Estimated COVID-19 Periodicity and Correlation with SARS-CoV-2 Spike Protein S1 Antigenic Diversity, United States
Erica Billig Rose, Clinton R. Paden, Peter W. Cook, C. Kevin, Amber Winn, Juan E. De Castro, Lakshmi Panagiotakopoulos, Benjamin J. Silk
Abstract
Emergence of antigenically diverse SARS-CoV-2 variants may be correlated with temporal circulation patterns. We analyzed positive SARS-CoV-2 tests in the United States reported to a national, laboratory-based surveillance network and unique amino acid sequences of the S1 region of the spike protein reported to national genomic surveillance during October 2020-September 2024. We estimated SARS-CoV-2 dominant periodicities using a discrete Fourier transform, described S1 variation using the Simpson diversity index (SDI), and estimated Spearman cross-correlation coefficients between percentage change in SDI and percentage positivity. SARS-CoV-2 activity consistently peaked during July-September and December-February, and dominant periodicities were at weeks 52.2 and 26.1. Percentage positivity and percentage change in SDI were negatively correlated (ρ = -0.30; p<0.001). SARS-CoV-2 peaks occurred in late summer and winter, a pattern likely related to rapid SARS-CoV-2 evolution and cyclical diversity. Monitoring associations between percentage positivity and SDI can help forecast expected surges and optimize prevention and preparedness.