Measures from AIHG diagnostic testing strongly explain variance in the South Dakota state positivity percentage (R2 = 0.758), a two-week delay in hospitalizations (R2 = 0.856), and a four-week delay in deaths (R2 = 0.854). Based on factor analysis of patient symptoms, three groups could be distinguished which had different presentations of age, Ct value, and time from collection. Additionally, conflicting Ct value results among SARSCoV- 2 variants during variant transition may reflect the community transmission dynamics.
Measures of Ct value in RT-PCR diagnostic assays combined with routine screening have valuable applications in monitoring the dynamics of SARS-CoV-2 within communities.
在 2019 年冠状病毒病（COVID-19）大流行期间，实时逆转录聚合酶链反应（RT-PCR）成为实验室为患者提供高灵敏度定性诊断检测和向公共卫生官员提供实时数据的重要工具。在这里，我们探讨了 RT-PCR 循环阈值（Ct）值定量数据在流行病学指标、症状表现和变异转变中的预测价值。
为了研究与住院和死亡的关联，我们将 2020 年向 Avera 人类遗传学研究所（AIHG）进行 COVID-19 检测的 74479 名患者的数据按日历周与南达科他州卫生部报告的流行病学数据相匹配。我们探讨了 101 名患者的症状数据、患者年龄和 Ct 值之间的关联。我们还研究了在 2021 年通过对 AIHG 检测人群的基因组监测测序检测到的变异转变期间 Ct 值的变化。
AIHG 诊断检测的措施强烈解释了南达科他州阳性百分比（R2=0.758）、住院延迟两周（R2=0.856）和死亡延迟四周（R2=0.854）的差异。基于对患者症状的因子分析，可以区分出三组，它们在年龄、Ct 值和采集后时间方面的表现不同。此外，在变异转变期间 SARSCoV-2 变体之间出现相互矛盾的 Ct 值结果可能反映了社区传播动态。
RT-PCR 诊断检测中的 Ct 值测量值与常规筛查相结合，在监测社区内 SARS-CoV-2 的动态方面具有重要应用价值。
