Spatiotemporal Analyses of 2 Co-Circulating SARS-CoV-2 Variants, New York State, USA

Abstract

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in late 2020 and early 2021 raised alarm worldwide because of their potential for increased transmissibility and immune evasion. Elucidating the evolutionary and epidemiologic dynamics among novel SARS-CoV-2 variants is essential for understanding the trajectory of the coronavirus disease pandemic. We describe the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) variants in New York State, USA, during December 2020-April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 probably evolved in New York City, where it was displaced as the dominant lineage by B.1.1.7 months after its initial appearance. In contrast, B.1.1.7 became dominant earlier in regions with fewer B.1.526 infections. These results suggest that B.1.526 might have delayed the initial spread of B.1.1.7 in New York City. Our combined spatiotemporal methodologies can help disentangle the complexities of shifting SARS-CoV-2 variant landscapes.

Keywords: COVID-19; New York; SARS-CoV-2; United States; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; spatiotemporal analyses; vaccine-preventable diseases; viruses; zoonoses.

Figure 1

Geographically weighted mean centers of total and estimated coronavirus disease cases attributable to B.1.526 and B.1.1.7 variants, New York State, USA, December 2020–April 2021. Cluster centroids refer to the results of the multinomial space-time scan analysis (Figure 2). New York’s centroid and geographic center of population are added as reference points.

Figure 2

Severe acute respiratory syndrome coronavirus 2 variant clusters identified from retrospective multinomial space-time scan analysis and coronavirus disease incidence by ZIP code tabulation area, New York State, USA, December 2020–April 2021. Circles indicate clusters with relative risk >1. 1, variant includes B.1.526, B.1.526.1, and B.1.526.2; 2, variant includes B.1.526 and B.1.526.2.

Figure 3

Time-calibrated phylogeny of severe acute respiratory syndrome coronavirus 2 variant B.1.526, New York and other states, USA, December 2020–April 2021. Left panel represents a maximum-likelihood phylogeny of 980 genomes from New York and other US states generated in IQTree 1.6.12 (20) with timescale inferred by TreeTime 0.7.6 (22) and ancestral state reconstruction performed in BEAST 2.6.2 (23). Faceted panels indicate the source of B.1.526 introductions into different regions of New York and other states (domestic). Only introductions supported by an ancestral state probability of >0.7 are shown. Bottom panel shows locations sampled and sample sizes. A, April; J, January; O, October.

Figure 4

Time-calibrated phylogeny of severe acute respiratory syndrome coronavirus 2 variant B.1.1.7, New York and other states, USA, December 2020–April 2021. Left panel represents a maximum-likelihood phylogeny of 1,195 genomes from New York and other states generated in IQTree 1.6.12 (20) with timescale inferred by TreeTime 0.7.6 (22) and ancestral state reconstruction performed in BEAST 2.6.2 (23). The tree was rooted with a P.1 genome (not shown). Faceted panels indicate the source of B.1.1.7 introductions into different regions of New York and other states (domestic). Only introductions supported by an ancestral state probability of >0.7 are shown. Bottom panel shows locations sampled and sample sizes. A, April; J, January; O, October.