Abstract
By August 1, 2022, the SARS-CoV-2 virus had caused over 90 million cases of COVID-19 and
one million deaths in the United States. Since December 2020, SARS-CoV-2 vaccines have
been a key component of US pandemic response; however, the impacts of vaccination are not
easily quantified. Here, we use a dynamic county-scale metapopulation model to estimate the
number of cases, hospitalizations, and deaths averted due to vaccination during the first six
months of vaccine availability. We estimate that COVID-19 vaccination was associated with
over 8 million fewer confirmed cases, over 120 thousand fewer deaths, and 700 thousand fewer
hospitalizations during the first six months of the campaign.
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Introduction
By August 1, 2022, SARS-CoV-2, the virus responsible for the COVID-19 pandemic, had
caused over 90 million cases and 1 million deaths in the United States (1). While these numbers
are likely affected by the widespread availability of SARS-CoV-2 vaccines, the precise impact of
vaccination on the burden of COVID-19 disease is uncertain. Here we use a dynamic model,
coupled with historical data, statistical inference methods, and hospitalization costs, to quantify
the clinical and economic burdens of infections, hospitalizations, and deaths averted due to
vaccination in the US, both cumulatively and in individual states, during the first approximately
six months of vaccine availability when the wild type and alpha variants of SARS-CoV-2 were
the predominant drivers of infection.
In mid-December 2020, the first SARS-CoV-2 vaccine received emergency use authorization in
the US and was initially recommended for healthcare workers and long-term care facility
residents, followed by adults aged 65 years and older, adults aged 16-64 with high-risk medical
conditions and essential workers (2). By early April 2021, the vaccine recommendation was
extended to the general population aged 16 years and older. Subsequent steps have seen
recommended vaccine use for 12-15 year-olds (May 2021) and 5-11 year-olds (November 2021).
Three different vaccines (two mRNA vaccines and one antiviral vector vaccine) with varying
efficacy and estimates of duration of protection have been authorized for use in the US.
However, vaccination delivery has been variable: it was initially limited by vaccine availability,
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with roughly 15 million doses provided in the first month, but reached a peak of roughly 90
million doses administered during April, 2021(1).
By early November 2021, 78% of the US population aged 12 years and older had received at
least one dose of a SARS-CoV-2 vaccine, with heterogeneous distribution across age groups
(97% of adults aged 65+ years vs 60% of persons aged 12-18 years) and across states (90% in CT, MA, HI, VT, PA [2]).
During the time period of vaccine rollout, variable levels of non-pharmaceutical interventions
(NPIs), such as social distancing, closures of restaurants and bars, mask mandates and travel
restrictions, were implemented across states with different start and end dates.
Here, we use a dynamic county-scale metapopulation model, previously used COVID-19
inference and projections (3-5), to conduct counterfactual simulations representing the effects of
vaccination. These simulations are used to estimate the number of cases, hospitalizations, and
deaths averted due to vaccination during the first six months of vaccine roll out.
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Methods
We used a metapopulation model with a Susceptible-Exposed-Infected-Recovered (SEIR)
structure run at the county level, coupled with a data assimilation method (EAKF, the ensemble
adjustment Kalman filter). We have previously used this framework for inference, forecasting
and projections of influenza and SARS-CoV-2 infections at various locations and spatial scales
(3-5). Here, we simulated SARS-CoV-2 transmission within and among the 3142 counties of the
United States (see Supplementary Material).
Specifically, we first used the model-inference system to fit reported case counts in each county
of the US [3] from the time of identification of the first COVID-19 cases in the United States in
February 2020, through December 14, 2020, the date of first authorized SARS-CoV-2
vaccination in the US. The inferred values of parameters and state variables on December 14,
2020 served as initial conditions for the averted burden analysis.
We then included vaccination in the dynamical model structure using documented daily rates of
vaccine administration (1, 6) (see Supplementary Materials). State-level daily vaccination data
from the CDC COVID Data Tracker (1) were allocated proportionally to each county based on
population size. Within each county, we assumed equal probability of vaccination regardless of
prior infection status. We modeled the vaccine as producing direct effects only, with 90%
effectiveness against infection (7-9) – i.e. 90% of vaccinated individuals with no prior immunity
were fully protected while the remaining 10% receive no protection. Specifically, 90% of
vaccinated individuals with no prior immunity were removed from the Susceptible pool and
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placed in the Recovered compartment 24 days after administration of the first dose. In the
Recovered compartment, we did not distinguish between vaccinated individuals and individuals
recovered from infection; given uncertainty and limited data on re-infections and waning, both
were considered immune for the remainder of the simulation period. With the 24-day delay, the
impact of vaccinations on the simulation begins on January 8th. This baseline scenario,
retrospectively fitted to case counts, enabled estimation of the daily timeseries of
epidemiological parameters, including Rt, the time-varying reproductive number, for each county
location from December 14, 2020 through June 3, 2021.
We ran the simulations through June 3, 2021 to focus on the impact of vaccination prior to the
predominance of the Delta and Omicron variants (1). Given that the higher transmissibility and
immune escape properties of the Delta and Omicron variants require substantial additional
modifications of the dynamical model structure, as well as re-parametrization, we restricted our
analysis to the December 14, 2020 through June 3, 2021, or the pre-Delta, time period, during
which the vaccine provided strong protection against infection. To quantify the burden averted
by vaccination, we compared the baseline vaccination scenario to 3 counterfactual no-
vaccination scenarios simulated over the same time period. All counterfactual scenarios
assumed no vaccinations (or, equivalently, 0% vaccine effectiveness) but varied transmissibility
to mimic different levels of non-pharmaceutical intervention (NPI) response in the absence of
vaccination:
Counterfactual Scenario 1; A no-transmission-change, no-vaccination scenario in which
the Rt daily time series for each location was as inferred for the baseline scenario;
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Counterfactual Scenario 2: A no-vaccination scenario in which Rt for each location-day
was increased 10% with respect to the baseline scenario; and
Counterfactual Scenario 3: A no-vaccination scenario in which Rt for each location-day
was decreased 10% with respect to the baseline scenario.
These counterfactual scenarios represent potential population behaviors and policies that might
have been effected in the absence of vaccination. Scenario 3 represents increased NPIs through
policies and individual action; Scenario 2 represents a decrease of NPIs, perhaps due to
pandemic fatigue. We compared cumulative SARS-COV-2 cases in the 3 no-vaccination
scenarios to the baseline scenario at national and state levels, analyzed differences in averted
cases among states, and identified factors correlating with vaccination success.
Hospitalizations and Deaths
To calculate hospitalizations and deaths in the counterfactual scenarios, we made the assumption
that excess cases would have continued to lead to hospitalizations and deaths at the same overall
rate as they did in each state during the summer and fall of 2020, prior to vaccine availability.
We applied a state-specific pre-vaccine Case Hospitalization Rate (CHR) and a Case Fatality
Rate (CFR) multiplier to the total number of averted cases in each scenario. CHR was calculated
as the number of COVID-19 hospitalizations divided by cases during August 1 – December 14,
2020. Hospitalization data were compiled from the HHS dataset (10) and cases from the Johns
Hopkins Center for Systems Science and Engineering (JHU CSSE) COVID-19 data set (11, 12).
August 2020 was the first full month with all states reporting daily COVID-19 hospitalizations.
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CFR was calculated as the number of COVID-19 deaths divided by the number of cases in each
state during August 1 - December 14, 2020, using the JHU CSSE COVID-19 Data (11). We
excluded deaths and cases prior to August 1, 2020, for consistency with the hospitalization data
set, and because both the ascertainment rate (fraction of true infections that are reported as
confirmed cases) and the infection fatality rate (fraction of true infections that resulted in death)
were unstable during the initial wave of the pandemic (4).
Hospitalization Costs
We calculated averted hospitalization costs by multiplying the distribution of estimated COVID-
19 associated hospitalizations averted by the distribution of costs per hospitalization episode,
obtained from the US-based Premier Healthcare COVID-19 claims database (13). The median
(interquartile range Q1-Q3) cost per hospitalization episode was $12,046 ($6,309-$25,361).
Results
Initialization
At the start of the simulation period, December 14, 2020, it was estimated 74.1% (95% credible
interval: 70.2 – 78.6) of the US population was susceptible, 0.8% (95% CrI 0.6-1.2%) exposed,
0.8% (95% CrI 0.6-1.0%) infectious and 24.3% (95% CrI 19.2-28.6%) recovered. Figure 1
shows the distribution of the estimated epidemiological parameters across states at the beginning
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of vaccine administration. The median estimated susceptible fraction, corresponding to the
fraction of the population that had not yet been infected since the beginning of the pandemic
varied by state and ranged from 58% (95% CrI 56%-61%) in North Dakota to 94% (93%-95%)
in Vermont. The susceptible fraction was highest in northwestern and northeastern states. The
time dependent reproductive number ranged from median 0.8 (0.7-1.4 95% CrI) in Minnesota to
2.0 (1.7-2.3 95% CrI) in Tennessee. The CFR prior to the start of vaccination varied from 0.5%
in Alaska (95% CrI 0.3-0.7%) to 2.3% (95% CrI 2.1-2.6%) in Rhode Island. The CHR in the
same period ranged from 3.8% (95% CrI 3.6-4.0%) in Alaska to 20.7% in Kentucky (95% CrI
20.5-20.9%). While there was a modest reduction in CHR at the national scale from the pre-
vaccine period (8.8% August 1, 2020 – December 14, 2020) to the analysis period (7.8%
December 15, 2020 – June 2, 2021), we did not observe consistent population level differences
in CFR at the national level (1.5% during both time periods) nor to CHR and CFR at the state
level.
Figure 1 Caption: Upper Left: Population susceptibility, S (proportion of the population
not yet infected), at the start of vaccine administration; Upper Right: Time-varying
reproductive number, Rt, at the start of vaccine administration; Lower Left: State-specific
case hospitalization rate, CHR; Lower Right: State-specific case fatality rate, CFR. Color
scales show the median values.
Model results
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Between December 14 and June 3, 2021, the baseline model estimated 16.1 million (95% CrI
15.1 – 18.3 million) total cases, 1.4 million (95% CrI 1.3 – 1.6 million) hospitalizations, and
246.7 thousand (95% CrI 230.4 – 279.6 thousand) deaths. These estimates were generally
consistent with data reported by CDC COVID Data Tracker (1).
The time series of Rt resulting from fitting the baseline scenario from December 14, 2020
through June 4, 2021 is shown at the state and national level in Supplementary Figure S2. Note
that Rt in this analysis refers to the time-varying basic reproductive number, not to be confused
with the effective reproductive number Reff(t), which is Rt multiplied with the fractional
susceptible population.
By June 4, 2021, 51% of the population in the US had received at least one dose of vaccine (1).
Vaccine coverage differed widely by location, ranging from 35% of the population in Mississippi
up to 74% in Vermont. The weekly number of vaccinations administered increased over time:
initially at less than 5 million vaccinated per week but reaching a peak of 14 million vaccinated
per week in April when vaccination was extended to the general population aged 16 and older
(Figure S2).
Table 1 reports the cumulative averted COVID-19 cases, deaths, hospitalizations and
hospitalization cost savings for the 3 scenarios, while Figure 2 shows the counterfactual
scenarios and trends.
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Table 1: Total cumulative COVID-19 cases, deaths, hospitalizations and hospitalization cost
savings.
Scenario 1
No change in
transmission
Scenario 2
10% higher
transmission
Scenario 3
10% lower
transmission
Cases averted 8.1 million 17.0 million -1.6 million
median, (95% CrI) (-4.8, 26.3 million) (1.5, 32.0 million) (-8.8, 18.2 million)
Deaths averted 123.2 thousand 260.1 thousand -25.1 thousand
median, (95% CrI) (-74.3, 403.0 thousand) (23.0, 489.7 thousand) (-134.8, 278.8 thousand)
Hospitalizations averted 0.7 million 1.5 million -0.1 million
median, (95% CrI) (-0.4, 2.3 million) (0.1, 2.8 million) (-0.8, 1.6 million)
Hospitalization cost
savings $7.0 billion $17.3 billion -$0.9 billion
median, (95% CrI) ($-11.9, 112.0 billion) ($0.9, 170.3 billion) (-$44.7, 70.1 billion)
Figure 2 Caption: Modeled total COVID-19 Cases in Counterfactual Scenarios 1 (top
panel), 2 (middle panel) and 3 (bottom panel) in the United States. The black line
presents observed cases, the blue line indicates the median counterfactual projection, and
the blue shaded area shows the 95% credible interval
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In the scenario with no change in transmission, we estimated that vaccination averted 8.1 million
cases at the national level (median value, 95% CrI :[-4.8, 26.3] millions cases), 123.2 thousand
deaths (median value, 95% CrI. :[-74.3, 403.0] thousand deaths) and 0.7 million hospitalizations
(median value, 95% CrI :[-0.4, 2.3] millions hospitalizations). The median cost savings
associated with averted hospitalization was $7.0 billion (median value, 95% CrI:[-$11.9,
$112.0]) (see Table 1).
Increasing Rt by 10% with no vaccination in Counterfactual Scenario 2 roughly doubled the
median cases averted nationally whereas decreasing Rt by 10% with no vaccination in
Counterfactual Scenario 3 considerably reduced the averted burden during the approximately 6
months of analysis (Figure 2 and Table 1). In effect, the decreased Rt, representing increased
NPIs, initially offsets the effects of no vaccination during the first 3 months when a more limited
percentage of the population is effectively vaccinated. However, this effect decreases in mid-
March as vaccination rates climb in the baseline scenario, and by May more cases are produced
per day in Counterfactual Scenario 3 due to the absence of vaccination.
In all three counterfactual scenarios, the majority of averted cases occurred between April and
June 2021 (Figure 2). For individual states, the median estimates of cases averted ranged from
roughly1000 to 6400 cases per hundred thousand population (Figure 3). Median cumulative
averted hospitalizations varied from 74 to 752 per hundred thousand and median cumulative
averted deaths varied from 16 to 128 per hundred thousand. Higher averted case burden
correlated with higher vaccination rate (R2=0.16) and higher population susceptibility at the
beginning of the vaccination campaign (R2=0.21).
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Figure 3 Caption: Total per capita averted cases (a), hospitalizations (b) and deaths (c)
in each state between December 14, 2020 and June 2, 2021. The x-axis is the percent
population vaccinated by June 2, 2021, and the y-axis is the averted
cases/hospitalizations/deaths per 100,000 people. Each state is represented by a dot; the
color scale of the dots indicate the estimated fraction of population susceptible at the
beginning of vaccine rollout.
Discussion
Evaluating the population-level impact of COVID-19 vaccination through mathematical
modeling can provide useful insights to policy makers. Here, we leveraged a validated dynamical
modeling approach, previously used for research and operationally to simulate county-level
COVID-19 transmission, to quantify the additional burden of disease in alternate scenarios
without vaccination. Our analyses show that under unchanged NPI levels, COVID-19
vaccination in the US cumulatively prevented 8.3 million cases, 681 thousand hospitalizations
and 118 thousand deaths in the first 6 months of implementation. States with high vaccination
coverage such as Maine averted as many as 6,000 cases per 100,000 individuals.
These simulations confirm findings from other modeling studies, set in the US and elsewhere,
that have found a substantial impact of vaccination in terms of averted burden of disease.
Shoukat et al found that vaccination was fundamental for reducing the spring/summer wave in
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NYC by reducing cases by one third and hospitalization and deaths by half during December
2020 through July 2021 (14). Vilches et al showed that vaccination may have averted more than
14 million cases, 241 thousand deaths and 1.1 million hospitalizations in the US by late June
2021(15). Moghadas et al. found an even stronger effect of vaccination with 26 million cases, 1.2
million hospitalizations and 279,000 deaths averted through the end of June 2021 (16). These
three studies are in general agreement with our findings and indicate the US would have
experienced a substantial wave of infections beginning in March/April 2021 in the absence of a
vaccine (14-16). Large effects were found also in Israel by Haas et al. where two thirds of
hospitalizations and deaths were averted with vaccination in the first four months of vaccine
implementation (17).
Our study augments prior research in this field by providing further geographical granularity.
The state-level analyses provide a dynamic picture revealing trends and differences in the public
health response to the COVID-19 pandemic, which may be informative for state and local
policymakers. Additionally, our study presents estimates of cost savings associated with vaccine-
preventable severe disease (i.e. hospitalizations). It showed that the benefits of vaccination due to
reduced hospitalization loads translated into cost-savings in the billions of dollars. Vaccination
may also lessen other societal impacts associated with the pandemic (e.g. work productivity
loss). The total economic impact may therefore be even greater than reported, and further studies
elucidating those impacts are warranted.
Our study also adds to the existing literature by considering 3 counterfactual scenarios, all
without vaccinations, but with varying Rt, that mimic different possible population responses to
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disease spread in the absence of a vaccine. The first counterfactual scenario is designed to
quantify what the SARS-COV-2 related burden would have been without vaccinations if the
population had maintained the same NPI measures as occurred with vaccination. The other two
counterfactual scenarios are designed to explore the uncertainties of these estimates, as it is
difficult to anticipate the public policy and population behavior response in the absence of a
vaccine. Specifically, Counterfactual Scenario 2 represents a stronger relaxation of NPIs,
possibly due to pandemic fatigue in the absence of an available vaccine, while Counterfactual
Scenario 3 represents a reinforcement of NPIs during the 6 months of projections, assuming that
the population would have responded with increased measures to control transmission.
Counterfactual 3 shows that in the early months of the vaccine rollout, an increase in NPIs could
have produced an even greater reduction of disease compared to vaccination as it occurred.
However, while increased NPIs may have slowed transmission in the short term (the first months
of vaccine rollout), those measures would not have been as effective as vaccination once the
Alpha variant became established in the United States (Figure 2). The benefits of vaccination are
seen in the difference between Counterfactual Scenario 3 and the baseline curve during the last
month of simulation.
All 3 scenarios show that vaccination benefits were limited during the early months of vaccine
rollout, and that most of the averted burden was realized in the last 2 months of the analyzed
period. The winter peak of COVID-19 cases was reached in the US during mid-January 2021 just
when the first vaccinations started to become effective. Vaccine availability constraints during
the first months of the campaign restricted administration to portions of the population with
increased risk of exposure and severe disease. It was not until April 2021 that vaccination was
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recommended for the general population aged >16 years. The combination of an initially slower
rate of vaccination and a decreasing trend in transmission, with some states having a significant
proportion of the population no longer susceptible to infection, narrowed the overall averted
burden in the first months of 2021. Some exceptions occurred in states with larger initial
susceptible fractions (e.g. Vermont); for these states the averted burden per hundred thousand
was already significant in the early months of the vaccination campaign.
By March 2021, the Alpha variant, a SARS-CoV-2 strain with increased transmissibility relative
to the wild type, became the predominant circulating serotype (1). This variant, combined with
progressive relaxation of NPIs in most states, likely produced the increase of Rt inferred at this
time. Simultaneously, the impact of vaccination, seen in the divergence between the baseline
scenario and the no-vaccination scenario case curves, becomes much more evident at the national
level (Figure 2).
A limitation of this analysis is that it relies on assumptions about whether and how the
parameters inferred from the true observed course of the pandemic would have changed in the
absence of a vaccine. Our primary counterfactual, Scenario 1, assumed that the parameters –
including the disease transmission rates and the case ascertainment rate – would have been the
same with or without a vaccine. We explored some of the sensitivity to this assumption by
altering the time-varying reproductive number in Counterfactual Scenarios 2 and 3. However,
these are very simplified representations, and one could just as well imagine dramatically
different counterfactual scenarios.
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We limit our analysis to a relatively short projection time: the first six months of the vaccination
campaign. Our estimates are therefore not generalizable to the entire period of the vaccination
campaign. In subsequent months, booster doses, the expansion of the Pfizer vaccine to children
aged 5-11, waning immunity, and the establishment of the more virulent Delta and immune-
evading Omicron variants have made estimation of vaccine effects more challenging. These
later phases of the pandemic driven by new variants led to tens of millions of Covid-19
infections. Nevertheless, these early averted cases were crucial, as this period was prior to the
widespread availability of antiviral medication, and with substantially lower population
immunity against severe outcomes.
Additional assumptions should also be noted. The model structure is parsimonious and does not
explicitly represent certain factors including population age structure, breakthrough infections or
reinfections. We used a constant case hospitalization rate (CHR) and case fatality rate (CFR) for
each state, computed based on COVID-19 outcomes during the 6 months before vaccination, to
calculate counterfactual hospitalization and deaths in all scenarios. These choices ignore
differences in age-specific behavior and probability of severe outcomes.
We also note that the full effect of COVID-19 vaccination on hospitalizations and deaths derives
from two effects: those averted due to averted cases; and those averted due to improved
outcomes in vaccinated individuals if infected. The estimates of averted hospitalizations and
deaths in this analysis are restricted to the effect of averted cases and do not include reductions in
the probability of hospitalization and death among the vaccinated if infected. Each of the
approved COVID-19 vaccines has been shown to be highly effective in preventing severe
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outcomes in individuals infected by SARS-CoV-2. Here, we assumed that the contribution of
the second effect was relatively small compared to the first, as the vaccines were shown to be
highly effective at preventing infections in the short term after inoculation and against the strains
circulating at the time of the study (18-20).
In conclusion, our analysis shows that COVID-19 vaccination reduced the burden of disease.
Base case results indicate that COVID-19 vaccination was associated with over 8 million fewer
confirmed cases, over 120 thousand fewer deaths, and 700 thousand fewer hospitalizations in the
first six months of the campaign. As such, COVID-19 vaccines represented a critical component
of the public health response to the COVID-19 pandemic in the US.
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Acknowledgements
This study was sponsored by Pfizer Inc. TKY, MG, SP and JS are employees of Columbia
University, which received funding from Pfizer in connection with the development of this study
and of this manuscript. JS and Columbia University disclose partial ownership of SK Analytics.
JS discloses consulting for BNI. MDF, FJA, MMM, and FK are employees of Pfizer and may
hold stock or stock options. DS was employed at Pfizer at the time this work was conducted
and he may own stock or stock options.
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