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Clinical Science and Epidemiology

  • Open Access
    Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area
    Research Article | Clinical Science and Epidemiology
    Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

    There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient...

    S. Wesley Long, Randall J. Olsen, Paul A. Christensen, David W. Bernard, James J. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Hung-Che Kuo, Heather Hendrickson, Ghazaleh Eskandari, Hoang A. T. Nguyen, J. Hunter Long, Muthiah Kumaraswami, Jule Goike, Daniel Boutz, Jimmy Gollihar, Jason S. McLellan, Chia-Wei Chou, Kamyab Javanmardi, Ilya J. Finkelstein, James M. Musser
  • Open Access
    The Interaction of Natural and Vaccine-Induced Immunity with Social Distancing Predicts the Evolution of the COVID-19 Pandemic
    Research Article | Clinical Science and Epidemiology
    The Interaction of Natural and Vaccine-Induced Immunity with Social Distancing Predicts the Evolution of the COVID-19 Pandemic

    The ability of our society to function effectively moving forward will depend on how the spread of the SARS-CoV-2 virus is contained. Immunity to the virus will be critical to this equation.

    Michael F. Good, Michael T. Hawkes
  • Open Access
    Immune Response and Microbiota Profiles during Coinfection with <span class="named-content genus-species" id="named-content-1">Plasmodium vivax</span> and Soil-Transmitted Helminths
    Research Article | Clinical Science and Epidemiology
    Immune Response and Microbiota Profiles during Coinfection with Plasmodium vivax and Soil-Transmitted Helminths

    Plasmodium (malaria) and helminth parasite coinfections are frequent, and both infections can be affected by the host gut microbiota. However, the relationship between coinfection and the gut microbiota is unclear. By performing comprehensive analyses on blood/stool samples from 130 individuals in Colombia, we found that the gut microbiota may have a stronger relationship with the number of...

    Alice V. Easton, Mayra Raciny-Aleman, Victor Liu, Erica Ruan, Christian Marier, Adriana Heguy, Maria Fernanda Yasnot, Ana Rodriguez, P’ng Loke
  • Open Access
    SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures
    Research Article | Clinical Science and Epidemiology
    SARS-CoV-2 Seroprevalence among a Southern U.S. Population Indicates Limited Asymptomatic Spread under Physical Distancing Measures

    This study suggests limited but accelerating asymptomatic spread of SARS-CoV-2. Asymptomatic infections, like symptomatic infections, disproportionately affected vulnerable communities in this population, and seroprevalence was higher in African American participants than in White participants. The low, overall prevalence may reflect the success of shelter-in-place mandates at the time this study was performed and of maintaining...

    Amir Barzin, John L. Schmitz, Samuel Rosin, Rameet Sirpal, Martha Almond, Carole Robinette, Samantha Wells, Michael Hudgens, Andrew Olshan, Stephanie Deen, Patrick Krejci, Eugenia Quackenbush, Kevin Chronowski, Caleb Cornaby, Janette Goins, Linda Butler, Julia Aucoin, Kim Boyer, Janet Faulk, Devena Alston-Johnson, Cristen Page, Yijun Zhou, Lynne Fiscus, Blossom Damania, Dirk P. Dittmer, David B. Peden
  • Open Access
    An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
    Research Article | Clinical Science and Epidemiology
    An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

    As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is...

    Jason T. Ladner, Brendan B. Larsen, Jolene R. Bowers, Crystal M. Hepp, Evan Bolyen, Megan Folkerts, Krystal Sheridan, Ashlyn Pfeiffer, Hayley Yaglom, Darrin Lemmer, Jason W. Sahl, Emily A. Kaelin, Rabia Maqsood, Nicholas A. Bokulich, Grace Quirk, Thomas D. Watts, Kenneth K. Komatsu, Victor Waddell, Efrem S. Lim, J. Gregory Caporaso, David M. Engelthaler, Michael Worobey, Paul Keim
  • Open Access
    Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials
    Editor's Pick Research Article | Clinical Science and Epidemiology
    Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials

    Due to the rapid spread of coronavirus disease 2019 (COVID-19), there is an increasing shortage of protective gear necessary to keep health care providers safe from infection. As of 9 April 2020, the CDC reported 9,282 cumulative cases of COVID-19 among U.S. health care workers (CDC COVID-19 Response Team, MMWR Morb Mortal Wkly Rep 69:477–481, 2020, https://doi.org/10.15585/mmwr.mm6915e6...

    Katelyn E. Zulauf, Alex B. Green, Alex N. Nguyen Ba, Tanush Jagdish, Dvir Reif, Robert Seeley, Alana Dale, James E. Kirby
  • Open Access
    Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis
    Research Article | Clinical Science and Epidemiology
    Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis

    DNA contamination from external sources (reagents, environment, operator, etc.) has long been assumed to be the main cause of spurious signals that appear under low-bacterial-biomass conditions. Here, we demonstrate that contamination can be separated from another, random signal generated during low-biomass-sample sequencing. This stochastic noise is not reproduced between technical replicates; however, results for any one replicate...

    John R. Erb-Downward, Nicole R. Falkowski, Jennifer C. D’Souza, Lisa M. McCloskey, Roderick A. McDonald, Christopher A. Brown, Kerby Shedden, Robert P. Dickson, Christine M. Freeman, Kathleen A. Stringer, Betsy Foxman, Gary B. Huffnagle, Jeffrey L. Curtis, Sara D. Adar
  • Open Access
    Pandemic COVID-19 Joins History’s Pandemic Legion
    Perspective | Clinical Science and Epidemiology
    Pandemic COVID-19 Joins History’s Pandemic Legion

    With great apprehension, the world is now watching the birth of a novel pandemic already causing tremendous suffering, death, and disruption of normal life. Uncertainty and dread are exacerbated by the belief that what we are experiencing is new and mysterious. However, deadly pandemics and disease emergences are not new phenomena: they have been challenging human existence throughout recorded history. Some have killed sizeable...

    David M. Morens, Peter Daszak, Howard Markel, Jeffery K. Taubenberger
  • Open Access
    Immune Profiling To Predict Outcome of <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Infection
    Research Article | Clinical Science and Epidemiology
    Immune Profiling To Predict Outcome of Clostridioides difficile Infection

    Clostridioides difficile infection is the most common health care-associated infection in the United States with more than 20% patients experiencing symptomatic recurrence. The complex nature of host-bacterium interactions makes it difficult to predict the course of the disease based solely on clinical parameters. In the present study, we built a robust prediction...

    Mayuresh M. Abhyankar, Jennie Z. Ma, Kenneth W. Scully, Andrew J. Nafziger, Alyse L. Frisbee, Mahmoud M. Saleh, Gregory R. Madden, Ann R. Hays, Mendy Poulter, William A. Petri
  • Open Access
    Emergence of Enteroaggregative <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> within the ST131 Lineage as a Cause of Extraintestinal Infections
    Research Article | Clinical Science and Epidemiology
    Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections

    E. coli ST131 is an important extraintestinal pathogenic lineage. A signature characteristic of ST131 is its ability to asymptomatically colonize the gastrointestinal tract and then opportunistically cause extraintestinal infections, such as cystitis, pyelonephritis, and urosepsis. In this study, we identified an ST131 H27 sublineage that has acquired the...

    Erik J. Boll, Søren Overballe-Petersen, Henrik Hasman, Louise Roer, Kim Ng, Flemming Scheutz, Anette M. Hammerum, Arnold Dungu, Frank Hansen, Thor B. Johannesen, Abigail Johnson, Divek T. Nair, Berit Lilje, Dennis S. Hansen, Karen A. Krogfelt, Timothy J. Johnson, Lance B. Price, James R. Johnson, Carsten Struve, Bente Olesen, Marc Stegger

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