While we recognize the scale of SARS-CoV-2 genomic surveillance is no longer feasible, sequencing 500/wk was enough to detect emerging lineages and identify growth earliest. However, sequencing 50/wk was enough to detect lineages along the same timeline as we would have otherwise

Across two genomic methods we found that more recent vaccination and booster doses reduced the likelihood of transmission. Boosted individuals ~35% less likely to initiate transmission than unvaccinated people.

In schools, colleges, and SNFs, we found much stronger evidence of within-facility transmission among student and resident-aged than among staff-aged. Staff-aged individuals had lower viral relatedness to their facility, suggesting more involvement in community transmission

Across three major Omicron lineages, new variants reached 50% frequency in college settings 4–13 days earlier than elsewhere. This early rise wasn’t observed in when colleges were out of session (during BA.5*), suggesting unique features of colleges that accelerate spread.

We also show that SARS-CoV-2 moved more quickly between metro areas than it did to the primarily rural areas between them. Overall, we find that viruses diffuse throughout the entire state in about 2 months

Using high-resolution spatial and temporal data, we tracked the introduction and spread of six Omicron lineages across Massachusetts. Urban areas played a central role—both as entry points for new lineages and as key drivers of their dissemination.

The Broad Clinical Labs generated >130k SC2 genomes 🧬 between Nov 2021 and Jan 2023. We were able to match >85k individuals to metadata like age, sex, city of residence, facility of collection, and vaccination status