Viral load in community SARS-CoV-2 cases varies widely and temporally
Walker AS., Pritchard E., House T., Robotham JV., Birrell PJ., Bell I., Bell JI., Newton JN., Farrar J., Diamond I., Studley R., Hay J., Vihta K-D., Peto T., Stoesser N., Matthews PC., Eyre DW., Pouwels KB.
<jats:title>ABSTRACT</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>Information on COVID-19 in representative community surveillance is limited, particularly regarding cycle threshold (Ct) values (a proxy for SARS-CoV-2 viral load) and symptoms.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We included all positive nose and throat swabs between 26 April-11 October 2020 from the UK’s national COVID-19 Infection Survey, tested by RT-PCR for the N, S and ORF1ab genes. We investigated predictors of median Ct value using quantile regression.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>1892(0.22%) of 843,851 results were positive, 1362(72%), 185(10%) and 345(18%) for 3, 2 or 1 genes respectively. Ct for different genes were strongly correlated (rho=0.99) with overall median Ct 26.2 (IQR 19.7-31.1; range 10.3-37.6), corresponding to ∼2,500 dC/ml (IQR 80-240,000). Ct values were independently lower in those reporting symptoms, with more genes detected, and in first (vs. subsequent) positives per-participant, with no evidence of independent effects of sex, ethnicity, age, deprivation or other test characteristics (p>0.20). Whilst single-gene positives without reported symptoms almost invariably had Ct>30, triple-gene positives without reported symptoms had widely varying Ct. Incorporating pre-test probability and Ct values, 1547(82%) and 112(6%) positives had “higher” or “lower” supporting evidence for genuine infection. Ct values, symptomatic percentages and supporting evidence changed over time. With lower positivity in the summer, there were proportionally more “lower” evidence positives, and “higher” evidence positives had higher Ct values (p<0.0001), suggesting lower viral burden. Declines in mean/median Ct values were apparent throughout August and preceded increases in positivity rates.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Community SARS-CoV-2 infections show marked variation in viral load. Ct values could be a useful epidemiological early-warning indicator.</jats:p></jats:sec><jats:sec><jats:title>SUMMARY</jats:title><jats:p>Cycle threshold (Ct) values in community SARS-CoV-2 infections from national surveillance vary markedly, including over time and by symptoms (1892 (0.22%) positive nose and throat swabs, 843,851 tested). Ct values could be a useful epidemiological early warning indicator.</jats:p></jats:sec>