NGS-SA: Publications and pre-prints of our genomics surveillance work

Track Omicron’s spread with molecular data

Authors: Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR, de Oliveira T

Journal: Science, 2021. DOI:


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 (?69–70) 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 ?69–70 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.

To put this data to use, countries should prioritize the release of daily counts of cases, hospitalizations, and deaths disaggregated by S+, S–, and unknown [e.g., (4)] as much as possible while taking logistical and privacy concerns into account. S-gene data could serve as a proxy for estimates of Omicron VOC prevalence (5) and help to understand the fraction of infections caused by Omicron (versus Delta) and the severity of Omicron cases, as measured by mortality and hospitalization. In low-resource settings where genomic sampling is absent, infrequent, or characterized by long turnaround times (6), S-gene data will help reveal the risk Omicron poses to pandemic control. Finally, through synthesis with serological data (7), S-gene data—shared in real time—could help to evaluate the degree of immune protection conferred by natural- and vaccine-elicited immunity in Omicron cases.