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1. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform

   https://doi.org/10.1186/s40537-021-00423-z  

   Villanustre, Flavio ; Chala, Arjuna ; Dev, Roger ; Xu, Lili ; LexisNexis, Jesse Shaw ; Furht, Borko ; Khoshgoftaar, Taghi ( December 2021 , Journal of Big Data)

   Abstract This project is funded by the US National Science Foundation (NSF) through their NSF RAPID program under the title “Modeling Corona Spread Using Big Data Analytics.” The project is a joint effort between the Department of Computer & Electrical Engineering and Computer Science at FAU and a research group from LexisNexis Risk Solutions. The novel coronavirus Covid-19 originated in China in early December 2019 and has rapidly spread to many countries around the globe, with the number of confirmed cases increasing every day. Covid-19 is officially a pandemic. It is a novel infection with serious clinical manifestations, including death, and it has reached at least 124 countries and territories. Although the ultimate course and impact of Covid-19 are uncertain, it is not merely possible but likely that the disease will produce enough severe illness to overwhelm the worldwide health care infrastructure. 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 infected 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 %. Public health efforts depend heavily on predicting how diseases such as those caused by Covid-19 spread across the globe. During the early days of a new outbreak, when reliable data are still scarce, researchers turn to mathematical models that can predict where people who could be infected are going and how likely they are to bring the disease with them. These computational methods use known statistical equations that calculate the probability of individuals transmitting the illness. Modern computational power allows these models to quickly incorporate multiple inputs, such as a given disease’s ability to pass from person to person and the movement patterns of potentially infected people traveling by air and land. This process sometimes involves making assumptions about unknown factors, such as an individual’s exact travel pattern. By plugging in different possible versions of each input, however, researchers can update the models as new information becomes available and compare their results to observed patterns for the illness. In this paper we describe the development a model of Corona spread by using innovative big data analytics techniques and tools. We leveraged our experience from research in modeling Ebola spread (Shaw et al. Modeling Ebola Spread and Using HPCC/KEL System. In: Big Data Technologies and Applications 2016 (pp. 347-385). Springer, Cham) to successfully model Corona spread, we will obtain new results, and help in reducing the number of Corona patients. We closely collaborated with LexisNexis, which is a leading US data analytics company and a member of our NSF I/UCRC for Advanced Knowledge Enablement. The lack of a comprehensive view and informative analysis of the status of the pandemic can also cause panic and instability within society. Our work proposes the HPCC Systems Covid-19 tracker, which provides a multi-level view of the pandemic with the informative virus spreading indicators in a timely manner. The system embeds a classical epidemiological model known as SIR and spreading indicators based on causal model. The data solution of the tracker is built on top of the Big Data processing platform HPCC Systems, from ingesting and tracking of various data sources to fast delivery of the data to the public. The HPCC Systems Covid-19 tracker presents the Covid-19 data on a daily, weekly, and cumulative basis up to global-level and down to the county-level. It also provides statistical analysis for each level such as new cases per 100,000 population. The primary analysis such as Contagion Risk and Infection State is based on causal model with a seven-day sliding window. Our work has been released as a publicly available website to the world and attracted a great volume of traffic. The project is open-sourced and available on GitHub. The system was developed on the LexisNexis HPCC Systems, which is briefly described in the paper. 

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2. A prospective cohort study of preconception COVID-19 vaccination and miscarriage

   https://doi.org/10.1093/humrep/dead211  

   Yland, Jennifer J. ; Wesselink, Amelia K. ; Regan, Annette K. ; Hatch, Elizabeth E. ; Rothman, Kenneth J. ; Savitz, David A. ; Wang, Tanran R. ; Huybrechts, Krista F. ; Hernández-Díaz, Sonia ; Eisenberg, Michael L. ; et al ( October 2023 , Human Reproduction)

   To what extent is preconception maternal or paternal coronavirus disease 2019 (COVID-19) vaccination associated with miscarriage incidence?

   COVID-19 vaccination in either partner at any time before conception is not associated with an increased rate of miscarriage.

   Several observational studies have evaluated the safety of COVID-19 vaccination during pregnancy and found no association with miscarriage, though no study prospectively evaluated the risk of early miscarriage (gestational weeks [GW] <8) in relation to COVID-19 vaccination. Moreover, no study has evaluated the role of preconception vaccination in both male and female partners.

   An Internet-based, prospective preconception cohort study of couples residing in the USA and Canada. We analyzed data from 1815 female participants who conceived during December 2020–November 2022, including 1570 couples with data on male partner vaccination.

   Eligible female participants were aged 21–45 years and were trying to conceive without use of fertility treatment at enrollment. Female participants completed questionnaires at baseline, every 8 weeks until pregnancy, and during early and late pregnancy; they could also invite their male partners to complete a baseline questionnaire. We collected data on COVID-19 vaccination (brand and date of doses), history of SARS-CoV-2 infection (yes/no and date of positive test), potential confounders (demographic, reproductive, and lifestyle characteristics), and pregnancy status on all questionnaires. Vaccination status was categorized as never (0 doses before conception), ever (≥1 dose before conception), having a full primary sequence before conception, and completing the full primary sequence ≤3 months before conception. These categories were not mutually exclusive. Participants were followed up from their first positive pregnancy test until miscarriage or a censoring event (induced abortion, ectopic pregnancy, loss to follow-up, 20 weeks’ gestation), whichever occurred first. We estimated incidence rate ratios (IRRs) for miscarriage and corresponding 95% CIs using Cox proportional hazards models with GW as the time scale. We used propensity score fine stratification weights to adjust for confounding.

   Among 1815 eligible female participants, 75% had received at least one dose of a COVID-19 vaccine by the time of conception. Almost one-quarter of pregnancies resulted in miscarriage, and 75% of miscarriages occurred <8 weeks’ gestation. The propensity score-weighted IRR comparing female participants who received at least one dose any time before conception versus those who had not been vaccinated was 0.85 (95% CI: 0.63, 1.14). COVID-19 vaccination was not associated with increased risk of either early miscarriage (GW: <8) or late miscarriage (GW: 8–19). There was no indication of an increased risk of miscarriage associated with male partner vaccination (IRR = 0.90; 95% CI: 0.56, 1.44).

   The present study relied on self-reported vaccination status and infection history. Thus, there may be some non-differential misclassification of exposure status. While misclassification of miscarriage is also possible, the preconception cohort design and high prevalence of home pregnancy testing in this cohort reduced the potential for under-ascertainment of miscarriage. As in all observational studies, residual or unmeasured confounding is possible.

   This is the first study to evaluate prospectively the relation between preconception COVID-19 vaccination in both partners and miscarriage, with more complete ascertainment of early miscarriages than earlier studies of vaccination. The findings are informative for individuals planning a pregnancy and their healthcare providers.

   This work was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the National Institute of Health [R01-HD086742 (PI: L.A.W.); R01-HD105863S1 (PI: L.A.W. and M.L.E.)], the National Institute of Allergy and Infectious Diseases (R03-AI154544; PI: A.K.R.), and the National Science Foundation (NSF-1914792; PI: L.A.W.). The funders had no role in the study design, data collection, analysis and interpretation of data, writing of the report, or the decision to submit the paper for publication. L.A.W. is a fibroid consultant for AbbVie, Inc. She also receives in-kind donations from Swiss Precision Diagnostics (Clearblue home pregnancy tests) and Kindara.com (fertility apps). M.L.E. received consulting fees from Ro, Hannah, Dadi, VSeat, and Underdog, holds stock in Ro, Hannah, Dadi, and Underdog, is a past president of SSMR, and is a board member of SMRU. K.F.H. reports being an investigator on grants to her institution from UCB and Takeda, unrelated to this study. S.H.-D. reports being an investigator on grants to her institution from Takeda, unrelated to this study, and a methods consultant for UCB and Roche for unrelated drugs. The authors report no other relationships or activities that could appear to have influenced the submitted work.

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3. Excess mortality in the United States during the first three months of the COVID-19 pandemic

   https://doi.org/10.1017/S0950268820002617  

   Rivera, R. ; Rosenbaum, J. E. ; Quispe, W. ( January 2020 , Epidemiology and Infection)

   null (Ed.)

   Abstract Deaths are frequently under-estimated during emergencies, times when accurate mortality estimates are crucial for emergency response. This study estimates excess all-cause, pneumonia and influenza mortality during the coronavirus disease 2019 (COVID-19) pandemic using the 11 September 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance System (MSS) from 27 September 2015 to 9 May 2020, using semiparametric and conventional time-series models in 13 states with high reported COVID-19 deaths and apparently complete mortality data: California, Colorado, Connecticut, Florida, Illinois, Indiana, Louisiana, Massachusetts, Michigan, New Jersey, New York, Pennsylvania and Washington. We estimated greater excess mortality than official COVID-19 mortality in the U.S. (excess mortality 95% confidence interval (CI) 100 013–127 501 vs. 78 834 COVID-19 deaths) and 9 states: California (excess mortality 95% CI 3338–6344) vs. 2849 COVID-19 deaths); Connecticut (excess mortality 95% CI 3095–3952) vs. 2932 COVID-19 deaths); Illinois (95% CI 4646–6111) vs. 3525 COVID-19 deaths); Louisiana (excess mortality 95% CI 2341–3183 vs. 2267 COVID-19 deaths); Massachusetts (95% CI 5562–7201 vs. 5050 COVID-19 deaths); New Jersey (95% CI 13 170–16 058 vs. 10 465 COVID-19 deaths); New York (95% CI 32 538–39 960 vs. 26 584 COVID-19 deaths); and Pennsylvania (95% CI 5125–6560 vs. 3793 COVID-19 deaths). Conventional model results were consistent with semiparametric results but less precise. Significant excess pneumonia deaths were also found for all locations and we estimated hundreds of excess influenza deaths in New York. We find that official COVID-19 mortality substantially understates actual mortality, excess deaths cannot be explained entirely by official COVID-19 death counts. Mortality reporting lags appeared to worsen during the pandemic, when timeliness in surveillance systems was most crucial for improving pandemic response. 

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4. Ensemble machine learning of factors influencing COVID-19 across US counties

   https://doi.org/10.1038/s41598-021-90827-x  

   McCoy, David ; Mgbara, Whitney ; Horvitz, Nir ; Getz, Wayne M. ; Hubbard, Alan ( December 2021 , Scientific Reports)

   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 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. 

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5. Which nursing home workers were at highest risk for SARS-CoV-2 infection during the November 2020–February 2021 winter surge of COVID-1?

   https://doi.org/10.1017/ash.2022.66  

   Kellogg, Joseph ; Dube, William ; Adams, Carly ; Collins, Matthew ; Lopman, Theodore ; Johnson, Theodore ; Amin, Avnika ; Weitz, Joshua ; Fridkin, Scott ( July 2022 , Antimicrobial Stewardship & Healthcare Epidemiology)

   Background: Nursing home (NH) residents and staff were at high risk for COVID-19 early in the pandemic; several studies estimated seroprevalence of infection in NH staff to be 3-fold higher among CNAs and nurses compared to other staff. Risk mitigation added in Fall 2020 included systematic testing of residents and staff (and furlough if positive) to reduce transmission risk. We estimated risks for SARS-CoV-2 infection among NH staff during the first winter surge before widespread vaccination. Methods: Between February and May 2021, voluntary serologic testing was performed on NH staff who were seronegative for SARS-CoV-2 in late Fall 2020 (during a previous serology study at 14 Georgia NHs). An exposure assessment at the second time point covered prior 3 months of job activities, community exposures, and self-reported COVID-19 vaccination, including very recent vaccination (≤4 weeks). Risk factors for seroconversion were estimated by job type using multivariable logistic regression, accounting for interval community-incidence and interval change in resident infections per bed. Results: Among 203 eligible staff, 72 (35.5%) had evidence of interval seroconversion (Fig. 1). Among 80 unvaccinated staff, interval infection was significantly higher among CNAs and nurses (aOR, 4.9; 95% CI, 1.4–20.7) than other staff, after adjusting for race and interval community incidence and facility infections. This risk persisted but was attenuated when utilizing the full study cohort including those with very recent vaccination (aOR, 1.8; 95% CI, 0.9–3.7). Conclusions : Midway through the first year of the pandemic, NH staff with close or common resident contact continued to be at increased risk for infection despite enhanced infection prevention efforts. Mitigation strategies, prior to vaccination, did not eliminate occupational risk for infection. Vaccine utilization is critical to eliminate occupational risk among frontline healthcare providers. Funding: None Disclosures: None 

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