Tracking the Omicron variant in Massachusetts

New data suggest the Omicron variant is spreading as a new wave of COVID-19 infections continues in Massachusetts. 

Broad Institute Communications
Credit: Broad Institute Communications

Through a partnership with the Massachusetts Department of Public Health (MDPH), researchers at the Broad Institute are using mCARMEN, a CRISPR-based technology that can rapidly differentiate between Omicron, Delta, and other COVID-19 variants, to get a provisional look at the rising prevalence of Omicron in the state. 

The MDPH requested Broad use mCARMEN to test COVID-19 specimens from across Massachusetts, enabling a faster, preliminary analysis of the prevalence of the variant for public health situational awareness, while viral genome sequencing is underway in parallel.

Of the 1,108 specimens tested in the first round of analysis, the team found that by December 16th, 45 percent of infections showed strong evidence of the Omicron variant. The specimens were from December 13–16 and suggest Omicron’s spread is rapidly increasing across the state. Based on the trends observed during this time period, the team estimates Omicron has been the dominant COVID-19 variant in Massachusetts since December 17.

Caption: Percent of Omicron cases in MA based on viral sequencing, mCARMEN, and extrapolation data.

mCARMEN, an acronym for “Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids,” uses microfluidic chips, enabling it to run many tests simultaneously. The team first developed the CARMEN platform in 2020 and refined the technology in 2021.

In partnership with the US Centers for Disease Control and Prevention and the MDPH, the Broad Institute has been conducting large-scale viral sequencing to support COVID-19 genomic surveillance since March 2021. Variant detection is performed as part of public health surveillance, and results are not returned to individuals or physicians.

Broad Institute will continue to monitor Omicron and other SARS-CoV-2 variants using both mCARMEN and viral sequencing.

mCARMEN is made possible by DARPA D18AC00006 and by support from Flu lab and a cohort of generous donors through TED's Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy.