SARS-CoV-2 Vaccine Breakthrough by Omicron and Delta Variants, New York, USA

Abstract

Recently emerged SARS-CoV-2 variants have greater potential than earlier variants to cause vaccine breakthrough infections. During emergence of the Delta and Omicron variants, a matched case-control analysis used a viral genomic sequence dataset linked with demographic and vaccination information from New York, USA, to examine associations between virus lineage and patient vaccination status, patient age, vaccine type, and time since vaccination. Case-patients were persons infected with the emerging virus lineage, and controls were persons infected with any other virus lineage. Infections in fully vaccinated and boosted persons were significantly associated with the Omicron lineage. Odds of infection with Omicron relative to Delta generally decreased with increasing patient age. A similar pattern was observed with vaccination status during Delta emergence but was not significant. Vaccines offered less protection against Omicron, thereby increasing the number of potential hosts for emerging variants.

Keywords: 2019 novel coronavirus disease; COVID-19; Delta; New York; Omicron; SARS-CoV-2; United States; conditional logistic regression; coronavirus disease; respiratory infections; severe acute respiratory syndrome coronavirus 2; vaccine breakthrough; variants; viruses; zoonoses.

Figure 1

Matched case–control pairs used in the conditional logistic regression by analysis for the SARS-CoV-2 Delta variant (March 19, 2021–August 15, 2021) and the Omicron variant (November 28, 2021–January 24, 2022) emergence periods, by economic region (map), New York, USA. The bars correspond to the order given in the legend; New York City is on top when present and Long Island on bottom when present. The dashed line separates the 2 datasets used in the analyses; the Delta emergence period is on the left and the Omicron emergence period on the right. Map base layer was derived from a combination of 2 public domain layers (US Census data, https://www.census.gov/geo/maps-data/data/tiger-line.html) and Natural Earth Administrative boundaries (https://www.naturalearthdata.com/downloads/50m-cultural-vectors/50m-admin-1-states-provinces).

Figure 2

Visualization of the fixed effects from the second Omicron emergence analysis on a log-odds scale (without age matching) in a study of SARS-CoV-2 vaccine breakthrough by Omicron and Delta variants, New York, USA. Odds scale in Appendix. Stratum-specific effects were often strong but were excluded for visual clarity. Increased values indicate an increased probability of infection with Omicron instead of Delta. Lines show ± 1 SE.