Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19 in England.
Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19 in England. Jefferson T, Heneghan C.
Published on August 19, 2020
Transmission Dynamics of COVID-19
|| Singanayagam A, Patel M, Charlett A, Lopez Bernal J, Saliba V, Ellis J, et al. Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Eurosurveillance. 2020;25(32):2001483. 2020
||Droplets, viral load
RT-PCR cycle threshold (Ct) values correlate strongly with cultivable virus and likelihood of infectiousness.
The RT-PCR cycle threshold (Ct) values as a measure of SARS-CoV-2 viral load showed that the level of SARS-CoV-2 RNA in the Upper Respiratory tract was greatest around symptom onset, steadily decreased during the first 10 days after illness onset and then plateaued.
- In days −2 to 7 since symptom onset geometric mean (GM) Ct was 28 (95% CI 27.8 to 28.6).
- In the second week (days 8 to 14), GM Ct was 31 (95% CI: 9.8 to 32; p < 0.001 compared with week 1)
- After 14 days, GM Ct was 32 (95% CI: 31.6–34.5; p = 0.01 compared with week 1 (there was no significant difference in Ct values between days 8–14 and after 14 days).
Cultivable virus was isolated from 133 (41%) samples (from 111 cases).
Detection of cultivable virus peaked around the time of symptom onset.
In the 246 samples from 176 symptomatic cases where the date of symptom onset was known, 103 (42%) from 81 cases were culture positive Implying that 30 samples from which the virus was cultured, were asymptomatic.
Median Ct of all 324 samples was 31 (interquartile range (IQR): 27.5–33.9; range: 17.5–41.8). 233 cases (92%) were classified as non-severe (asymptomatic or mild-to-moderate) and 20 (8%) had severe illness (requiring intensive care admission and/or fatal).
There was no difference in Ct values between those with asymptomatic (median Ct = 31; IQR: 28–33), mild-to-moderate (median Ct = 31; IQR: 27–35) or severe (median Ct = 33; IQR 28.–34) illness (p = 0.79).
A stratified comparison of the severe cases over time showed a similar result.
Ct values were lower in week 1 than week 2. There was no difference in culture positivity rate from 62 samples of 61 asymptomatic cases: 21 of 62 samples from asymptomatic individuals vs 112 of 262 samples from symptomatic individuals (estimated odds ratio (OR) = 0.66; 95% CI: 0.34–1.31.
Similar to Bullard and colleagues’ and Piralla’s findings there was a strong relationship between Ct value and ability to recover infectious virus. The estimated OR of recovering infectious virus decreased by 0.67 for each unit increase in Ct value (95% CI: 0.58–0.77).
Virus propagation was successful from 5/60 samples with Ct > 35; all five were from symptomatic cases and none had severe illness. The estimated probability of recovery of virus from samples with Ct > 35 was 8% (95% CI: 2.8%–18%).
When symptom onset was based on symptom recall, median duration of virus shedding as measured by culture was 4 days (IQR: 1–8; range: −13 to 12).
Culture positivity rate was significantly higher during week 1 than week 2 (74% vs 20%; p = 0.002).
Ten days after symptom onset, the probability of culturing virus declined to 6.0% (95% CI: 0.9–31.2%). Again this observation is in line with what we already know.
Table 2 in the paper reports the breakdown by age and positivity of 324 cases. There was no difference in culture positivity or ct values by age group although the younger age group 0-20 contributed only 14 cases to the dataset.
What did they do?
The study reports the testing for correlation between RT PCR results and cycle threshold (ct) and day of onset of symptoms and probability of culturing live SARS CoV-2 in 324 samples from 253 positive cases (from an original set of 754 URT samples from 425 symptomatic cases that tested positive).
All samples had to be related to a clear day of onset of symptoms and sample taking. Samples were nose, throat, combined nose-and throat and nasopharyngeal swabs nasopharyngeal aspirates either taken by staff or self-sampled nose swabs. The PCR targeted the RNA polymerase gene called RdRp. Evidence of cytopathic effect in cultured Vero cells with the presence of SARSCoV-2 was confirmed by nucleoprotein staining by enzyme immunoassay on infected cells.
The authors specifically state that they cannot be absolutely certain of the circumstances of collection or symptom onset. However in the text they appear to contradict their earlier statement that all samples came from symptomatic cases reporting that the specimens came “from a range of clinical scenarios including community and healthcare worker surveillance, symptomatic persons tested as part of the early epidemic response and samples acquired in outbreak investigations. Selection of asymptomatic cases was through swabbing of contacts or facility/family/household testing in the context of outbreak investigations”.
|Clearly defined setting
||Demographic characteristics described
||Follow-up length was sufficient
||Transmission outcomes assessed
||Main biases are taken into consideration
What else should I consider?
This study is part of a growing body of evidence linking symptom onset, with PCR ct values and infectiousness
About the authors
Carl is Professor of EBM & Director of CEBM at the University of Oxford. He is also a GP and tweets @carlheneghan. He has an active interest in discovering the truth behind health research findings
Tom Jefferson, epidemiologist.