Longitudinal SARS-CoV-2 Testing among the Unvaccinated Is Punctuated by Intermittent Positivity and Variable Rates of Increasing Cycle Threshold Values

Abstract

The coronavirus disease 2019 (COVID-19) pandemic is complicated by cases of vaccine breakthrough and reinfection and widespread transmission of variants of concern (VOCs). Consequently, the need to interpret longitudinal positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests is crucial in guiding clinical decisions regarding infection control precautions and treatment. Although diagnostic real-time reverse transcription (RT)-PCR tests yield C_T values that are inversely correlated with RNA quantity, these tests are only approved for qualitative interpretation. In this study, we performed a retrospective review of 72,217 SARS-CoV-2 positive tests and identified 264 patients with longitudinal positivity prior to vaccination and VOC circulation. Patients with longitudinal positivity fell into two categories: short-term (207, 78%) or prolonged (57, 22%) positivity, defined as ≤28 (range, 1 to 28; median, 16) days and >28 (range, 29 to 152; median, 41) days, respectively. In general, C_T values increased over time in both groups; however, 11 short-term-positive patients had greater amounts of RNA detected at their terminal test than at the first positive test, and 6 patients had RNA detected at C_T values of <35 at least 40 days after initial infection. Oscillating positive and negative results occurred in both groups, although oscillation was seen three times more frequently in prolonged-positive patients. Patients with prolonged positivity had diverse clinical characteristics but were often critically ill and were discharged to high-level care or deceased (22%). Overall, this study demonstrates that caution must be emphasized when interpreting C_T values as a proxy for infectivity, a predictor of severity, or a guide for patient care decisions in the absence of additional clinical context, particularly among the unvaccinated population. IMPORTANCE We describe the duration of positivity and the COVID-19 treatment and outcome characteristics of an unvaccinated population of patients with prolonged SARS-CoV-2 positivity. This investigation serves to highlight challenges in using C_T values to guide clinical decisions among unvaccinated individuals.

Keywords: SARS-CoV-2; cycle threshold; infectivity; longitudinal positive.

FIG 1

Summary of time between first and last positive tests for patients with multiple positive tests. y axis indicates days between first and last positive tests, and individual dots indicate individual patients. Blue indicates prolonged-positive patient defined at natural breakpoint of >3rd quartile duration, and gray indicates short-term-positive patient. Violin-and-box plot indicates overall distribution of days between first and last positive tests.

FIG 2

Distribution of C_T values over time for patients with and without prolonged positivity. x axis indicates days between positive tests, and y axis indicates cycle threshold value of clinical tests. (A) Patients without prolonged positivity (<28 days). (B) Patients with prolonged positivity. Symbols indicate nasopharyngeal swab or other specimen type. Violin-and-box plot indicates distribution of C_T values in time frames specified on the x axis.

FIG 2

Distribution of C_T values over time for patients with and without prolonged positivity. x axis indicates days between positive tests, and y axis indicates cycle threshold value of clinical tests. (A) Patients without prolonged positivity (<28 days). (B) Patients with prolonged positivity. Symbols indicate nasopharyngeal swab or other specimen type. Violin-and-box plot indicates distribution of C_T values in time frames specified on the x axis.

FIG 3

SARS-CoV-2 testing summary for patients with slow C_T value increase, defined as C_T values of <35 after 40 days post-initial positive test. x axis indicates time, and y axis indicates 1 patient per gray line. Red and blue dots indicate positive and negative SARS-CoV-2 tests, respectively. C_T values are indicated.