key: cord-0866669-gcku08s7 authors: Skidmore, P. T.; Kaelin, E. A.; Holland, L. A.; Maqsood, R.; Wu, L. I.; Mellor, N. J.; Blain, J. M.; Harris, V.; LaBaer, J.; Murugan, V.; Lim, E. S. title: Emergence of a SARS-CoV-2 E484K variant of interest in Arizona date: 2021-03-28 journal: nan DOI: 10.1101/2021.03.26.21254367 sha: 8aff07b09ad847a4a87663c3df431f58e803ad1d doc_id: 866669 cord_uid: gcku08s7 SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunity and escape mutations. The E484K mutation in the spike protein reduces neutralization by post-vaccination sera and monoclonal antibody therapeutics. We detected the emergence of an E484K harboring variant B.1.243.1 from a common circulating variant (B.1.243) in the United States. In contrast to other instances when the E484K mutation was acquired independently in the parental lineage, genomic surveillance indicates that the B.1.243.1 variant of interest is in the process of being established in Arizona and beginning to cross state borders to New Mexico and Texas. Genomic, epidemiologic and phylogenetic evidence indicates that the B.1.243.1 variant of interest is poised to emerge. These findings demonstrate the critical need to continue tracking SARS-CoV-2 in real-time to inform public health strategies, diagnostics, medical countermeasures and vaccines. Main there are 3 VOIsall of which harbor the E484K mutation in the spike glycoprotein S gene: B.1.525 and B.1.526 both first detected in New York in the US 11 , and P.2 that was first identified in Brazil 12 . In an effort to provide state-wide genomic surveillance, we sequenced the SARS-CoV-2 genome from 688 positive samples collected from December 28 2020 to March CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Sequencing analysis. Illumina sequencing reads were quality filtered to remove adaptors and low-quality bases using BBTools. High-quality-filtered reads were mapped to the SARS-CoV-2 Wuhan1 reference genome (NC_045512.2) using BWA-MEM 25 and amplicon primers were trimmed using Primerclip (version 0.3.8) 26 . Consensus sequence was called using iVar (version 1.0; parameters -q 20, -t 0.75, -m 20, -n N) 27 . Sequence alignments were performed with . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The authors declare no competing interests. Cumulative case incidence is plotted as a line graph. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted March 28, 2021 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted March 28, 2021 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 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