Pictured: The city of Oxnard’s wastewater treatment facility. City of Oxnard photo.
by Kimberly Rivers
Last week the city of Oxnard reported that a Colorado lab found two mutations of the coronavirus in samples of sewage wastewater from Oxnard and that levels of the virus in the wastewater are decreasing.
“The overall prevalence of the virus is measured by the overall amount of the virus, variant or otherwise, present in the sample,” said Rose Nash, PhD, director of research and development with GT Molecular in Fort Collins, Colorado. She spoke with the the Ventura County Reporter on Feb. 1. about data from the company’s testing of virus levels and targeting mutations. The company developed a test that provides results within 24 hours. The goal in creating the rapid response test being used in Oxnard as well as about 100 other wastewater facilities across the country is to provide timely test results that are “actionable” for community leaders.
Nash’s team receives samples from Oxnard twice a week. “Oxnard was very proactive. They got involved early and have great research ideas.”
Oxnard has been testing sewage water samples for “overall viral copies per liter concentration since September and started testing at a weekly interval beginning in December,” said Mike Shaffer, GIS manager for the city of Oxnard. The first variant test was done on Jan. 22.
Shaffer said Oxnard has grant funding from the Ventura County Community Foundation to cover five to six more weeks that will include “a few more variant tests, which are twice as expensive as the standard viral copies per liter analysis.”
Staff from Oxnard’s Wastewater Division learned about the work being done by GT Molecular labs when they attended a webinar last year hosted by the California Association of Water Agencies and the California Water Environment Association
Oxnard’s sewage facility manages waste from about 250,000 people, nearly a third of Ventura County’s population. The complete coronavirus genome can be found in the stools of those infected (“Full COVID genome found in stools: What does this mean for prevention and treatments?” by Kimberly Rivers, Ventura County Reporter, Sept. 24, 2020).
Nash clarified that they are “not doing DNA sequencing,” and the tests are “not mapping all mutations on the same strand.” The test being used looks “for key mutational signatures” that are known and can be targeted. Specifically, they are looking for mutations that are known to “drive the transmission” of the virus, like the N501Y and L69/70 mutations. She said mapping the entire genome of viruses in the samples would be very expensive and take several weeks.
Mutations detected locally
The first mutation detected in Oxnard, reported on Tuesday, Jan. 26, by Dr. Robert Levin, health officer with Ventura County Public Health, makes the virus more transmissible.
Almost all, 99.6%, of the virus detected in Oxnard’s wastewater samples are the original “Wuhan” coronavirus strain. A mere 0.4% of the viruses found in the wastewater contain this first detected mutation.
Shortly thereafter, on Friday, Jan. 29, in a written statement, Ventura County announced the discovery of a second mutation found in Oxnard’s wastewater. This additional mutation is being called “N501Y,” and it occurs in both the UK and South African variants already identified. N501Y made up a smaller percentage of the virus sample than the first mutation found, representing 0.283% of the detected virus.
N501Y enables the virus to attach more tightly to ACE2 receptors in the body — the receptors the coronavirus targets.
“The presence of this mutation in such a small amount of the sample tells me that this virus is not widespread in our county yet,” said Levin.
“We cannot say the UK variant is absolutely present [ in the Oxnard samples],” said Nash, adding that the “two mutations that make the UK [variant] more transmissible are present in your community.”
Additional testing, that will take one to two weeks, is needed to confirm whether these samples are the UK variant, which was first detected in the state on Dec. 30, or just share a mutation and represent a unique strain. That testing will be done in a partnership between GT Molecular and Stanford University through a “deep sequencing” project.
Nash clarified that these two mutations have been found in the same sample of wastewater from Oxnard, but she “can’t say they came from the same particle,” or even from the same person. She explained that a mutation is a change in the nucleic acid code in the DNA of the virus and that a single change is a mutation. “Any virus that has a mutation is by definition a variant,” she said. Sometimes particular mutations can lead to “variants of interest,” which are “viruses that have changes that become interesting.” “Interesting” can mean numerous things, such as the virus becoming more transmissible or more virulent, or causing more deaths. So far, variants detected have not been more virulent than the original version of the virus.
Three variants currently recognized
Health officials emphasize the discovery of new mutations and unique strains is not surprising and should be expected as mutations are a normal part of virus replication.
There are currently three main variants from the original virus being tracked globally. All have been found in the United States. The United Kingdom (UK) variant that was found in California in December. The other variants come from South Africa and Brazil. (1)
Nash pointed to the UK variant, which hosts both of the mutations found in Oxnard, representing two of “about 20 different mutations [on that variant]. Some of those mutations are hitchhiker mutations, they are just along for the ride and happen near each other.” Other mutations happen to “improve” the virus in some way. “Right now, we know the UK [variant] has two to three mutations that are really driving it to become more infectious,” giving the virus a “fitness advantage.” Those are the mutations Nash and her team are focusing on.
Nash is scheduled to speak at a webinar on Feb. 17 for the California Water Environmental Association. She will be presenting the data from Oxnard’s samples along with those from Palm Springs and other clients.
As of today, the manufacturers of both available vaccines report their formulations are effective against all three variants, but with less efficacy than against the original virus. But the data behind those statements have not yet been peer reviewed. On Jan. 25, Moderna announced the testing of a third shot of its current vaccine as a “booster” and the development of a new vaccine to address “emerging variants.” (2)