Abstract
Prior infection and vaccination both contribute to population-level SARS-CoV-2 immunity. We used a Bayesian model to synthesize evidence and estimate population immunity to prevalent SARS-CoV-2 variants in the United States over the course of the epidemic until December 1, 2021, and how this changed with the introduction of the Omicron variant. We used daily SARS-CoV-2 infection estimates and vaccination coverage data for each US state and county. We estimated relative rates of vaccination conditional on previous infection status using the Census Bureau’s Household Pulse Survey. We used published evidence on natural and vaccine-induced immunity, including waning and immune escape. The estimated percentage of the US population with a history of SARS-CoV-2 infection or vaccination as of December 1, 2021, was 88.2% (95%CrI: 83.6%-93.5%), compared to 24.9% (95%CrI: 18.5%-34.1%) on January 1, 2021. State-level estimates for December 1, 2021, ranged between 76.9% (95%CrI: 67.6%-87.6%, West Virginia) and 94.4% (95%CrI: 91.2%-97.3%, New Mexico). Accounting for waning and immune escape, the effective protection against the Omicron variant on December 1, 2021, was 21.8% (95%CrI: 20.7%-23.4%) nationally and ranged between 14.4% (95%CrI: 13.2%-15.8%, West Virginia), to 26.4% (95%CrI: 25.3%-27.8%, Colorado). Effective protection against severe disease from Omicron was 61.2% (95%CrI: 59.1%-64.0%) nationally and ranged between 53.0% (95%CrI: 47.3%-60.0%, Vermont) and 65.8% (95%CrI: 64.9%-66.7%, Colorado). While over three-quarters of the US population had prior immunological exposure to SARS-CoV-2 via vaccination or infection on December 1, 2021, only a fifth of the population was estimated to have effective protection to infection with the immune-evading Omicron variant.
Significance Both SARS-CoV-2 infection and COVID-19 vaccination contribute to population-level immunity against SARS-CoV-2. This study estimates the immunity and effective protection against future SARS-CoV-2 infection in each US state and county over 2020-2021. The estimated percentage of the US population with a history of SARS-CoV-2 infection or vaccination as of December 1, 2021, was 88.2% (95%CrI: 83.6%-93.5%). Accounting for waning and immune escape, protection against the Omicron variant was 21.8% (95%CrI: 20.7%-23.4%). Protection against infection with the Omicron variant ranged between 14.4% (95%CrI: 13.2%-15.8%%, West Virginia) and 26.4% (95%CrI: 25.3%-27.8%, Colorado) across US states. The introduction of the immune-evading Omicron variant resulted in an effective absolute increase of approximately 30 percentage points in the fraction of the population susceptible to infection.
Competing Interest Statement
VEP has received reimbursement from Merck and Pfizer for travel expenses to Scientific Input Engagements unrelated to the topic of this manuscript. All other authors have declared that no competing interest exist.
Funding Statement
VEP reports grants from National Institute of Allergy and Infectious Diseases R01 AI137093 TC reports grants from National Institute of Allergy and Infectious Diseases R01 AI112438 NAM reports grants from National Institute of Allergy and Infectious Diseases R01 AI146555-01A1, the Centers for Disease Control and Prevention though the Council of State and Territorial Epidemiologists (NU38OT000297-03), and the Centers for Disease Control and Prevention (75D30121F0003). JAS reports funding from the Centers for Disease Control and Prevention though the Council of State and Territorial Epidemiologists (NU38OT000297-02) and the National Institute on Drug Abuse (3R37DA01561217S1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
Yes
The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
All data used in the main analysis are available from The Covid Tracking Project, Johns Hopkins CSSE, Github, US Census Bureau, Ipsos and a JAMA publication. Code for analyses is available from GitHub.
I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.
Yes
I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
Yes
I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.
Yes
Footnotes
Competing interest statement: VEP has received reimbursement from Merck and Pfizer for travel expenses to Scientific Input Engagements unrelated to the topic of this manuscript. All other authors have declared that no competing interest exist.
Funding updated. Minor textual revisions.
Data Availability
All data used in the main analysis are available from The Covid Tracking Project, Johns Hopkins CSSE, Github, US Census Bureau, Ipsos and a JAMA publication. Code for analyses is available from GitHub. https://covidtracking.com/ https://www.mass.gov/info-details/covid-19-response-reporting https://www.openicpsr.org/openicpsr/project/144903/version/V1/view https://github.com/bansallab/vaccinetracking/tree/main/vacc_data https://www.census.gov/programs-surveys/household-pulse-survey/data.html https://github.com/covidestim/covidestim/immunity-waning https://jamanetwork.com/journals/jama/fullarticle/2784013
https://covidtracking.com/
https://www.mass.gov/info-details/covid-19-response-reporting
https://www.openicpsr.org/openicpsr/project/144903/version/V1/view
https://github.com/bansallab/vaccinetracking/tree/main/vacc_data
https://www.census.gov/programs-surveys/household-pulse-survey/data.html
https://github.com/covidestim/covidestim/immunity-waning
https://jamanetwork.com/journals/jama/fullarticle/2784013