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Title: Ensemble machine learning of factors influencing COVID-19 across US counties
Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causal agent for COVID-19, is a communicable disease spread through close contact. It is known to disproportionately impact certain communities due to both biological susceptibility and inequitable exposure. In this study, we investigate the most important health, social, and environmental factors impacting the early phases (before July, 2020) of per capita COVID-19 transmission and per capita all-cause mortality in US counties. We aggregate county-level physical and mental health, environmental pollution, access to health care, demographic characteristics, vulnerable population scores, and other epidemiological data to create a large feature set to analyze per capita COVID-19 outcomes. Because of the high-dimensionality, multicollinearity, and unknown interactions of the data, we use ensemble machine learning and marginal prediction methods to identify the most salient factors associated with several COVID-19 outbreak measure. Our variable importance results show that measures of ethnicity, public transportation and preventable diseases are the strongest predictors for both per capita COVID-19 incidence and mortality. Specifically, the CDC measures for minority populations, CDC measures for limited English, and proportion of Black- and/or African-American individuals in a county were the most important features for per capita COVID-19 cases within a month after the pandemic more » started in a county and also at the latest date examined. For per capita all-cause mortality at day 100 and total to date, we find that public transportation use and proportion of Black- and/or African-American individuals in a county are the strongest predictors. The methods predict that, keeping all other factors fixed, a 10% increase in public transportation use, all other factors remaining fixed at the observed values, is associated with increases mortality at day 100 of 2012 individuals (95% CI [1972, 2356]) and likewise a 10% increase in the proportion of Black- and/or African-American individuals in a county is associated with increases total deaths at end of study of 2067 (95% CI [1189, 2654]). Using data until the end of study, the same metric suggests ethnicity has double the association as the next most important factors, which are location, disease prevalence, and transit factors. Our findings shed light on societal patterns that have been reported and experienced in the U.S. by using robust methods to understand the features most responsible for transmission and sectors of society most vulnerable to infection and mortality. In particular, our results provide evidence of the disproportionate impact of the COVID-19 pandemic on minority populations. Our results suggest that mitigation measures, including how vaccines are distributed, could have the greatest impact if they are given with priority to the highest risk communities. « less
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Scientific Reports
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National Science Foundation
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  1. Turner, Richard (Ed.)
    Background With the availability of multiple Coronavirus Disease 2019 (COVID-19) vaccines and the predicted shortages in supply for the near future, it is necessary to allocate vaccines in a manner that minimizes severe outcomes, particularly deaths. To date, vaccination strategies in the United States have focused on individual characteristics such as age and occupation. Here, we assess the utility of population-level health and socioeconomic indicators as additional criteria for geographical allocation of vaccines. Methods and findings County-level estimates of 14 indicators associated with COVID-19 mortality were extracted from public data sources. Effect estimates of the individual indicators were calculated with univariate models. Presence of spatial autocorrelation was established using Moran’s I statistic. Spatial simultaneous autoregressive (SAR) models that account for spatial autocorrelation in response and predictors were used to assess (i) the proportion of variance in county-level COVID-19 mortality that can explained by identified health/socioeconomic indicators (R 2 ); and (ii) effect estimates of each predictor. Adjusting for case rates, the selected indicators individually explain 24%–29% of the variability in mortality. Prevalence of chronic kidney disease and proportion of population residing in nursing homes have the highest R 2 . Mortality is estimated to increase by 43 per thousand residentsmore »(95% CI: 37–49; p < 0.001) with a 1% increase in the prevalence of chronic kidney disease and by 39 deaths per thousand (95% CI: 34–44; p < 0.001) with 1% increase in population living in nursing homes. SAR models using multiple health/socioeconomic indicators explain 43% of the variability in COVID-19 mortality in US counties, adjusting for case rates. R 2 was found to be not sensitive to the choice of SAR model form. Study limitations include the use of mortality rates that are not age standardized, a spatial adjacency matrix that does not capture human flows among counties, and insufficient accounting for interaction among predictors. Conclusions Significant spatial autocorrelation exists in COVID-19 mortality in the US, and population health/socioeconomic indicators account for a considerable variability in county-level mortality. In the context of vaccine rollout in the US and globally, national and subnational estimates of burden of disease could inform optimal geographical allocation of vaccines.« less
  2. Importance Prior research has established that Hispanic and non-Hispanic Black residents in the US experienced substantially higher COVID-19 mortality rates in 2020 than non-Hispanic White residents owing to structural racism. In 2021, these disparities decreased. Objective To assess to what extent national decreases in racial and ethnic disparities in COVID-19 mortality between the initial pandemic wave and subsequent Omicron wave reflect reductions in mortality vs other factors, such as the pandemic’s changing geography. Design, Setting, and Participants This cross-sectional study was conducted using data from the US Centers for Disease Control and Prevention for COVID-19 deaths from March 1, 2020, through February 28, 2022, among adults aged 25 years and older residing in the US. Deaths were examined by race and ethnicity across metropolitan and nonmetropolitan areas, and the national decrease in racial and ethnic disparities between initial and Omicron waves was decomposed. Data were analyzed from June 2021 through March 2023. Exposures Metropolitan vs nonmetropolitan areas and race and ethnicity. Main Outcomes and Measures Age-standardized death rates. Results There were death certificates for 977 018 US adults aged 25 years and older (mean [SD] age, 73.6 [14.6] years; 435 943 female [44.6%]; 156 948 Hispanic [16.1%], 140 513 non-Hispanic Black [14.4%], and 629 578more »non-Hispanic White [64.4%]) that included a mention of COVID-19. The proportion of COVID-19 deaths among adults residing in nonmetropolitan areas increased from 5944 of 110 526 deaths (5.4%) during the initial wave to a peak of 40 360 of 172 515 deaths (23.4%) during the Delta wave; the proportion was 45 183 of 210 554 deaths (21.5%) during the Omicron wave. The national disparity in age-standardized COVID-19 death rates per 100 000 person-years for non-Hispanic Black compared with non-Hispanic White adults decreased from 339 to 45 deaths from the initial to Omicron wave, or by 293 deaths. After standardizing for age and racial and ethnic differences by metropolitan vs nonmetropolitan residence, increases in death rates among non-Hispanic White adults explained 120 deaths/100 000 person-years of the decrease (40.7%); 58 deaths/100 000 person-years in the decrease (19.6%) were explained by shifts in mortality to nonmetropolitan areas, where a disproportionate share of non-Hispanic White adults reside. The remaining 116 deaths/100 000 person-years in the decrease (39.6%) were explained by decreases in death rates in non-Hispanic Black adults. Conclusions and Relevance This study found that most of the national decrease in racial and ethnic disparities in COVID-19 mortality between the initial and Omicron waves was explained by increased mortality among non-Hispanic White adults and changes in the geographic spread of the pandemic. These findings suggest that despite media reports of a decline in disparities, there is a continued need to prioritize racial health equity in the pandemic response.« less
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Emerging viral pandemics can place extraordinary and sustained demands on public health and health systems and on providers of essential community services. Modeling the Covid-19 pandemic spread is challenging. But there are data that can be used to project resource demands. Estimates of the reproductive number (R) of SARS-CoV-2 show that at the beginning of the epidemic, each infectedmore »person spreads the virus to at least two others, on average (Emanuel et al. in N Engl J Med. 2020, Livingston and Bucher in JAMA 323(14):1335, 2020). A conservatively low estimate is that 5 % of the population could become infected within 3 months. Preliminary data from China and Italy regarding the distribution of case severity and fatality vary widely (Wu and McGoogan in JAMA 323(13):1239–42, 2020). A recent large-scale analysis from China suggests that 80 % of those infected either are asymptomatic or have mild symptoms; a finding that implies that demand for advanced medical services might apply to only 20 % of the total infected. Of patients infected with Covid-19, about 15 % have severe illness and 5 % have critical illness (Emanuel et al. in N Engl J Med. 2020). Overall, mortality ranges from 0.25 % to as high as 3.0 % (Emanuel et al. in N Engl J Med. 2020, Wilson et al. in Emerg Infect Dis 26(6):1339, 2020). Case fatality rates are much higher for vulnerable populations, such as persons over the age of 80 years (> 14 %) and those with coexisting conditions (10 % for those with cardiovascular disease and 7 % for those with diabetes) (Emanuel et al. in N Engl J Med. 2020). Overall, Covid-19 is substantially deadlier than seasonal influenza, which has a mortality of roughly 0.1 %. 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  5. Goller, Carlos C. (Ed.)
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