Track Omicron’s spread with molecular data
Lesley Scott, Marvin Hsiao, Sikhuline Moyo, Lavanya Singh, Houriiyah Tegally, Graeme Dor, Piet Maes, Oliver G. Pybus, Moritz U. G. Kraemer, Elizaveta Semenova, Samir Bhatt, Seth Flaxman, Nuno R. Faria, Túlio de Oliveira
Abstract
On 26 November, the newly emerged variant Omicron was designated a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VOC) (1). Rapid polymerase chain reaction (PCR) test results could improve estimates of the prevalence of Omicron around the world. The widely used Thermo Fisher TaqPath COVID-19 PCR assay was valuable in tracking the spread of the Alpha (B.1.1.7) VOC (2) because a deletion of amino acids 69 and 70 in Alpha’s spike gene (Δ69–70) yields a distinct absent S-gene (S−) despite positive test results. The Delta VOC lacks this deletion and is therefore S-gene positive (S+) on TaqPath PCR tests (3). The Omicron VOC shares the spike Δ69–70 deletion with Alpha, which has dropped to negligible levels worldwide. Therefore, the frequency of S− results can be used as a rapid proxy for the frequency of Omicron cases, provided initial detection of local circulation had been confirmed by sequencing.