Virus World

Federal public health officials are turning to wastewater surveillance to help fill in the gaps in efforts to track H5N1 bird flu outbreaks in dairy cows. R eluctance among dairy farmers to report H5N1 bird flu outbreaks within their herds or allow testing of their workers has made it difficult to keep up with the virus’s rapid spread, prompting federal public health officials to look to wastewater to help fill in the gaps. On Tuesday, the Centers for Disease Control and Prevention is expected to unveil a public dashboard tracking influenza A viruses in sewage that the agency has been collecting from 600 wastewater treatment sites around the country since last fall. The testing is not H5N1-specific; H5N1 belongs to the large influenza A family of viruses, as do two of the viruses that regularly sicken people during flu season. But flu viruses that cause human disease circulate at very low levels during the summer months. So the presence of high levels of influenza A in wastewater from now through the end of the summer could be a reliable indicator that something unusual is going on in a particular area.

Wastewater monitoring, at least at this stage, cannot discern the sources — be they from dairy cattle, run-off from dairy processors, or human infections — of any viral genetic fragments found in sewage, although the agency is working on having more capability to do so in the future. CDC wastewater team lead Amy Kirby told STAT that starting around late March or early April, some wastewater collection sites started to notice unusual increases in influenza A virus in their samplings. Those readings stood out because by the last week of March, data the CDC tracks on the percentage of people seeking medical care for influenza-like illnesses suggested that the 2023-2024 flu season was effectively over. The increases were very site-specific, she said, and were not reflected in other areas. In fact, she called it “a very limited phenomenon. … The vast majority of our sites are not seeing this.” To date there has been little information in the public sphere about where infected cattle herds have been located. When the U.S. Department of Agriculture announces positive test results, it merely names the state in which the herd was located when the testing took place. Last week, the USDA reported that six additional herds — in Michigan, Idaho, and Colorado — had tested positive for H5N1, bringing the total to 42....

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples.

Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Nature  preprint (July 2022):

https://www.nature.com/articles/s41586-022-05049-6_reference.pdf 

Scientists say samples from Milan and Turin showed virus traces long before cases were confirmed. Italian scientists say sewage water from two cities contained coronavirus traces in December, long before the country's first confirmed cases. The National Institute of Health (ISS) said water from Milan and Turin showed genetic virus traces on 18 December. It adds to evidence from other countries that the virus may have been circulating much earlier than thought. Chinese officials confirmed the first cases at the end of December. Italy's first case was in mid-February.

In May French scientists said tests on samples showed a patient treated for suspected pneumonia near Paris on 27 December actually had the coronavirus. Meanwhile in Spain a study found virus traces in waste water collected in mid-January in Barcelona, some 40 days before the first local case was discovered. In their study, ISS scientists examined 40 sewage samples collected from wastewater treatment plants in northern Italy between last October and February. Samples from October and November came back negative, showing that the virus had not yet arrived, ISS water quality expert Giuseppina La Rosa said. Waste water from Bologna began showing traces of the virus in January. The findings could help scientists understand how the virus began spreading in Italy, Ms La Rosa said.

However she said the research did not "automatically imply that the main transmission chains that led to the development of the epidemic in our country originated from these very first cases". 

Italy's first known non-imported virus case was a patient in the town of Codogno in the Lombardy region. The town was closed off and declared a "red zone" on 21 February. Nine other towns in Lombardy and neighbouring Veneto followed and the entire country went into lockdown in early March....

If you believe it's now safe to fly without a protective mask, you might want to think again. New research shows the COVID-19 virus has been found on nearly every flight tested. Scientists who analyzed wastewater samples taken from 29 flights in Kuala Lumpur have found the coronavirus in 28 of them, according to the National Public Health Laboratory Malaysia. Testing on the 29th sample has not yet been completed, per the laboratory. The samples were taken at international entry points from June through December 2022. During the same time frame, the lab also tested 301 samples from 15 sentinel locations representing each state in the country. All totaled, "SarsCoV-2 was detected in 288 samples," or 95.7% of all flights, health director-general Dr. Noor Hisham Abdullah said in a statement to Malaysian newspaper Sinar Harian. The aircraft sewage surveillance process involves systematic sampling and testing for untreated wastewater and sewer contamination. RNA fragments of the SARS-CoV-2 virus are found in the feces of infected individual regardless of health status (symptomatic, asymptomatic, pre-symptomatic, recovered) and can be detected in sewage. This form of the virus is not infectious and can't be transmitted via feces.

The sewage is taken out of the airplane through a septic tank truck to the aircraft waste disposal facility. Once the targeted flights are identified, officials obtain samples of the sewage water before it undergoes treatment and send them to the lab for testing. Dr. Abdullah said sewage water sampling from aircraft is carried out twice a week. "For the sewage water surveillance from this aircraft, as many as one liter of sewage water samples are taken from selected aircraft," Abdullah told Sinar Harian. The testing is continuously carried out by Malaysia's Ministry of Health as supplementary surveillance to identify countries at risk for COVID-19. Abdullah said the surveillance is intended as an early warning and is one of the control measures the country is using in facing the current situation of the coronavirus. The concentration of a virus in wastewater can paint a picture of how much COVID-19 is present in that community. Testing at airports can help provide context for how prevalent the virus is among international travelers, and provide clues as to what new variants are emerging. Within the last week, the Center for Disease Control announced it is considering use of wastewater testing at airports, mainly on incoming international flights, to track any emerging new variants as COVID-19 surges in China. Health officials in Australia and the United Kingdom announced similar plans.

Scientists not involved in the study seriously doubt the findings, which challenge the current consensus on where and when the virus originated. In a study not yet published in a journal, scientists have reported that the new coronavirus was present in wastewater in Barcelona, Spain in March 2019, a finding that, if confirmed, would show that the pathogen had emerged much earlier than previously thought. But independent experts who reviewed the findings said they doubted the claim. The study was flawed, they said, and other lines of evidence strongly suggest the virus emerged in China late last year. Up until now, the earliest evidence of the virus anywhere in the world has been from December 2019 in China and it was only known to have hit mainland Spain in February 2020.

“Barcelona is a city that is frequented by Chinese people, in tourism and business, so probably this happened also elsewhere, and probably at the same time,” said the lead author, Albert Bosch, a professor in the Department of Microbiology of the University of Barcelona who has been studying viruses in wastewater for more than 40 years. Several experts not involved in the research pointed out problems with the new study, which has not yet been subjected to the critical review by outside experts that occurs before publication in a scientific journal. They suggested that the tests might very well have produced false positives because of contamination or improper storage of the samples. 

“I don’t trust the results,” said Irene Xagoraraki, an environmental engineer at Michigan State University. Researchers at the University of Barcelona posted their findings online on June 13. Most of their report described research on wastewater treatments from early 2020. 

Preprint available at medRxiv (June 13, 2020):

https://doi.org/10.1101/2020.06.13.20129627

We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area.

SARS-CoV-2 RNA was detected in all environmental samples and, when adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99). SARS-CoV-2 RNA concentrations were a seven-day leading indicator ahead of compiled COVID-19 testing data and led local hospital admissions data by three days. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community....

Our results demonstrate: (1) the utility of SARS-CoV-2 primary sludge monitoring to accurately track outbreaks in a community and (2) primary sludge SARS-CoV-2 RNA concentrations can be a leading indicator over other commonly used epidemiology approaches including summarized COVID-19 test results and hospital admissions.

Preprint available in medRxiv (May 22, 2020):

https://doi.org/10.1101/2020.05.19.20105999