March 21, 2021 Analysis of USA state data

Individual state histories

The plots below show the case / hospitalization / deaths data for all 50 states, DC, and PR. The data fits were done using data up until March 15, 2021.

The green points are the daily cases, the grey points the daily hospitalizations, and indigo points are the daily deaths (each averaged over a week). The case data are used to define the periods for which transmission rate appears to be constant. The vertical lines show where the transmission rate is changed. In absence of immunity, constant transmission rates lead to steady exponential growth or decline during, which appear as straight lines on these log-scale plots. With immunity growing, these lines are no longer straight - bending downwards due to the herd effect. The curves are the model expectations for cases, hospitalizations, and deaths, as determined from the case data. The dashed curves separately show the reported cases from the original variant and the B117 variant.

Below the set of individual state plots, summary plots are provided that indicate the degree that natural and vaccination immunization is helping to bring down infections.

The final set of plots show the 4 week forecast for the USA and for each state.

Genomic data

For some staes, genomic screening data is available to estimate the growth advantage (aka selection coefficient, s) of the B117 variant as well as the current fraction of cases dues to that variant.

Below is a figure showing fits to the ratio of the SGTF cases to non-SGTF cases used to estimate the selection coefficient and current “frequency” of these cases.

usa_v_r

State	s	w	f_v (Mar 20)
Arizona	0.093 +/- 0.008	0.001 +/- 0.000	0.467 +/- 0.065
California	0.066 +/- 0.002	0.002 +/- 0.000	0.469 +/- 0.018
Florida	0.063 +/- 0.001	0.005 +/- 0.000	0.683 +/- 0.009
Georgia	0.090 +/- 0.003	0.001 +/- 0.000	0.727 +/- 0.017
Illinois	0.061 +/- 0.007	0.000 +/- 0.000	0.304 +/- 0.056
Indiana	0.090 +/- 0.005	0.001 +/- 0.000	0.450 +/- 0.034
Louisiana	0.107 +/- 0.020	0.002 +/- 0.001	0.665 +/- 0.099
Massachusetts	0.095 +/- 0.007	0.030 +/- 0.002	0.538 +/- 0.033
Michigan	0.098 +/- 0.005	0.000 +/- 0.000	0.766 +/- 0.019
Minnesota	0.094 +/- 0.010	0.001 +/- 0.000	0.757 +/- 0.042
North Carolina	0.086 +/- 0.005	0.001 +/- 0.000	0.422 +/- 0.031
New Jersey	0.059 +/- 0.010	0.000 +/- 0.001	0.372 +/- 0.084
New York	0.069 +/- 0.011	0.003 +/- 0.003	0.622 +/- 0.080
Pennsylvania	0.079 +/- 0.003	0.003 +/- 0.000	0.462 +/- 0.018
Texas	0.090 +/- 0.003	0.000 +/- 0.000	0.714 +/- 0.021

s: selection coefficient
w: SGTF false identification probability
f_v: fraction of cases due to the variant on March 20, 2021

States with genomic data

The states with independent genomic data allow for better constraint on the growth advantage and current case fraction. With the variant potentially causing growth in the weeks to come, predictions for these states are much better established.

Arizona

California

Florida

Georgia

Illinois

Indiana

Louisiana

Massachusetts

Michigan

Minnesota

North Carolina

New Jersey

New York

Pennsylvania

Texas

States without genomic data

In absence of genomic data, the growth advantage s = 0.08 is assumed. The current strength of the B117 is estimated from the fit to case data. Essentially this is derived by how fare the case data deviate from the expected trajectory for the original strain model (orange dashed curve). For states where the deviation is just beginning, there will be significant uncertainty on the timing of the next peak.

These model fits assume that there is no change to NPI (non-pharmiceutical intervention) between the vertical dotted lines. Such NPI changes can lead to large changes in the projections for the future growth of the variant.

Alaska

Alabama

Arkansas

Colorado

Connecticut

District Of Columbia

Delaware

Hawaii

Iowa

Idaho

Kansas

Kentucky

Maryland

Maine

Missouri

Mississippi

Montana

North Dakota

Nebraska

New Hampshire

New Mexico

Nevada

Ohio

Oklahoma

Oregon

Puerto Rico

Rhode Island

South Carolina

South Dakota

Tennessee

Utah

Virginia

Vermont

Washington

Wisconsin

West Virginia

Wyoming

Summary of growth rates (with and without immunity)

The following plots summarize the infection history. The upper plot shows the daily growth/decline of infections (% per day) for the orginal strain. The dashed curve are the growths that would have been experienced in absense of immunity. Natural immunity built up during the course of the epidemic has helped reduce infections and this is now being overtaken by vaccine immunity in many of the states. Note that the daily growth rate for the B117 variant is typically 8% more than that of the original strain.

The lower plot shows an estimate of the contagious fraction of the population as a function of time.