Speaker
Description
Despite intensive study, surprising gaps remain in our knowledge of transmission patterns during the COVID-19 pandemic, particularly transmission as new lineages emerge. We analyzed 134,785 SARS-CoV-2 genomes from 7 lineages collected in Massachusetts from November 1, 2021, to January 17, 2023; this includes 85,125 genomes with individualized epidemiological data across 666 testing facilities. Urban centers were identified as sources of new lineages in Massachusetts, while colleges were sentinels for variant predominance. Resident populations concentrated within college campuses and nursing homes exhibited higher rates of within-facility transmission. We find that increased vaccination was associated with reduced infection and transmission. As our previous scale of sequencing is no longer accessible nor sustainable, we note that 500 genomes per week is sufficient to detect a new lineage at 1% prevalence and monitor its growth. We present these findings to help guide future surveillance strategies for emerging pathogens.
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