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  1. Article: Counties with Lower Insurance Coverage and Housing Problems Are Associated with Both Slower Vaccine Rollout and Higher COVID-19 Incidence.

    Donadio, Gregory / Choudhary, Mayank / Lindemer, Emily / Pawlowski, Colin / Soundararajan, Venky

    Vaccines

    2021  Volume 9, Issue 9

    Abstract: Equitable vaccination distribution is a priority for outcompeting the transmission of COVID-19. Here, the impact of demographic, socioeconomic, and environmental factors on county-level vaccination rates and COVID-19 incidence changes is assessed. In ... ...

    Abstract Equitable vaccination distribution is a priority for outcompeting the transmission of COVID-19. Here, the impact of demographic, socioeconomic, and environmental factors on county-level vaccination rates and COVID-19 incidence changes is assessed. In particular, using data from 3142 US counties with over 328 million individuals, correlations were computed between cumulative vaccination rate and change in COVID-19 incidence from 1 December 2020 to 6 June 2021, with 44 different demographic, environmental, and socioeconomic factors. This correlation analysis was also performed using multivariate linear regression to adjust for age as a potential confounding variable. These correlation analyses demonstrated that counties with high levels of uninsured individuals have significantly lower COVID-19 vaccination rates (Spearman correlation: -0.460,
    Language English
    Publishing date 2021-08-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9090973
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein.

    Suratekar, Rohit / Ghosh, Pritha / Niesen, Michiel J M / Donadio, Gregory / Anand, Praveen / Soundararajan, Venky / Venkatakrishnan, A J

    Molecular systems biology

    2022  Volume 18, Issue 2, Page(s) e10673

    Abstract: The highly contagious Delta variant of SARS-CoV-2 has become a prevalent strain globally and poses a public health challenge around the world. While there has been extensive focus on understanding the amino acid mutations in the Delta variant's Spike ... ...

    Abstract The highly contagious Delta variant of SARS-CoV-2 has become a prevalent strain globally and poses a public health challenge around the world. While there has been extensive focus on understanding the amino acid mutations in the Delta variant's Spike protein, the mutational landscape of the rest of the SARS-CoV-2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS-CoV-2 proteins from nearly 2 million SARS-CoV-2 genomes from 176 countries/territories. Six highly prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, and Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant. Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of amino acid mutations in the Delta variant's proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.
    MeSH term(s) COVID-19 ; Humans ; Mutation ; Mutation, Missense ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2022-01-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2193510-5
    ISSN 1744-4292 ; 1744-4292
    ISSN (online) 1744-4292
    ISSN 1744-4292
    DOI 10.15252/msb.202110673
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Counties with lower insurance coverage are associated with both slower vaccine rollout and higher COVID-19 incidence across the United States

    Lindemer, Emily / Choudhary, Mayank / Donadio, Gregory / Pawlowski, Colin / Soundararajan, Venky

    medRxiv

    Abstract: Efficient and equitable vaccination distribution is a priority for effectively outcompeting the transmission of COVID-19 globally. A recent study from the Centers for Disease Control and Prevention (CDC) identified that US counties with high social ... ...

    Abstract Efficient and equitable vaccination distribution is a priority for effectively outcompeting the transmission of COVID-19 globally. A recent study from the Centers for Disease Control and Prevention (CDC) identified that US counties with high social vulnerability according to metrics such as poverty, unemployment, low income, and no high school diploma, have significantly lower rates of vaccination compared to the national average1. Here, we build upon this analysis to consider associations between county-level vaccination rates and 68 different demographic, socioeconomic, and environmental factors for 1,510 American counties with over 228 million individuals for which vaccination data was also available. Our analysis reveals that counties with high levels of uninsured individuals have significantly lower COVID-19 vaccination rates (Spearman correlation: -0.264), despite the fact that the CDC has mandated that all COVID-19 vaccines are free and cannot be denied to anyone based upon health insurance coverage or immigration status. Furthermore, we find that the counties with high levels of uninsured individuals tend to have the highest COVID-19 incidence rates in March 2021 relative to December 2020 (Spearman correlation: 0.388). Among the 68 factors analyzed, insurance coverage is the only factor which is highly correlated with both vaccination rate and change in COVID-19 incidence during the vaccination period (|Spearman correlation| > 0.25). We also find that counties with higher percentages of Black and Hispanic individuals have significantly lower vaccination rates (Spearman correlations: -0.128, -0.136) and lesser declines of COVID-incidence rates (Spearman correlations: 0.334, 0.330) during the vaccination period. Surprisingly however, after controlling for race, we find that the association between lack of insurance coverage and vaccination rate as well as COVID-19 incidence rates is largely driven by counties with a majority white population. Among the counties with high proportions of white residents (top 10% decile), the association between insurance coverage and vaccination rate is significant (Spearman correlation: -0.210, p-value: 0.002), but among counties with low proportions of white residents (bottom 10% decile) this association is not significant (Spearman correlation: 0.072, p-value: 0.088). Taken together, this study highlights the fact that intricate socioeconomic factors are correlated not just to COVID-19 vaccination rates, but also to COVID-19 incidence fluctuations, underscoring the need to improve COVID-19 vaccination campaigns in marginalized communities. The strong positive correlation between low levels of health insurance coverage and low vaccination rates is particularly concerning, and calls for improved public health messaging to emphasize the fact that health insurance is not required to be eligible for any of the FDA-authorized COVID-19 vaccines in the United States.
    Keywords covid19
    Language English
    Publishing date 2021-03-26
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.03.24.21254270
    Database COVID19

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  4. Article ; Online: High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein

    Ghosh, Pritha / Suratekar, Rohit / Niesen, Michiel J.M. / Anand, Praveen / Donadio, Gregory / Soundararajan, Venky / Venkatakrishnan, AJ

    bioRxiv

    Abstract: The highly contagious Delta variant of SARS-CoV-2 has emerged as the new dominant global strain, and reports of reduced effectiveness of COVID-19 vaccines against the Delta variant are highly concerning. While there has been extensive focus on ... ...

    Abstract The highly contagious Delta variant of SARS-CoV-2 has emerged as the new dominant global strain, and reports of reduced effectiveness of COVID-19 vaccines against the Delta variant are highly concerning. While there has been extensive focus on understanding the amino acid mutations in the Delta variant9s Spike protein, the mutational landscape of the rest of the SARS-CoV-2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS-CoV-2 proteins from nearly 2 million SARS-CoV-2 genomes from 176 countries/territories. Six highly-prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant (cosine similarity: meanAlpha = 0.94, S.D.Alpha = 0.05; meanDelta = 0.86, S.D.Delta = 0.1; Cohen9s dAlpha-Delta = 1.17, p-value < 0.001). Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of targetable amino acid mutations in the Delta variant9s proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.
    Keywords covid19
    Language English
    Publishing date 2021-09-02
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.09.01.458647
    Database COVID19

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  5. Article ; Online: Comparison of Resource Utilization and Clinical Outcomes Following Screening with Digital Breast Tomosynthesis Versus Digital Mammography: Findings From a Learning Health System.

    Alsheik, Nila H / Dabbous, Firas / Pohlman, Scott K / Troeger, Kathleen M / Gliklich, Richard E / Donadio, Gregory M / Su, Zhaohui / Menon, Vandana / Conant, Emily F

    Academic radiology

    2018  Volume 26, Issue 5, Page(s) 597–605

    Abstract: Rationale and objectives: To compare outcomes associated with breast cancer screening with digital mammography (DM) alone versus in combination with digital breast tomosynthesis (DBT) in a large representative cohort.: Materials and methods: A total ... ...

    Abstract Rationale and objectives: To compare outcomes associated with breast cancer screening with digital mammography (DM) alone versus in combination with digital breast tomosynthesis (DBT) in a large representative cohort.
    Materials and methods: A total of 325,729 screening mammograms from 247,431 women were analyzed, across two healthcare systems, from June 2015 to September 2017. Patient level demographic, calculated risk levels, and clinical outcomes were extracted from radiology information system and electronic medical records. Multivariable regression modeling adjusting for institution, age, breast density, and first exam was conducted to compare patient characteristics, recall rates, time to biopsy and final diagnosis, clinical outcomes, and diagnostic performance. Participating institutions and the Coordinating Center received Institutional Review Board approval for a waiver of consent to collect and link data and perform analysis.
    Results: A total of 194,437 (59.7%) screens were DBT versus 131,292 (40.3%) with DM. Women with dense breasts and higher calculated risk were more likely to be screened with DBT. Recall rates were lower for DBT overall (8.83% DBT vs 10.98% DM, adjusted odds ratio, 95% confidence interval = 0.85, 0.83-0.87) and across all age groups, races, and breast densities, and at facilities that used predominantly DBT (8.05%) versus predominantly DM (11.22%), or a combination (10.73%). The most common diagnostic pathway after recall was mammography and ultrasound. Women recalled from DBT were more likely to proceed directly to ultrasound. The median time to biopsy (18 vs 22 days) and final diagnosis (10 vs 13 days) was shorter for DBT. The adjusted cancer rate, cancer detection rate, and specificity were higher for DBT.
    Conclusion: DBT demonstrated a more efficient screening pathway and improved quality measures with lower recall rates in all patient types, reduced diagnostic mammography and shorter time to biopsy and final diagnosis.
    MeSH term(s) Adult ; Aged ; Biopsy/statistics & numerical data ; Breast Density/physiology ; Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/epidemiology ; Breast Neoplasms/pathology ; Cohort Studies ; Early Detection of Cancer/statistics & numerical data ; Facilities and Services Utilization ; Female ; Humans ; Learning Health System ; Mammography/statistics & numerical data ; Mass Screening/statistics & numerical data ; Middle Aged ; Odds Ratio ; Sensitivity and Specificity ; United States/epidemiology
    Language English
    Publishing date 2018-07-26
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 1355509-1
    ISSN 1878-4046 ; 1076-6332
    ISSN (online) 1878-4046
    ISSN 1076-6332
    DOI 10.1016/j.acra.2018.05.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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