key: cord-0704840-et65kom2
authors: Smith, Benjamin F.; Graven, Peter F.; Yang, Doris Y.; Downs, Siouxzanna M.; Hansel, Donna E.; Fan, Guang; Qin, Xuan
title: Using Spike Gene Target Failure to Estimate Growth Rate of the Alpha and Omicron Variants of SARS-CoV-2
date: 2022-03-07
journal: J Clin Microbiol
DOI: 10.1128/jcm.02573-21
sha: 2a8a1a733fa885e1b7e187753131b1d957803e2b
doc_id: 704840
cord_uid: et65kom2

nan

This shortened case doubling time is additional evidence of the increased transmissibility of Omicron. Using SGTF provides a real-time estimate of viral epidemiology for Omicron; however, there are limitations with this analysis. Rarely, SGTF can be detected in sublineages of the Delta variant that are simultaneously in circulation (8) . Also, the time it took for Delta to come to predominance was complicated by several factors including remote schooling, increased outdoor activities during summer, the protection from vaccination in the population, and the simultaneous presence of Alpha, Beta, and Gamma variants in circulation. All of these may have contributed to Delta's prolonged case doubling time compared with that of Alpha and Omicron. Nonetheless, clinical laboratory data are essential for monitoring the SARS-CoV-2 pandemic. The case doubling time in our community reflects the nationwide trend toward Omicron predominance and immune evasion, and can inform local pandemic mitigation efforts. In conjunction with early reports of the clinical severity of and immunologic responses to a given variant, case doubling time can be used to inform whether to implement a variety of public health measures, e.g., masking policies, hospital visitor policies, vaccination booster recommendations, scale-up of laboratory testing, and widespread distribution of at-home testing.

SARS-CoV-2 genome sequencing was funded in part by the Oregon Public Health Authority (OHA Agreement Number 170015). We thank OHSU clinical laboratory scientists for their high-quality performance and documentation of SARS-CoV-2 test results. We thank Brian O'Roak's lab for their sustained contributions to OHSU's sequencing operations. Doris Y. Yang was a freshman attending Harvard College while working as a student intern on Weekly Oregon State Genome Dashboard for OHSU.

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