Page 14 - Abacoa Community News - August '22

Page 14, Abacoa

Scripps Research from page 11 but you also have the problem of
asymptomatic people not getting
Now, scientists at Scripps Research and University of tested and those who only use
California, San Diego, in collaboration with the San Diego home tests not contributing to
Epidemiology and Research for COVID Health (SEARCH) the pool of data,” says Levy. “But
alliance, have changed that. The team has reported that with wastewater, we don’t have
with just two teaspoons of raw sewage, they can accurately those blind spots.”
determine the genetic mixture of SARS-CoV-2 variants In addition to Levy,
present within a population and identify new variants of Karthikeyan, Andersen and
concern up to 14 days before traditional clinical testing. Knight, authors of the study,
In San Diego wastewater, the group detected the Omicron “Wastewater sequencing uncovers
variant 11 days before it was first reported clinically. early, cryptic SARS-CoV-2 variant
Their algorithm, named “Freyja,” for identifying transmission,” include Christine
SARS-CoV-2 variants in wastewater, described today in Aceves, Catelyn Anderson, Using wastewater virus concentration measurements and genome sequencing, researchers
Nature, has quickly been adapted by many public health Karthik Gangavarapu, Emory tracked the rapid spread of SARS-CoV-2 during the Omicron wave of the pandemic.
labs, and is a boon to surveillance efforts that aim to detect Hufbauer, Ezra Kurzban, Justin
new variants of SARS-CoV-2. Lee, Nathaniel Matteson, Edyth
“In a lot of places, standard clinical surveillance for Parker, Sarah Perkins, Karthik
new variants of concern is not only slow but extremely Ramesh, Refugio Robles-Sikisaka,
cost-prohibitive,” says Kristian Andersen, Ph.D., professor Madison Schwab, Emily Spencer,
of immunology and microbiology at Scripps Research and Shirlee Wohl, Laura Nicholson, and
a senior author of the new work. “But with this new tool, Mark Zeller of Scripps Research,
you can take one wastewater sample and basically profile as well as collaborators at U.C. San
the whole city.” Diego, Rady Children’s Institute
The project required a tight collaboration between for Genomic Medicine, Scripps
hospitals, state and local governments, sequencing facilities, Health, Sharp Healthcare, Helix,
and academic scientists – including researchers in the the County of San Diego Health
Andersen lab and that of U.C. San Diego microbiologist and Human Services Agency,
Rob Knight, Ph.D. The Knight lab deployed 131 wastewater the California Department of
autosamplers to collect wastewater from 343 buildings on the Public Health, and the Centers for
UCSD campus and 17 public schools across four San Diego Disease Control and Prevention. Researchers devised a new way of analyzing wastewater to monitor the prevalence of
school districts and acquired samples from large wastewater different SARS-CoV-2 variants over time (shown here for San Diego, from September
treatment facilities in the county. Over the course of nearly Scripps Research on page 15 2021 to May 2022).
a year, the group analyzed more than 20,000 wastewater
samples. In the process, they developed improved methods
being widely used by public health labs across the country Experience Dentistry with a Woman’s Touch
for concentrating viral RNA in wastewater, which are now

and world. Then, the Andersen lab took on the challenge of
quantifying viral variants from the sequencing data.
“It’s challenging to take all these tiny pieces of virus Cosmetic & Comprehensive Restorative Dentistry
floating around in wastewater and figure out which ones are
from different variants and what their relative abundance State of the Art & Same Day Restorations
is,” says Scripps Research postdoctoral fellow Joshua
Levy, Ph.D., a co-first author of the new paper with Smruthi Nitrous Oxide/Oxygen Sedation Available
Karthikeyan of U.C. San Diego.
Many variants of SARS-CoV-2, including Omicron and
Delta, differ by a small number of mutations. But since Joanne Green, D.D.S.
these changes can impact how the virus spreads or infects
people, public health officials must carefully track them. 10887 N. Military Trail, Suite 6
They have typically done this by sequencing virus genomes Palm Beach Gardens, FL 33410
from patients, which is a slow and costly process and has
become less effective at capturing the extent and diversity of (561) 622-2815 • www.joannegreendds.com
COVID-19 variants as many people turn to at-home testing.
Levy developed a library of “barcodes” that identify Medical College of Virginia School of Dentistry - Cum Laude
SARS-CoV-2 variants based on short snippets of their Hospital of the University of Penn - General Practice Residency Training
RNA that are unique to each variant. Then, he coded a new Harvard Dental School - Former Instructor
computational tool that sifts through the mass of genetic Boston Brigham and Women’s Dental Group - Staff Dentist
information in wastewater to find these barcodes. He made
the new Freyja program easy to use and free.
“If you’re in a lab that can already sequence a wastewater
sample, you’re good to go – you just run this code and in
another 20 seconds you’re done,” he says. BUILDING LIFE’S CHAMPIONS
When the researchers applied Freyja to their wastewater
samples and compared the results to clinical data collected
from around San Diego by SEARCH, they discovered that the imagine collaborative personalized insightful creative learning
tool detected variants of concern, including Alpha, Delta, and
Omicron, in wastewater up to 14 days before it was reported
clinically. The Mu (B.1.621) variant was detected in U.C.
San Diego wastewater on July 27, 2021 – four weeks before
its first clinical detection on campus. And, using more recent
data not included in the original study period, the team also
reported that the Omicron variant could be detected at the Point
Loma wastewater treatment plant – at an abundance of just
over 1 percent of all SARS-CoV-2 viruses in a contributing
population of over two million people – on Nov. 27, 2021, 11
days before its clinical detection in the city.
“Wastewater contains a massive amount of very
valuable information about our health, including these
viral genomes that can let us track the course of a
pandemic or epidemic,” says Karthikeyan.
“It took a lot of collaboration between public health
and academic players to get this system established in San
Diego, and now that we’ve shown its effectiveness, we
hope it inspires other localities to use these tools,” adds
Knight. “We’re also very excited about expanding them LEARN MORE
to pathogens beyond SARS-CoV-2.”
The researchers say they are continuing to improve
upon the set of tools they use to analyze viruses in
wastewater, but that the current suite of methods is Scan to view
Website
already a leap forward from previous approaches. The
same strategies could be used to not only track variants A Catholic College Preparatory High School
of SARS-CoV-2 but other human pathogens. cardinalnewman.com
“When you rely on clinical sampling, you not only West Palm Beach, FL
introduce a lot of socioeconomic and geographic bias 561-683-6266
into who is contributing to genomic surveillance data,