COVID-19 Cycle Threshold/Cycle Number Testing at a Community Living Center

This is the first study in the English literature to track CT/CN values as part of serial testing of a veteran CLC. Widescale testing and repeat screening in the absence of symptoms of nursing home residents would identify those who are infected and allow providers to track viral load clearance. ^9-14 CT/CN values, when serially tracked during the infection course, appear to increase with illness resolution, consistent with earlier reports that CT/CN correlates with viral load. ^8-14 Serial CT/CN values that are high (> 25) and continue to increase with each test suggest progression toward disease resolution or viral RNA clearance. ^8-14 After symptom resolution, patients can have a persistent low level of viral shedding (corresponding to a high CT/CN value). ^10-14,25 Near the end of disease resolution, a negative serial RT-PCR sample test before a subsequent positive might be a promising clinical sign of near disease recovery. Once the viral load is low with a CT/CN significantly higher than 25, some specimens might result as negative but turn up positive on subsequent sampling with a high CT/CN value. This pattern, with attendant high CT/CN values for the positive results, are consistent with the known effect of viral load (ie, a low viral load correlates to a high CT/CN) and adequacy of specimen collection on CT/CN values ^.25 If the patient’s viral load is low, the sample collected might have a viral load at or near the testing platform’s LOD.

For Abbott m2000, the manufacturer provided LOD is 100 virus copies/mL, although the instrument was able to detect virus concentrations below that level during the initial validation. ²⁰ The actual LOD of the instrument at our institution is < 100 virus copies/mL. For the Cepheid Xpert Xpress SARS-CoV-2 assay, the manufacturer-provided LOD is 250 virus copies/mL.19 An LOD study including samples below the manufacturer-provided LOD was not part of the initial validation study for the Xpert Xpress assay. Nonetheless, the virus concentration of samples with very high CT values at or near the maximum CT value of 45 is expected to be at or near the platform’s actual LOD.

If the samples collected near the end of the patient’s disease course have viral loads near these low concentrations, the encouraging positive-negative-positive pattern with high CT/CN values might be a promising sign for viral clearance. On the other hand, a positive-negative-positive pattern in the setting of low CT/CN values before and after the negative test might indicate poor sampling for the negative specimen. The back-and-forth or positive-negative-positive pattern generally appears to indicate near resolution of the infection course, although clinical correlation is necessary to rule out inadequate sampling earlier in the disease course or prolonged viral RNA shedding. ^9-14 In all of the surviving symptomatic patients who showed the positive-negative-positive pattern, this sign occurred around or after symptom resolution. It also is important to consider that in some patients, SARS-CoV-2 RNA might remain detectable with increasing CT/CN after symptom resolution, and samples from these patients might not result positive. Therefore, CT/CN values cannot be interpreted without considering the clinical picture. ²⁵