Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas

Abstract

Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.

Figure 1

Epidemiologic curve showing five COVID-19 disease waves in Houston Methodist patients. Number of new COVID-19 cases (y axis) totals are shown as a ±3-day moving average. Each of the five waves is shown in a different color. The first and second waves were composed of a heterogeneous array of SARS-CoV-2 genotypes. The Alpha variant of concern (VOC) shown in the third wave, the Delta VOC shown in the fourth wave, and the Omicron VOC shown in the fifth wave indicate their numeric prominence in those waves. The figure should not be interpreted to mean that all cases in the third, fourth, and fifth waves were caused by Alpha, Delta, and Omicron VOCs, respectively. Rather, they are the dominant single VOCs causing disease in Houston Methodist system patients in those waves. The fifth wave shown includes data through January 5, 2022. The figure was generated with Tableau version 2021.2.7 (Tableau Software, LLC, Seattle, WA), and is adapted with permission from the version presented in Christensen et al. The curve is essentially superimposable on COVID-19 activity in all metropolitan Houston, Texas.

Figure 2

Increase in Omicron frequency over time and distribution in metropolitan Houston, Texas. The study time frame was November 27, 2021, through January 5, 2022. A: Omicron logistic growth model. The estimated case doubling time is 1.8 days. B: Cumulative increase in Omicron during the study period; y axis is the cumulative number of new COVID-19 Omicron cases. At the end of the study period, Omicron caused 98% of all COVID-19 cases. The plateau between December 24, 2021, and December 30, 2021, exists because samples obtained during this period were not sequenced due to the massive number of daily positive specimens, as described in Materials and Methods. C–F: Geospatial distribution of Omicron based on home address zip code for each patient. C: November 27 to December 6. D: November 27 to December 16. E: November 27 to December 26. F: November 27 to January 5. Note differences in heat map scale for each panel. Figures were generated using Tableau version 2021.2.7. (Tableau Software, LLC, Seattle, WA).