Letter: Track Omicron’s spread with molecular data

Rapid polymerase chain reaction test results could improve global estimates of the prevalence of Omicron, the newly emerged variant of SARS-CoV-2, say Lesley Scott and colleagues in a Letter. Given that the Omicron variant of concern (VOC) exhibits a particular amino acid deletion in its spike gene – which yields a distinct absent S-gene (S^-) – the frequency of S^- results can be used to provide a rapid proxy for the frequency of Omicron cases, they say. The authors argue that countries should prioritize the release of daily counts of cases, hospitalizations, and deaths disaggregated by S-gene data – either S^-, S⁺, or unknown. This could help to understand the fraction of infections caused by Omicron versus Delta, which, unlike Omicron, is designated S⁺ on PCR tests. It could also help inform the severity of Omicron cases, as measured by mortality and hospitalization. In low-resource settings, S-gene data will help reveal the risk Omicron poses to pandemic control, the authors add. Finally, 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. The authors discuss ways to control for preferential sequencing of samples with an S^- result, as global scientists prepare to contribute sample data. “To evaluate risk and guide policy, there is an urgent need to incentivize the quick sharing of well-annotated genomic and S-gene-stratified surveillance data globally,” they conclude.