An ongoing program that monitors wastewater for the presence of SARS-CoV-2 and effectively predicted the subsequent spike in COVID-19 cases in San Diego has been expanded to detect the presence of monkeypox.
Since the first confirmed case of monkeypox in California in late May, the number of reported cases has steadily increased statewide and nationwide, now at nearly 100 in San Diego County and more than 1,300 in California.
On August 1, 2022, the state declared a public health emergency; San Diego County followed suit the next day. On August 4, 2022, a federal public health emergency was declared with more than 7,000 reported cases nationwide. This is only the fifth such state of emergency in the country since 2001. The nation is still in a state of emergency due to the coronavirus pandemic.
Auto-robotic samplers scattered around the UC San Diego campus and at other sites, such as the Point Loma Wastewater Treatment Plant, help monitor levels of the SARS-CoV-2 virus — and now the monkeypox virus. Photo: Erik Jepsen/UC San Diego
Monitoring and testing for monkeypox virus is a relatively simple addition to the current wastewater surveillance program for SARS-CoV-2, said Dr. Rob Knight, professor and director of the Center for Microbiome Innovation at the University of California, San Diego.
“It’s the same process as SARS-CoV-2 qPCR monitoring, except we tested for a different virus. Monkeypox is a DNA virus, so it’s a bit of a surprise that our process optimized for SARS-CoV-2, which is an RNA virus, works so well,” he said.
The researchers began experimenting with the possibility that their test might work with both types of virus in May and began monitoring wastewater from the Point Loma treatment plant, which serves 2.2 million San Diegans, for the monkeypox virus in early June.
The first positive indicator occurred on July 10, 2022, at levels close to the detection limit: 10,565.54 viral copies per liter of wastewater. Levels have increased dramatically since then, rising and falling slightly but trending upward with a current high concentration of 189,309.81 viral copies per liter of wastewater on August 2, 2022.
Knight said it remains to be seen whether monitoring monkeypox virus load levels in wastewater can predict future infection or case rates.
“We don’t know yet if the data will predict an increase in the number of cases like with COVID,” he said. “It depends on when the virus is cleared from the body versus how bad the symptoms are that people seek care. It is, in principle, different for each virus, although in practice wastewater seems to predict more viruses.”
And the system is not yet set up to sequence monkeypox genomes, which is necessary to detect emerging variants. But, in general, Knight said, “DNA viruses evolve much more slowly than RNA viruses, so we wouldn’t expect variants to emerge and spread so quickly.”
Christopher Longhurst, MD, chief medical officer at UC San Diego Health, said monkeypox surveillance is an important innovation in what he called “anticipatory surveillance.”
“The increase in levels of monkeypox in wastewater clearly correlates with the increasing spread of this virus. Detection and monitoring will help alert us to situations before they become crises, giving health systems and public agencies time to respond, prepare and act.”
Wilma Wooten, MD, MPH, San Diego County Public Health Officer, agreed, “As we’ve seen with COVID-19, it can serve as an additional window into how the virus moves and affects our community. The county appreciates the work of all partners and looks forward to our further work on solving threats to citizens’ health.”
Evidence and experience
People infected with SARS-CoV-2 shed the virus in their waste, even before they show symptoms of COVID-19. That fact prompted the development of the first wastewater screening program in late 2020, when researchers from UC San Diego and UC San Diego Health began an ambitious collaboration to collect wastewater samples across campus using automated sampling robots for subsequent analysis. The program is designed to help students safely return to campus.
Wastewater monitoring and sequencing was eventually extended to the region.
Central to these efforts has been SEARCH (San Diego Epidemiology and Research for COVID Health), a consortium of scientists from UC San Diego, Scripps Research and Rady Children’s Hospital-San Diego, working with San Diego County public health officials and others.
Also included: Laboratory for Expedited Identification of COVID (EXCITE), a Knight collaboration; Louise Laurent, MD, PhD, Professor in the Department of Obstetrics, Gynecology and Reproductive Sciences; and Gene Yeo, PhD, professor of cellular and molecular medicine, both at UC San Diego School of Medicine.
“Based on SEARCH’s success over the past few years, it is fantastic to see wastewater surveillance here in San Diego expand to include monkeypox, while creating a flexible system for future human pathogens,” said Dr. Kristian Andersen, prof. at Scripps Research. “This work is only possible because of the close collaboration between UC San Diego, Scripps Research and San Diego County. It really sets the standard for effective public health-academic partnerships for the country.”
In July, SEARCH collaborators published a report in the journal Nature describing the success of the wastewater sequencing and virus detection, reporting that the program effectively identified new viral “variants of concern” up to 14 days before traditional clinical testing and could be reliably used to predict looming increase in local infections and case rates.
A previously published study estimated that wastewater surveillance enabled early detection of 85 percent of COVID-19 cases on the UC San Diego campus, allowing for more effective mitigation and prevention efforts.
The researchers said they are exploring the possibility of adding other pathogens to the wastewater surveillance program, including poliovirus, which has re-emerged in parts of the United States.
“It’s pretty easy to add new pathogens to the process,” said Dr. Smruthi Karthikeyan, an environmental engineer and postdoctoral researcher in Knight’s lab who oversaw the wastewater monitoring at UC San Diego. “It is feasible in the short term. We can get more information in the same time frame.”
You can find the SEARCH dashboard for waste water monitoring here.
About monkeypox
Monkeypox is a rare disease caused by infection with the monkeypox virus, part of the same family of viruses that cause smallpox. Symptoms of monkeypox, which include painful rashes or itching, fever, low energy, and swollen lymph nodes, are similar to those of measles, but milder and rarely fatal, monkeypox is rare. Monkeypox is not related to chickenpox.
Monkey pox is primarily spread by direct contact with infected sores, scabs, or body fluids during activities such as kissing, hugging, massage, petting, and sex. Monkey pox can be spread by touching materials used by a person with monkey pox that have not been cleaned, such as clothing and bedding. It can also be spread by respiratory secretions during prolonged, close, face-to-face contact. It is not spread by short conversations or walking by someone with monkeypox.
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