Mortality data on deaths due to pneumonia & influenza through the week ending 2020-03-28
Background Tracking the severity and public health impact of emerging diseases, such as the novel coronavirus diseases COVID-19, is a critical need. These efforts are often hampered by testing issues and reporting lags for key epidemiological data. Evaluating unexplained increases in deaths attributed to non-specific causes, such as pneumonia, can provide a more complete picture of the burden caused by COVID-19.
Methods We evaluated increases in the occurrence of deaths due to P&I above a seasonal baseline across the United States and compared the rate of excess deaths to reported rates of death due to COVID-19, as well as state-level coronavirus testing rates and excess rates of influenza-like illness.
Results There were notable increases in the rate of death due to pneumonia and influenza. In a number of states, these increases pre-dated the increase in testing rates and went uncounted. There was substantial variability between states in the discrepancy between reported rates of death due to COVID-19 and the estimated burden of excess deaths due to P&I. In some states, the burden of reported deaths was 10-fold lower than the burden of excess deaths due to P&I.
Conclusions Given the lack of consistent virological testing, tracking spikes in deaths due to non-specific causes provides the most complete estimate of the burden of COVID-19. This approach provides a framework for tracking the progression of the epidemic and its public health impact.
The black line shows the observed proportion of deaths that were due to Pneumonia & Influenza (P&I) per week. The red line and shaded area represent the 95% Prediction Interval. The latest P&I data is for the week ending 2020-03-28.
Excess Deaths due to pneumonia and influenza
These plots show the Observed/Expected number of deaths due to pneumonia and influenza in each week for the 2019-20 year (red) compared to previous years (gray). Values close to 1 indicate that the values for that week are close to what would be expected based on the time of year and influenza activity.
The blue line shows the number of excess P&I cases, the red solid line shows the reported number of COVID-19 deaths for the same week (as compiled by the Johns Hopkins CSEE), and the dotted red line shows the reported COVID-19 deaths for weeks in which the CDC data were not yet available. Excess P&I estimates from recent weeks are adjusted for incomplete records using the “percent_complete” variable.
Observed and Excess deaths due to pneumonia & influenza, and COVID-19, from February 9, 2020 through Mar 28, 2020 | ||||
State | Total P&I deaths | Excess P&I deaths | Reported COVID-19 deaths | Excess P&I deaths/1,000,000 people |
---|---|---|---|---|
NY | 2654 | 620(526, 714) | 728 | 31.9 (27.1, 36.7) |
WA | 736 | 187(139, 235) | 207 | 24.6 (18.2, 30.9) |
NJ | 860 | 206(154, 258) | 140 | 23.2 (17.4, 29) |
IL | 1266 | 185(117, 253) | 47 | 14.6 (9.2, 20) |
PA | 1237 | 182(115, 249) | 34 | 14.2 (9, 19.4) |
CA | 3428 | 399(286, 512) | 101 | 10.1 (7.2, 13) |
ME,MA,NH,RI,VT | 1258 | 114(44, 183) | 59 | 10.1 (3.9, 16.3) |
IA,KS,MO,NE | 1498 | 124(47, 200) | 20 | 8.7 (3.3, 14.2) |
CO,MT,ND,SD,UT,WY | 953 | 105(45, 165) | 36 | 8.6 (3.7, 13.5) |
FL | 2039 | 180(93, 267) | 54 | 8.4 (4.3, 12.4) |
IN,MN,WI | 1795 | 150(65, 235) | 49 | 8.2 (3.6, 12.9) |
AK,ID,OR | 466 | 51(10, 93) | 19 | 7.6 (1.4, 13.8) |
AR,LA,NM,OK | 1402 | 95(21, 169) | 158 | 6.9 (1.5, 12.3) |
GA | 677 | 68(18, 118) | 69 | 6.4 (1.7, 11.2) |
TX | 2105 | 176(86, 266) | 27 | 6.1 (3, 9.2) |
AZ,HI,NV | 994 | 62(0, 125) | 25 | 5.3 (0, 10.6) |
DE,MD,VA | 1188 | 67(-3, 136) | 25 | 4.3 (-0.2, 8.7) |
OH | 973 | 44(-19, 106) | 25 | 3.7 (-1.6, 9.1) |
MI | 979 | 37(-27, 101) | 92 | 3.7 (-2.7, 10.1) |
AL,KY,MS,SC,TN | 2661 | 47(-58, 152) | 43 | 1.9 (-2.4, 6.2) |
Here we compare the observed vs expected number of deaths due to pneumonia and influenza in each week compare to the observed vs expected number of outpatient visits for influenza-like illness (ILI) in each week. we would expect ILI (blue line) to increase earlier than deaths (red line)
Table S1: Comparison of data sources: Observed and Excess deaths due to pneumonia & influenza, and COVID-19, from February 9, 2020 through Mar 28, 2020 | |||||
Week ending | Total P&I deaths | Excess P&I deaths | NCHS Reported COVID-19 Deaths, with pneumonia code | NCHS Reported COVID-19 Deaths | All reported COVID-19 deaths (covidtracking.com) |
---|---|---|---|---|---|
2020-02-15 | 3971 | -71(-202, 60) | 0 | 0 | 0 |
2020-02-22 | 3867 | -132(-262, -2) | 0 | 0 | 0 |
2020-02-29 | 3998 | 67(-62, 196) | 3 | 5 | 1 |
2020-03-07 | 4092 | 270(143, 397) | 11 | 19 | 22 |
2020-03-14 | 4046 | 455(332, 578) | 22 | 44 | 36 |
2020-03-21 | 4317 | 887(767, 1007) | 200 | 435 | 229 |
2020-03-28 | 4877 | 1622(1505, 1739) | 928 | 2034 | 1670 |
#> [1] "3098(2766, 3430)"
#> [1] 1958
#> [1] 2537
Now instead of modeling the proportion of deaths that were due to pneumonia and influenza, we will model all-caused deaths, using the proportion under-reporting as the denominator
The black line shows the observed number of all deaths per week, regardless of cause. The red line and shaded area represent the 95% Prediction Interval. The latest data is for the week ending 2020-03-28. Note that these are adjusted for percent completeness of the data. There are clear jumps in all-cause mortality in NY and NJ, other states less clear, probably due to reporting delays
Fold difference between excess all-cause mortality and excess P&I mortality in NJ and NY. Shows that excess P&I accounts for ~50-60% of the excess deaths
#> [1] 0.5667752
#> [1] 0.352065
Ratio of all-cause vs P&I deaths in NYC. In NYC, only 25% of excess deaths were coded as P&I
#> [1] 0.237500 0.283148
#> [1] 1409
Note these values will be greater than those in other tables, which are 2 weeks behind
State | NCHS Reported COVID-19 Deaths | NCHS Reported COVID-19 Deaths, with pneumonia code | Proportion with pneumonia | |
---|---|---|---|---|
25 | Total US | 6930 | 3161 | 0.46 |
26 | Alabama | 17 | 6 | 0.35 |
27 | Alaska | 1 | 1 | 1 |
28 | Arizona | 26 | 13 | 0.5 |
29 | Arkansas | 10 | 2 | 0.2 |
30 | California | 187 | 102 | 0.55 |
31 | Colorado | 107 | 60 | 0.56 |
33 | Delaware | 2 | 2 | 1 |
34 | District of Columbia | 5 | 5 | 1 |
35 | Florida | 157 | 93 | 0.59 |
36 | Georgia | 74 | 42 | 0.57 |
37 | Hawaii | 1 | 0 | 0 |
38 | Idaho | 13 | 4 | 0.31 |
39 | Illinois | 77 | 47 | 0.61 |
40 | Indiana | 43 | 19 | 0.44 |
41 | Iowa | 12 | 2 | 0.17 |
42 | Kansas | 9 | 3 | 0.33 |
43 | Kentucky | 6 | 3 | 0.5 |
44 | Louisiana | 154 | 64 | 0.42 |
45 | Maine | 10 | 5 | 0.5 |
46 | Maryland | 75 | 42 | 0.56 |
47 | Massachusetts | 172 | 85 | 0.49 |
48 | Michigan | 309 | 142 | 0.46 |
49 | Minnesota | 17 | 6 | 0.35 |
50 | Mississippi | 34 | 17 | 0.5 |
51 | Missouri | 22 | 9 | 0.41 |
52 | Montana | 3 | 1 | 0.33 |
53 | Nebraska | 3 | 2 | 0.67 |
54 | Nevada | 27 | 21 | 0.78 |
55 | New Hampshire | 15 | 8 | 0.53 |
56 | New Jersey | 593 | 303 | 0.51 |
57 | New Mexico | 1 | 0 | 0 |
58 | New York | 1130 | 650 | 0.58 |
59 | New York City | 2862 | 1065 | 0.37 |
61 | North Dakota | 1 | 0 | 0 |
62 | Ohio | 8 | 4 | 0.5 |
63 | Oklahoma | 17 | 5 | 0.29 |
64 | Oregon | 21 | 13 | 0.62 |
65 | Pennsylvania | 220 | 98 | 0.45 |
66 | Rhode Island | 1 | 1 | 1 |
67 | South Carolina | 36 | 13 | 0.36 |
68 | South Dakota | 4 | 1 | 0.25 |
69 | Tennessee | 25 | 11 | 0.44 |
70 | Texas | 47 | 18 | 0.38 |
71 | Utah | 8 | 3 | 0.38 |
72 | Vermont | 17 | 6 | 0.35 |
73 | Virginia | 39 | 15 | 0.38 |
74 | Washington | 278 | 142 | 0.51 |
76 | Wisconsin | 34 | 7 | 0.21 |
78 | Puerto Rico | 18 | 13 | 0.72 |
Observed and Excess deaths due to pneumonia & influenza, and COVID-19, from February 9, 2020 through Mar 28, 2020 | |||
State | Excess P&I deaths (unadjusted) | Excess P&I deaths (adjusted) | Reported COVID-19 deaths |
---|---|---|---|
NY | 620(526, 714) | 620(526, 714) | 728 |
CA | 393(280, 506) | 399(287, 512) | 101 |
NJ | 206(154, 258) | 206(154, 258) | 140 |
WA | 187(139, 235) | 187(139, 235) | 207 |
IL | 185(117, 253) | 185(117, 253) | 47 |
FL | 180(93, 267) | 180(93, 267) | 54 |
TX | 159(71, 247) | 176(88, 264) | 27 |
PA | 156(96, 216) | 182(122, 242) | 34 |
IN,MN,WI | 146(62, 230) | 150(66, 234) | 49 |
ME,MA,NH,RI,VT | 110(40, 180) | 114(44, 183) | 59 |
IA,KS,MO,NE | 110(35, 185) | 124(48, 199) | 20 |
CO,MT,ND,SD,UT,WY | 101(41, 161) | 105(46, 165) | 36 |
AR,LA,NM,OK | 74(3, 145) | 95(24, 166) | 158 |
DE,MD,VA | 65(-4, 134) | 67(-2, 136) | 25 |
AZ,HI,NV | 61(-1, 123) | 62(0, 125) | 25 |
GA | 47(-2, 96) | 68(20, 117) | 69 |
AK,ID,OR | 45(5, 85) | 51(11, 92) | 19 |
AL,KY,MS,SC,TN | 38(-65, 141) | 47(-57, 150) | 43 |
MI | 37(-27, 101) | 37(-27, 101) | 92 |
OH | 34(-23, 91) | 44(-14, 101) | 25 |
Excess deaths due to pneumonia & influenza from February 9, 2020 through Mar 28, 2020 with or without adjustment for delayed reporting | ||
state | Excess P&I (unadjusted) | Excess P&I (adjusted for reporting delay) |
---|---|---|
NY | 514(420, 608) | 620(526, 714) |
CA | 370(257, 482) | 399(287, 512) |
NJ | 206(154, 258) | 206(154, 258) |
WA | 156(108, 204) | 187(139, 235) |
IL | 165(97, 233) | 185(117, 253) |
PA | 75(15, 135) | 182(122, 242) |
FL | 179(92, 266) | 180(93, 267) |
TX | 88(0, 177) | 176(88, 264) |
IN,MN,WI | 101(17, 185) | 150(66, 234) |
IA,KS,MO,NE | 62(-13, 137) | 124(48, 199) |
ME,MA,NH,RI,VT | 61(-9, 130) | 114(44, 183) |
CO,MT,ND,SD,UT,WY | 53(-7, 113) | 105(46, 165) |
AR,LA,NM,OK | 67(-5, 138) | 95(24, 166) |
GA | 40(-9, 88) | 68(20, 117) |
DE,MD,VA | 39(-30, 108) | 67(-2, 136) |
AZ,HI,NV | 46(-16, 109) | 62(0, 125) |
AK,ID,OR | 17(-23, 58) | 51(11, 92) |
AL,KY,MS,SC,TN | 42(-61, 145) | 47(-57, 150) |
OH | 13(-44, 70) | 44(-14, 101) |
MI | 46(-18, 110) | 37(-27, 101) |