Transmission dynamics and control of COVID-19 in Chile, March-October, 2020

Abstract

Since the detection of the first case of COVID-19 in Chile on March 3rd, 2020, a total of 513,188 cases, including ~14,302 deaths have been reported in Chile as of November 2nd, 2020. Here, we estimate the reproduction number throughout the epidemic in Chile and study the effectiveness of control interventions especially the effectiveness of lockdowns by conducting short-term forecasts based on the early transmission dynamics of COVID-19. Chile's incidence curve displays early sub-exponential growth dynamics with the deceleration of growth parameter, p, estimated at 0.8 (95% CI: 0.7, 0.8) and the reproduction number, R, estimated at 1.8 (95% CI: 1.6, 1.9). Our findings indicate that the control measures at the start of the epidemic significantly slowed down the spread of the virus. However, the relaxation of restrictions and spread of the virus in low-income neighborhoods in May led to a new surge of infections, followed by the reimposition of lockdowns in Greater Santiago and other municipalities. These measures have decelerated the virus spread with R estimated at ~0.96 (95% CI: 0.95, 0.98) as of November 2nd, 2020. The early sub-exponential growth trend (p ~0.8) of the COVID-19 epidemic transformed into a linear growth trend (p ~0.5) as of July 7th, 2020, after the reimposition of lockdowns. While the broad scale social distancing interventions have slowed the virus spread, the number of new COVID-19 cases continue to accrue, underscoring the need for persistent social distancing and active case detection and isolation efforts to maintain the epidemic under control.

Fig 1. Timeline of the milestones of the COVID-19 pandemic in Chile as of November 2^nd, 2020.

Fig 2. Daily incidence curve for all COVID-19 confirmed cases in Chile as of November 2^nd, 2020 [27].

Fig 3. Reproduction number with 95% CI estimated using the GGM model.

The estimated reproduction number of the COVID-19 epidemic in Chile as of March 28^th, 2020 is 1.80 (95% CI: 1.60, 1.90).

Fig 4. Reproduction number with 95% CI estimated by calibrating the GLM model from May 9^th-July 7^th, 2020.

The estimated reproduction number of the COVID-19 epidemic in Chile as of July 7^th, 2020 is 0.87 (95% CI: 0.84, 0.89).

Fig 5. Estimate of instantaneous reproduction number (R) for the COVID-19 epidemic in Chile as of November 2^nd, 2020 using the Cori method.

The most recent estimate of R~ 0.96 (95% CrI: 0.95, 0.98) as of November 2^nd, 2020. Black solid line represents the mean R and the gray shaded region represents the 95% credible interval around mean R.

Fig 6. 20-days ahead forecast of the COVID-19 epidemic in Chile by calibrating the GGM model until March 30^th, 2020.

Blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% prediction interval. The vertical black dashed line represents the time of the start of the forecast period.

Fig 7. 20-days ahead forecast of the COVID-19 epidemic in Chile by calibrating the GLM model from May 9^th-July 7^th, 2020.

Blue circles correspond to the data points; the solid red line indicates the best model fit, and the red dashed lines represent the 95% prediction interval. The vertical black dashed line represents the time of the start of the forecast period.

Fig 8. Laboratory results for the COVID-19 tests conducted in Chile as of November 2^nd, 2020.

The blue color represents the negative test results, and the yellow color represents the positive test results. The solid orange line represents the positivity rate of COVID-19 in Chile.