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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