Science - USA (2021-07-16)

Hayet al.,Science 373 , eabh0635 (2021) 16 July 2021 4 of 12

0

2

4

6

B 8

0

2

4

6

8

Count

0

2

4

6

8

30 2 0 01

Ct value

0.00

0.25

0.50

0.75

1.00

2020−04−10 2020−04−16 2020−05−04

PCR detectable prevalence

D

0.00

0.03

0.06

0.09

0.12

0.0

0.2

0.4

0.6

Per capita incidence

A PCR detectable prevalence

0.00

0.03

0.06

0.09

C 0.12

0.00

0.03

0.06

0.09

0.12

0.00

0.03

0.06

0.09

0.12

Mar 01 Mar 15 Apr 01 Apr 15 May 01

−0.6

−0.3

0.0

0.3

0.6

Mar 01 Mar 15 Apr 01 Apr 15 May 01

Date

Growth rate

E

Per capita incidence

Average growth rate, SEEIRR

Daily growth rate, SEEIRR

Average growth rate, Ct model

Daily growth rate, Ct model

Observed

Fitted

MAP

Posterior draw

Incidence

Prevalence

Observed prevalence

Fig. 2. Single cross-sectional distributions of observed Ct values can be used
to reconstruct epidemic trajectories in a Massachusetts long-term care
facility.(A) Estimated prevalence [faint orange lines show posterior samples,
solid orange line shows posterior median, and orange ribbon shows 95% credible
intervals (CrIs)] and incidence (red line shows posterior median and red ribbon
shows 95% CrI) from the standard compartmental (SEEIRR) model fit to
point prevalence at three sampling times (error bars show 95% binomial
confidence intervals). (B) Model-predicted Ct distributions (blue) fitted to the
observed Ct values (gray bars) from each of three cross-sectional samples.
Shown are the posterior median (black line) and 95% CrI for the expected Ct
distribution (dark blue ribbon) and 95% prediction intervals based on simulated

observations (light blue ribbon). Note that prediction intervals are much wider

than CrIs because they result from simulating observations with a small sample

size. (C) Each panel shows results from fitting the Ct-based SEIR model separately

to three cross sections of virologic data. Shown are random posterior samples

(red lines) and the maximum posterior probability (MAP) trajectory (black line)

for the incidence curve. (D) Fitted median (blue point) and 95% CrI (blue error

bars) for the proportion of samples testing positive based on the Ct model

compared with the observed proportion tested positive (gray cross). (E) Thirty-

fiveÐday (green) and 1-day (pink) average growth rates from the Ct model

estimates in (C) at three time points (violin plots) compared with growth-rate

estimates from the SEEIRR model in (A) (lines and shaded ribbons).

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