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coronavirus

  • Open Access
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
    Research Article | Clinical Science and Epidemiology
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

    Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread.

    Alexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson
  • Open Access
    Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion
    Research Article | Clinical Science and Epidemiology
    Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion

    Orf8 is one of the most puzzling genes in the SARS lineage of coronaviruses, including SARS-CoV-2. Using sophisticated sequence comparisons, we confirm its origins from Orf7a, another gene in the lineage that appears as more conserved, compared to Orf8.

    Russell Y. Neches, Nikos C. Kyrpides, Christos A. Ouzounis
  • Open Access
    SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia
    Research Article | Host-Microbe Biology
    SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia

    Understanding how SARS-CoV-2 spreads globally and within infected individuals is critical to the development of mitigation strategies. We found that most lineages in Philadelphia had resembled sequences from New York, suggesting infection primarily but not exclusively from this location.

    John Everett, Pascha Hokama, Aoife M. Roche, Shantan Reddy, Young Hwang, Lyanna Kessler, Abigail Glascock, Yize Li, Jillian N. Whelan, Susan R. Weiss, Scott Sherrill-Mix, Kevin McCormick, Samantha A. Whiteside, Jevon Graham-Wooten, Layla A. Khatib, Ayannah S. Fitzgerald, Ronald G. Collman, Frederic Bushman
  • Open Access
    Coronaviruses Associated with the Superfamily <em>Musteloidea</em>
    Minireview | Host-Microbe Biology
    Coronaviruses Associated with the Superfamily Musteloidea

    Among the animal superfamily Musteloidea, which includes those commonly known as mustelids, naturally occurring and species-specific alphacoronavirus infections have been observed in both mink (Mustela vison/Neovison vison) and domestic ferrets (...

    Alison E. Stout, Qinghua Guo, Jean K. Millet, Ricardo de Matos, Gary R. Whittaker
  • Open Access
    Do an Altered Gut Microbiota and an Associated Leaky Gut Affect COVID-19 Severity?
    Perspective | Clinical Science and Epidemiology
    Do an Altered Gut Microbiota and an Associated Leaky Gut Affect COVID-19 Severity?

    Coronavirus disease 2019 (COVID-19), which has been declared a pandemic, has exhibited a wide range of severity worldwide. Although this global variation is largely affected by socio-medical situations in each country, there is also high individual-level variation attributable to elderliness and certain underlying medical conditions, including high blood pressure, diabetes, and obesity.

    Heenam Stanley Kim
  • Open Access
    Analysis of Measles-Mumps-Rubella (MMR) Titers of Recovered COVID-19 Patients
    Research Article | Therapeutics and Prevention
    Analysis of Measles-Mumps-Rubella (MMR) Titers of Recovered COVID-19 Patients

    COVID-19 has presented various paradoxes that, if understood better, may provide clues to controlling the pandemic, even before a COVID-19 vaccine is widely available. First, young children are largely spared from severe disease. Second, numerous countries have COVID-19 death rates that are as low as 1% of the death rates of other countries. Third, many people, despite prolonged close contact with someone who is COVID-19 positive, never...

    Jeffrey E. Gold, William H. Baumgartl, Ramazan A. Okyay, Warren E. Licht, Paul L. Fidel, Mairi C. Noverr, Larry P. Tilley, David J. Hurley, Balázs Rada, John W. Ashford
  • Open Access
    Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals
    Editor's Pick Observation | Therapeutics and Prevention
    Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals

    While waiting for an efficient vaccine to protect against SARS-CoV-2 infection, alternative approaches to treat or prevent acute COVID-19 are urgently needed. Transfusion of convalescent plasma to treat COVID-19 patients is currently being explored; neutralizing activity in convalescent plasma is thought to play a central role in the efficacy of this treatment. Here, we observed that plasma neutralization activity decreased a few weeks...

    Guillaume Beaudoin-Bussières, Annemarie Laumaea, Sai Priya Anand, Jérémie Prévost, Romain Gasser, Guillaume Goyette, Halima Medjahed, Josée Perreault, Tony Tremblay, Antoine Lewin, Laurie Gokool, Chantal Morrisseau, Philippe Bégin, Cécile Tremblay, Valérie Martel-Laferrière, Daniel E. Kaufmann, Jonathan Richard, Renée Bazin, Andrés Finzi
  • 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
    Rescue of SARS-CoV-2 from a Single Bacterial Artificial Chromosome
    Research Article | Therapeutics and Prevention
    Rescue of SARS-CoV-2 from a Single Bacterial Artificial Chromosome

    The pandemic coronavirus (CoV) disease 2019 (COVID-19) caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is a major threat to global human health. To date, there are no approved prophylactics or therapeutics available for COVID-19. Reverse genetics is a powerful approach to understand factors involved in viral pathogenesis, antiviral screening, and vaccine development. In this study, we describe the feasibility of...

    Chengjin Ye, Kevin Chiem, Jun-Gyu Park, Fatai Oladunni, Roy Nelson Platt, Tim Anderson, Fernando Almazan, Juan Carlos de la Torre, Luis Martinez-Sobrido
  • Open Access
    Antiviral Drug Discovery To Address the COVID-19 Pandemic
    Commentary | Therapeutics and Prevention
    Antiviral Drug Discovery To Address the COVID-19 Pandemic

    The magnitude of the morbidity and mortality inflicted upon the global population in less than 1 year has driven the inescapable conclusion that the discovery and development of effective antiviral drugs for COVID-19 are urgent and should be prioritized. The antiviral drug discovery programs that emerged for HIV and hepatitis C virus have enabled technology and expertise to accelerate this process for SARS-CoV-2. The description of...

    Douglas D. Richman

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