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Predicting infectious SARS-CoV-2 from diagnostic samples

Our take —

This retrospective cross-sectional study examined the correlation between SARS-CoV-2 RT-PCR results (RNA testing) from Canada, and time since symptom onset with virus culture in vitro. While they used the largest sample size to date of non-epidemiologically linked samples to assess these associations, they do not assess actual infectivity in vivo, and the sample size per day since symptom onset is very limited. They also do not assess the relationship between RNA testing and infectiousness in asymptomatic or pre-symptomatic individuals, who may be contributing a significant amount to viral spread in the real-world. Given the limited sample size, we recommend caution when interpreting the peak infectivity.

Study design

Cross-Sectional; Other

Study population and setting

Nasopharangeal (NP) and endotracheal (ETT) samples collected as part of routine care and surveillance in Manitoba, Canada, were tested for SARS-CoV-2 RNA using RT-PCR targeting the viral envelope at the provincial public health laboratory (n=90 total samples). Samples were linked with epidemiological data including time from symptom onset to test (STT). Researchers assessed the relationship between RT-PCR cycle threshold (Ct), which has an inverse relationship with viral concentration, STT, and infectivity of Vero cells in vitro.

Summary of Main Findings

Overall, 26/90 (28.9%) of the samples were deemed infectious, though none past day 8 STT. Infectious samples were more likely to have a lower Ct (<24) and a lower STT (<8 days) than non-infectious samples. Ct was found to be statistically associated with positive culture (infectivity) (OR 0.64 [95% CI: 0.49 – 0.84])—which can be interpreted as for each 1 unit increase in Ct value the odds of infectivity decreased by 32%. Similarly, STT was associated with culture as well (OR 0.63 [95% CI: 0.42 – 0.94]). The peak probability of infectivity was on day 3 STT and decreased thereafter.

Study Strengths

The study used the largest sample size to date collected from epidemiologically unrelated individuals to examine the relationship between test result and infectivity. They integrated PCR results, with epidemiological data and in-vitro infectivity data.

Limitations

Although the largest sample to date, 26 infectious cases remains limited and it is not clear how many samples were available by day, potentially leading to a misinterpretation of results that infectiousness is highest at Day 3 STT given limited sample sizes. In vitro culture is not directly equivalent to in vivo infectivity, especially with respect to actual factors related to transmission events. All individuals were symptomatic, part of the criteria for testing in Manitoba, so the relationship between PCR results and infectivity remains unknown in asymptomatic individuals who have been shown to be infectious. Ct values can vary by assay and lab even when using the same assay. Ct values can be converted into a viral load with a properly run standard curve, which may be more useful in drawing hypotheses across platforms and laboratories about viral PCR results and infectiousness.

Value added

This study links epidemiologic, laboratory, and diagnostic data using a large and epidemiologically unrelated sample set to examine the relationship between RNA testing, time since symptom onset, and potential infectiousness (in vitro).

This review was posted on: 25 June 2020