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Differential effects of intervention timing on COVID-19 spread in the United States

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Science Advances  04 Dec 2020:
Vol. 6, no. 49, eabd6370
DOI: 10.1126/sciadv.abd6370
  • Fig. 1 Model fit and parameter inference.

    Posterior fitting to daily cases and deaths in the United States (A and B) and the New York metropolitan area (C and D). Orange dots represent observations. Blue and gray lines are the median estimate and 95% CIs, respectively. The estimated effective reproductive number, Re, in six metropolitan areas are shown in (E). The black dotted line indicates Re = 1. (F) The estimated ascertainment rate over time. The blue line and gray dashed lines are the median estimates and 95% CIs, respectively. (G) The estimated cumulative infections (both reported and unreported) in six metropolitan areas. We compare the reported seroprevalence (%) in nine locations on different dates with the inferred percentage cumulative infections on those dates in (H). Whiskers show 95% CIs. Details on the serological survey are provided in Materials and Methods.

  • Fig. 2 Asynchronous reduction of effective reproductive numbers.

    For each county, we show the date when the local effective reproductive number dropped below 1.5 (A), 1.25 (B), 1 (C), and 0.75 (D) and stayed below that threshold until 3 May. Counties in gray are those that either never reached the threshold or failed to remain below the threshold.

  • Fig. 3 Counterfactual simulations with control interventions beginning in early March, 1 and 2 weeks earlier than implemented.

    Daily cases and deaths in the United States (A, B, E, and F) and the New York metropolitan area (C, D, G, and H) under early interventions are compared with the observations (orange crosses). The top and bottom rows present counterfactuals with interventions implemented on 8 and 1 March, respectively. The black lines and surrounding bands show the median estimate, interquartile, and 95% CIs.

  • Fig. 4 Effects of response time after control measures are relaxed.

    We assume a control relaxation (a weekly 5% increase of the transmission rate) starting on 4 May in all U.S. counties. If the local weekly case number in a county increases for 2 or 3 consecutive weeks, a weekly 25% reduction of the transmission rate is imposed for that county. Daily cases and deaths in the United States for a response time of 2 weeks (A and C) and 3 weeks (B and D) are compared. The black lines and bands show the median estimate, interquartile, and 95% CIs.

  • Table 1 Estimated basic reproductive numbers.

    Estimated basic reproductive numbers (Rt) for the New York, New Orleans, Los Angeles, Chicago, Boston, and Miami metropolitan areas on 15 March, 29 March, 12 April, 26 April, and 3 May. Mean estimate (95% CIs) are presented.

    15 March29 March12 April26 April3 May
    New York3.10 (2.76, 3.45)1.63 (1.41, 1.88)0.60 (0.52, 0.66)0.38 (0.32, 0.43)0.34 (0.30, 0.40)
    New Orleans2.50 (2.11, 2.89)1.91 (1.65, 2.27)0.44 (0.34, 0.55)0.29 (0.22, 0.36)0.27 (0.21, 0.34)
    Los Angeles3.12 (2.56, 3.72)1.35 (1.06, 1.71)1.16 (0.89, 1.38)1.17 (0.89, 1.44)1.18 (0.91, 1.44)
    Chicago2.84 (2.41, 3.34)2.04 (1.74, 2.36)1.11 (0.92, 1.29)1.39 (1.14, 1.66)1.13 (0.92, 1.34)
    Boston3.86 (3.28, 4.47)2.19 (1.73, 2.57)0.95 (0.77, 1.08)0.41 (0.32, 0.54)0.33 (0.26,0.40)
    Miami2.96 (2.56, 3.45)1.38 (1.12, 1.68)0.78 (0.60, 0.96)0.76 (0.57, 0.88)1.32 (1.07, 1.52)
  • Table 2 Setting initial parameters and variables.

    The prior transmission rate in each county is scaled by population density using a baseline transmission rate β0 as inferred through 13 March 2020. The relative transmission rate (μ), latency period (Z), infectious period (D), and mobility factor (θ) are fixed at posterior values inferred through 13 March 2020. Values are shown for the median and 95% CIs in the parentheses. The initial numbers of exposed individuals E and unreported infected individuals Iu are drawn from uniform distributions U(0,18C) and U(0,20C) 9 days before the reporting date (T0) of the first case. Here, C is the total number of reported cases between days T0 and T0 + 4.

    Parameter/variableValues
    Baseline transmission rate (β0, day−1)0.95 (0.84, 1.06)
    Relative transmission rate (μ)0.64 (0.56, 0.70)
    Latency period (Z, day)3.59 (3.28, 3.99)
    Infectious period (D, day)3.56 (3.21, 3.83)
    Mobility factor (θ)0.15 (0.12, 0.17)
    Reporting rate (α), prior0.080 (0.069, 0.093)
    Initial exposed population (E)U(0,20C)
    Initial unreported infected population (Iu)U(0,18C)

Supplementary Materials

  • Supplementary Materials

    Differential Effects of Intervention Timing on COVID-19 Spread in the United States

    Sen Pei, Sasikiran Kandula and Jeffrey Shaman

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    This PDF file includes:

    • Materials and Methods
    • Figs. S1 to S9
    • Table S1

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