A modified Susceptible-Infected-Recovered model for observed under-reported incidence data.

Fitting Susceptible-Infected-Recovered (SIR) models to incidence data is problematic when not all infected individuals are reported. Assuming an underlying SIR model with general but known distribution for the time to recovery, this paper derives the implied differential-integral equations for observed incidence data when a fixed fraction of newly infected individuals are not observed. The parameters of the resulting system of differential equations are identifiable. Using these differential equations, we develop a stochastic model for the conditional distribution of current disease incidence given the entire past history of reported cases. We estimate the model parameters using Bayesian Markov Chain Monte-Carlo sampling of the posterior distribution. We use our model to estimate the transmission rate and fraction of asymptomatic individuals for the current Coronavirus 2019 outbreak in eight American Countries: the United States of America, Brazil, Mexico, Argentina, Chile, Colombia, Peru, and Panama, from January 2020 to May 2021. Our analysis reveals that the fraction of reported cases varies across all countries. For example, the reported incidence fraction for the United States of America varies from 0.3 to 0.6, while for Brazil it varies from 0.2 to 0.4.

Assessing the impact of human mobility to predict regional excess death in Ecuador.

COVID-19 outbreaks have had high mortality in low- and middle-income countries such as Ecuador. Human mobility is an important factor influencing the spread of diseases possibly leading to a high burden of disease at the country level. Drastic control measures, such as complete lockdown, are effective epidemic controls, yet in practice one hopes that a partial shutdown would suffice. It is an open problem to determine how much mobility can be allowed while controlling an outbreak. In this paper, we use statistical models to relate human mobility to the excess death in Ecuador while controlling for demographic factors. The mobility index provided by GRANDATA, based on mobile phone users, represents the change of number of out-of-home events with respect to a benchmark date (March 2nd, 2020). The study confirms the global trend that more men are dying than expected compared to women, and that people under 30 show less deaths than expected, particularly individuals younger than 20 with a death rate reduction between 22 and 27%. The weekly median mobility time series shows a sharp decrease in human mobility immediately after a national lockdown was declared on March 17, 2020 and a progressive increase towards the pre-lockdown level within two months. Relating median mobility to excess deaths shows a lag in its effect: first, a decrease in mobility in the previous two to three weeks decreases excess death and, more novel, we found an increase of mobility variability four weeks prior increases the number of excess deaths.

Excess deaths reveal unequal impact of COVID-19 in Ecuador.

Latin America has struggled to control the transmission of COVID-19. Comparison of excess death (ED) rates during the pandemic reveals that Ecuador is among the highest impacted countries. In this analysis, we update our previous findings with the most complete all-cause mortality records available for 2020, disaggregated by sex, age, ethnicity and geography. Our study shows that in 2020, Ecuador had a 64% ED rate (95% CI 63% to 65%) or 64% more deaths than expected. Men had a higher ED rate, 75% (95% CI 73% to 76%), than women's 51% (95% CI 49% to 52%), and this pattern of higher EDs for men than women held for most age groups. The only exception was the 20-29 age group, where women had 19% more deaths, compared to 10% more deaths for men, but that difference is not statistically significant. The analysis provides striking evidence of the lack of COVID-19 diagnostic testing in Ecuador: the confirmed COVID-19 deaths in 2020 accounted for only 21% of total EDs. Our significant finding is that indigenous populations, who typically account for about 5% of the deaths, show almost four times the ED rate of the majority mestizo group. Indigenous women in each age group have higher ED rates than the general population and, in ages between 20 and 49 years, they have higher ED rates than indigenous men. Indigenous women in the age group 20-29 years had an ED rate of 141%, which is commensurate to the ED rate of indigenous women older than 40 years.

Excess deaths reveal the true spatial, temporal and demographic impact of COVID-19 on mortality in Ecuador.

BACKGROUND: In early 2020, Ecuador reported one of the highest surges of per capita deaths across the globe. METHODS: We collected a comprehensive dataset containing individual death records between 2015 and 2020, from the Ecuadorian National Institute of Statistics and Census and the Ecuadorian Ministry of Government. We computed the number of excess deaths across time, geographical locations and demographic groups using Poisson regression methods. RESULTS: Between 1 January and 23 September 2020, the number of excess deaths in Ecuador was 36 402 [95% confidence interval (CI): 35 762-36 827] or 208 per 100 000 people, which is 171% of the expected deaths in that period in a typical year. Only 20% of the excess deaths are attributable to confirmed COVID-19 deaths. Strikingly, in provinces that were most affected by COVID-19 such as Guayas and Santa Elena, the all-cause deaths are more than double the expected number of deaths that would have occurred in a normal year. The extent of excess deaths in men is higher than in women, and the number of excess deaths increases with age. Indigenous populations had the highest level of excess deaths among all ethnic groups. CONCLUSIONS: Overall, the exceptionally high level of excess deaths in Ecuador highlights the enormous burden and heterogeneous impact of COVID-19 on mortality, especially in older age groups and Indigenous populations in Ecuador, which was not fully revealed by COVID-19 death counts. Together with the limited testing in Ecuador, our results suggest that the majority of the excess deaths were likely to be undocumented COVID-19 deaths.