• Scientists detect novel SARS-CoV-2 varia

    From ScienceDaily@1:317/3 to All on Thu Feb 3 21:30:40 2022
    Scientists detect novel SARS-CoV-2 variants in NYC wastewater
    Study suggests these novel mutations of the virus that causes COVID-19
    could help identify where the next variant of concern could originate

    Date:
    February 3, 2022
    Source:
    University of Missouri-Columbia
    Summary:
    Researchers have detected at least four 'cryptic' variants of
    SARS-CoV-2, the virus that causes COVID-19, in samples of wastewater
    from New York City's public sewer system.



    FULL STORY ========================================================================== First delta, then omicron. The latest Covid variants have spread like
    wildfire across the globe in recent months, leading many scientists to
    wonder when the next variant will appear. Now, scientists may be one
    step closer to making that determination.


    ==========================================================================
    A multi-institutional team of researchers, including virologist Marc
    Johnson, a professor of molecular microbiology and immunology at the
    University of Missouri, has detected at least four "cryptic" variants
    of SARS-CoV-2, the virus that causes COVID-19, in samples of wastewater
    from New York City's public sewer system. Their findings were recently published in Nature Communications, a journal of Nature.

    According to the Centers for Disease Control and Prevention (CDC),
    viruses such as SARS-CoV-2 can continually evolve by acquiring
    mutations. Variants, such as delta or omicron, may contain one or more mutations within their viral sequence that help to distinguish themselves
    from other variants of SARS-CoV-2.

    Johnson, a co-corresponding author on the study, believes the results
    suggest the "cryptic" mutations they identified in New York City could
    be linked to possible animal origins. While these origins have not been verified yet, he believes one possible source could be the rats that
    frequent New York City's sewer system.

    "For instance, we still don't know where the omicron variant came from,
    but it had to come from somewhere," Johnson said. "These variants are
    bubbling up everywhere, including omicron, which eventually spilled into
    the general population and wreaked havoc. We think these weird lineages
    could be where the next variant of concern for COVID-19 comes from."
    Hunting for virus mutations The idea for this project started in March
    2020 after John Dennehy, a virologist and professor of biology at Queens College, City University of New York, began looking for different ways to analyze the impact of the COVID-19 pandemic. Monica Trujillo, an associate professor at Queensborough Community College, City University of New York, shared with Dennehy a study from Australia that described using wastewater
    to track the spread of a coronavirus, and it inspired Trujillo to ask
    officials from the New York City Department of Environmental Protection
    to send her wastewater samples in order to conduct similar work.



    ==========================================================================
    In the summer of 2020, Dennehy and Trujillo teamed up with Davida Smyth,
    the lead author on the study. Smyth, now an associate professor at
    Texas A&M University-San Antonio, was at The New School, New York at
    the time. They put together a team of researchers to begin tracking
    the spread of coronavirus via New York City's wastewater. Since then,
    Dennehy, a co-corresponding author on the study, found some interesting results. When he shared some of the more unusual results during a March
    2021 episode of Vincent Racaniello's podcast "This Week in Virology,"
    a popular podcast with virologists nationwide, Johnson happened to
    be listening.

    "The mutations that we were observing in our sample weren't typical
    among any of the known sequences circulating at that time," Dennehy said.

    Ironically, Johnson was simultaneously reaching out to various researchers across the United States who were doing similar work with wastewater
    after he observed some unusual results from his analysis of wastewater
    in some of his samples from the greater St. Louis area. On the podcast,
    he heard Dennehy describe their targeted approach, which happened to be
    the same method MU was using to test samples of wastewater for SARS-CoV-2
    in Missouri, but with one key difference -- MU was analyzing a larger
    region of the virus genome for possible mutations. Within a week, Johnson
    had samples of NYC wastewater delivered to MU for further analysis.

    "When we first started with the samples from New York City, I was looking
    to see if they had the same virus sequences that I saw in some of my
    samples from St. Louis," Johnson said. "They were different, but all of
    them had similar mutations in common at one particular location on the
    virus -- Q498. What's amazing is that in most of the samples from New York City, the Q in Q498 had turned into a Y, or glutamine into tyrosine. If
    you look at the database, there was not, and continues to not be, a
    human patient who has had that mutation." Dennehy believes a possible explanation could be a biological process called convergent evolution.



    ==========================================================================
    "An animal in Missouri is not going to mix with the same type of animal
    in New York City," Dennehy said. "Therefore, the evolution of the virus
    in each geographic area is independent of each other, but because it's
    the same animal, the virus looks the same in both places. For instance,
    we think conditions in South Africa that gave rise to the omicron variant
    are the same conditions in New York City that gave rise to our cryptic variants. As a biologist, I thought the spread of delta was menacing, but
    the speed in which omicron took over New York City is on another level." Understanding the broader impact Smyth joined the research team in part
    due to her passion for taking science from inside a laboratory to showing
    how it can be applied through a broader, real-world impact. A proud Irish immigrant, she transitioned from studying the basics of biology early
    in her career to now pursuing her passion by engaging her students in real-world health issues, such as antibiotic resistance, and tracking coronavirus in wastewater.

    "I'm interested in how we can take what we know and apply it to the
    real world where it is needed the most," said Smyth, who is also
    the deputy director for the National Center for Science and Civic
    Engagement. "Wastewater surveillance is really important in the context
    of community-based, public health measures where we have the ability
    to communicate health information at a level where decisions, practices
    and interventions can be implemented. Wastewater surveillance is fast, inexpensive and unbiased, and for that reason it has the ability to be implemented depending on resource availability in a variety of contexts, especially in areas with limited resources such as low testing and
    vaccine availability." "Tracking cryptic SARS-CoV-2 lineages detected
    in NYC wastewater," was published in Nature Communications. Funding
    was provided in part by the New York City Department of Environmental Protection, a donation from the Linda Markeloff Charitable Fund, and a
    grant from the National Institutes of Health (U01DA053893-01).

    Co-authors include Devon Gregory, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Terry Lyddon, Clayton Rushford, Reinier Suarez, Emma
    Teixeiro and Mark Daniels at MU; Davida Smyth and Geena Sompanya at Texas
    A&M University-San Antonio; Monica Trujillo at Queensborough Community
    College, City University of New York; Kristen Cheung, Anna Gao, Irene
    Hoxie, Sherin Kannoly, Nanami Kubota, Michelle Markman, and Kaung Myat
    San at the City University of New York; and Fabrizio Spagnolo at Long
    Island University.

    ========================================================================== Story Source: Materials provided by University_of_Missouri-Columbia. Note: Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Davida S. Smyth, Monica Trujillo, Devon A. Gregory, Kristen
    Cheung, Anna
    Gao, Maddie Graham, Yue Guan, Caitlyn Guldenpfennig, Irene Hoxie,
    Sherin Kannoly, Nanami Kubota, Terri D. Lyddon, Michelle Markman,
    Clayton Rushford, Kaung Myat San, Geena Sompanya, Fabrizio Spagnolo,
    Reinier Suarez, Emma Teixeiro, Mark Daniels, Marc C. Johnson,
    John J. Dennehy.

    Tracking cryptic SARS-CoV-2 lineages detected in NYC
    wastewater. Nature Communications, 2022; 13 (1) DOI:
    10.1038/s41467-022-28246-3 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/02/220203122941.htm

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