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

Alexis Russell; Collin O'Connor; Erica Lasek-Nesselquist; Jonathan Plitnick; John P. Kelly; Daryl M. Lamson; Kirsten St. George


Emerging Infectious Diseases. 2022;28(3):650-659. 

In This Article

Abstract and Introduction


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.


The emergence of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 (Alpha) in the United Kingdom in late 2020 raised alarm worldwide and prompted major reassessment of the management, surveillance, and projected future of coronavirus disease (COVID-19).[1,2] Evidence of increased transmissibility and potential immune evasion prompted the World Health Organization to designate B.1.1.7 a variant of concern (VOC) in December 2020 (;[3–5] W.A. Haynes et al., unpub. data, The emergence of B.1.1.7 and additional novel SARS-CoV-2 variants with competitive advantages has resulted in the localized dominance of single variants (E. Volz et al., unpub. data, and raised concern for increases in COVID-19 incidence.[6]

Novel variant B.1.526 (Iota) arose within New York State (NYS), USA, in late 2020 (E. Lasek-Nesselquist et al., unpub. data,[7] and quickly increased in proportion throughout the state, leading to a noticeable shift in lineage distribution during early 2021 (E. Lasek-Nesselquist et al., unpub. data,[31] The World Health Organization designated B.1.526 as a variant of interest (VOI) because of its increase in prevalence coupled with mutations associated with immune evasion.[8] Despite these concerns, an epidemiologic assessment of B.1.526 in NYC during January–April 2021 found that the lineage did not cause more severe disease and was not associated with increased risk for reinfection or vaccine breakthrough.[9] However, an epidemiologic study of NYS during late 2020–May 2021 concluded that B.1.526 was 35% more transmissible than non-VOC and non-VOI lineages circulating at the time.[10]

Genomic surveillance of COVID-19 is a crucial tool to monitor and assess the physiologic and epidemiologic characteristics of SARS-CoV-2 variants as they emerge. The New York State Department of Health (NYSDOH) substantially expanded its genomic surveillance program in December 2020, with the aim of sequencing a more representative subset of COVID-19 cases across the state to track the spread and impact of novel variants. A robust genomic surveillance system enables assessment of changes in variant distribution over precise temporal and spatial scales.

This study employed spatial scan statistics paired with phylogeographic analyses to describe the shifting SARS-CoV-2 variant landscape in NYS during December 2020–April 2021, specifically the interplay between co-circulating B.1.526 and B.1.1.7 lineages. Our findings elucidate the dynamics of competing SARS-CoV-2 variants at a time when the highly transmissible VOC Delta had overtaken B.1.1.7 worldwide and future variant displacements were likely to occur.