CDC unveils its latest weapon in Covid-19 detection: wastewater ...

CNN —

Three days before Thanksgiving, a planeload of passengers from South Africa touched down in San Francisco. One of them was a woman who was in the early stages of a Covid-19 infection, though she wouldn’t know it for almost another week.

It happened to be the same day that scientists 10,000 miles away in Botswana and South Africa began alerting the world to a new and highly mutated version of the virus that causes Covid-19.

Alexandria Boehm, a professor of civil engineering at Stanford University, read about the usual pattern of mutations in the yet-to-be-named variant and sprang into action.

For more than a year, Boehm and her team of 45 people at the Sewer Coronavirus Alert Network, or SCAN, have been collecting and testing daily sludge samples from wastewater processing plants across Northern California, hunting for fragments of the new coronavirus.

Wastewater-based epidemiology has proven to be so reliable in dozens of pilot projects across the US that the government has invested millions to create the National Wastewater Surveillance System, or NWSS, a network of 400 testing sites spread across 19 states that is coordinated by the US Centers for Disease Control and Prevention.

Boehm’s SCAN is part of that network, which has been quietly operating behind the scenes, generating data for public health departments across the country, since September 2020.

For the first time, the CDC has published data that looks at how much coronavirus is turning up in the country’s wastewater. It added this testing data to its Covid-19 dashboard.

Tests show that there’s been a decrease in the amount of virus at two-thirds of the 255 sites reporting data from the latest 15-day period. The NWSS includes 400 sites overall, and more than 500 more will begin submitting data in the coming weeks, the CDC says.

Data from anywhere with a sewer connection

SARS-CoV-2, the virus that causes Covid-19, is encased in an oily envelope. After it invades our bodies and begins to furiously clone itself, some of those copies are shed into our intestines, where the fatty parts of the virus stick to the fats in stool. When we poop, genetic material from the virus gets flushed down the toilet into the wastewater stream, where it can be detected by the same kinds of tests labs use to detect the virus from nasal swabs: real time polymerase chain reaction tests, or RT-PCR.

This kind of testing is highly sensitive. It can pick up the presence of the virus when just one person out of 100,000 in a given area, or sewershed, is infected.

And because wastewater testing doesn’t depend on people to realize they’re sick and seek out a test, or even to have symptoms at all, it’s often the earliest warning a community has that wave of Covid-19 infections is on the way.

The CDC estimates that it takes five to seven days after a toilet flushes to get the wastewater data to its COVID Tracker, and and the samples typically turn positive in an area four to six days before clinical cases show up.

“As long as people are using a toilet that’s connected to a sewer, we can get information on those cases in that community,” said Amy Kirby, a CDC microbiologist who leads the NWSS project.

Government investment has taken what had been a little-known branch of public health and brought it into the mainstream.

“It’s really exploded the field,” said Colleen Naughton, a civil engineer at the University of California at Merced who runs the @CovidPoops19 Twitter account. “We did wastewater monitoring for other pathogens before this, like poliovirus, but it’s really, the amount of people involved in everything has really increased exponentially.”

Jumping into action

Speed is essential to making wastewater testing useful. So when Boehm heard the gravity behind the alerts of a new variant emerging 10,000 miles away, she didn’t delay.

“It all happened very, very quickly, right around Thanksgiving and the holidays, which is a really inconvenient time for things to happen,” she said.

SCAN – a partnership between Stanford, Emory University and the University of Michigan – worked long hours to change the monitoring system over to a new test.

The Monday before Thanksgiving, Boehm alerted her team to the new variant. On Tuesday, they downloaded the handful of gene sequences for the new variant that had been sent to GISAID, a website used by researchers around the world to share information about the new coronavirus. They started to design a test that could pick up several of its telltale changes, including amino acids that were deleted from a chunk of sites in its spike protein and the addition of three amino acids at another place on its spike.

Boehm ordered supplies: the chemical probes they would need to run their new test. She knew that delivery could take weeks, but she says they got lucky and got the new chemicals in just seven days.

But it wasn’t just luck. She had done this many times over the past year, first for the Alpha variant and then Beta, Gamma, Delta and Mu.

While they waited for the supplies, Boehm dusted off an older test her team had been using to find signs of the Alpha variant. Like Omicron, Alpha is missing certain amino acids from a key location on its spike protein. These deletions cause a pattern on lab tests called an s-gene target failure.

“We knew Alpha was basically gone. It’s extinct in our region,” she said. That meant any hits on the Alpha tests were probably the new variant.

On Thursday, Thanksgiving, they got their first hit. A sample in Merced tested positive on the old test.

On Friday, the World Health Organization gave the variant they were hunting a name, Omicron, and officially listed it as a variant of concern.

The following Tuesday, another sample – this time from Sacramento – was positive, and on Wednesday, Gov. Gavin Newsom and the CDC announced that the first American had tested positive for Omicron in San Francisco.

The woman had recently traveled from South Africa, landing in San Francisco on Nov. 22. She didn’t seek out testing until nearly a week later, on Monday, Nov. 28, four days after the first wastewater sample in Merced was positive.

In the days that followed, more positive samples turned up from Sacramento.

And in Santa Clara County, they got their first hit in Palo Alto on Dec. 7, the same day a person living in same sewershed became that county’s first case.

What started as a trickle of positive samples quickly became a steady stream. On Dec. 16, the Santa Clara County Health Department hosted a news conference warn the public based, in large part, on what they were seeing in the wastewater data.

“When I look around the corner ahead, what I see is a deluge of Omicron. What I see is one of the most challenging moments that we’ve had yet in the pandemic,” said Dr. Sara Cody, director of public health for Santa Clara County.

The limitations of wastewater testing

The CDC’s Kirby says the system worked well for the arrival of Omicron in California. Colorado, Houston, and New York City. She published a snapshot of those efforts in the January 21 Morbidity and Mortality Weekly Report.

“What we hear most often is that our health department partners say this gives them confidence to know what’s going on in their communities. So truly, are cases going up or down? And that’s because it is completely independent of health care and clinical testing,” she says.

Kirby says it’s also a useful tool to let counties and cities know where to direct limited resources.

“So if you have, for example, mobile testing capacity, and you want to decide which communities could most use that additional testing capacity, wastewater surveillance is really useful for that,” she says.

There are some blind spots in the system. Although 80% of homes in the US are connected to sewers, the other 20% or so rely on septic systems. These homes, which are mostly in rural areas, wouldn’t be covered by the testing.

Wastewater testing is also harder to interpret and less useful in areas where people come and go often, like tourist destinations.

It’s also difficult to compare data between sewersheds because different areas use different sampling methods. Some take samples directly from the water with thin cotton swabs encased in 3-D printed submarines, while others collect and sample biosolids. Sewersheds can be very different sizes, which also complicated comparisons. The CDC’s new dashboard shows data at the ZIP code level.

Finally, this kind of testing can’t signal when a community is free from the virus because the threshold of detection – how many people have to be positive in an area to show up in a water sample – isn’t known.

For these reasons, the CDC says, wastewater surveillance is best used along with case-based surveillance.

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To avoid direct comparisons, Kirby says, the dashboard will compare each site to its own past results. The main metric will be the percent change concentration at the same site over the past 15 days. The other metric people will be able to see is how many detections there were over that same 15 days, how many samples tested positive at all.

“As you can imagine, right now, that’s not a very useful metric, because everywhere is positive. But as cases go down and we see much lower rates, that will become the metric you’ll want to follow to see if SARS-CoV-2 is re-emerging in your community,” Kirby said.

Kirby says wastewater monitoring will be around long after Covid is gone, too. By the end of the year, the CDC plans to expand the number of pathogens tracked on the dashboard to include influenza, a fungal superbug called Candida auris, and foodborne threats like E. coli and salmonella.

Wastewater monitoring for Covid-19 is picking up steam across the ...

CNN —

Interest in using wastewater surveillance to monitor Covid-19 continues to grow in the United States, as the values of the early detection tool come into clearer focus.

In September 2020, the US Centers for Disease Control and Prevention launched the National Wastewater Surveillance System, investing millions of dollars in an effort to coordinate and build upon programs that track coronavirus in samples collected in sewage systems.

Participation in the program has risen steadily since launch. But what’s driving interest now – and has led to the biggest bump yet – is the change in clinical testing strategies across the US, said Amy Kirby, a microbiologist who leads the CDC’s wastewater program.

With the growing prevalence of at-home Covid-19 tests and the public’s waning interest in testing in general, less case data is being officially reported. Local health departments are “recognizing that clinical surveillance isn’t going to have as much information about what’s going on in the community,” she said.

“Wastewater is a non-intrusive way to still have that early and reliable information of what’s going on in your community,” Kirby said.

The CDC launched a national public dashboard tracking Covid-19 wastewater data in February, and the number of participating sites has risen from about 400 to nearly 700 sites in the two months since.

In that same time, the daily average of reported Covid-19 tests dropped by two-thirds, according to data from the US Department of Health and Human Services.

The CDC’s wastewater program has enough money to sufficiently cover programs for all 50 states and 14 additional jurisdictions, with funding guaranteed through 2025.

There are 33 states currently funded through the agency’s epidemiology and laboratory capacity cooperative agreement – and another 14 that have a commercial testing contract – but the CDC hopes that all 50 states will be represented in the network by next year. Grant applications are now in process for 2023 funding.

Wastewater surveillance is not a new public health tool, but it was far from mainstream before Covid-19.

Local health departments are still figuring out how to best make use of this tool. They have questions about how to partner with utility companies to collect samples in the first place, as well as the best way to analyze and interpret the resulting data and more, said Deise Galan, lead analyst for the National Association of County and City Health Officials’ public health preparedness program.

Enough questions from members have poured in that NACCHO recently launched a mentorship program that has so far matched one local jurisdiction with lots of experience in wastewater surveillance to a couple of others that are just getting started.

About a dozen local health departments applied to be part of this mentorship program, and it has sparked the interest of many more that have reached out to learn more.

“It’s become something that has not only caught the desire of the local health officials, but also their elected officials as something that they can really implement and use not only for SARS-CoV-2, but for other pathogens as well,” Galan said.

Wastewater is a hyper-local surveillance tool, which only provides information about the specific community that is served by the participating wastewater treatment plant. But experts say there is clear value in bringing as many sites on board as possible.

“It’s both a strength that we get really good information about that community, but also a weakness because we need to get as many wastewater systems as we can doing this testing so that we get a more complete picture,” Kirby said.

It took the CDC about a year and a half – from the launch of the program in September 2020 until February 2022 – to work through how to best standardize and present the data they’d been collecting into a national dashboard.

Right now, data on the dashboard is limited. A map shows the relative change in coronavirus detection levels over a single 15-day period, with earlier trends in percent change only available through downloading a large data set.

But in the coming weeks, the CDC plans to update their national wastewater dashboard with more information about not just how levels change week-to-week, but how the absolute level of coronavirus detected in a sewershed compares to other points in the pandemic. They also plan to include an option to visualize trends over time for each site.

“Our focus is on using this system as an early warning of increases in the community. And we want that early warning system to be as early and as sensitive as it can be,” Kirby said.

This high-sensitivity can create “noise” in the system, she said. But with variants such as BA.2 picking in the US and others potentially looming over the horizon, they’d rather play it extra safe.

“We are working closely with our state and local public health officials to make sure that they are interpreting the data correctly to answer their questions. We’re monitoring those increases until we are either convinced they are just noise or see that they are real increases and we need to move on them.”

More participants bring more opportunities to share knowledge about a public health tool that many are just starting to become familiar with, too.

“Why are we going to reinvent the wheel, if there are other places that have been able to successfully implement this program?” Galan said. “At the local level, we can have that peer-to peer-sharing and collection of best practice.”

Putting it all on a national dashboard allows local health departments to explore what’s happening in similar places, said Chelsea Gridley-Smith, director of environmental health at NACCHO.

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“Local health departments know who they see as peers. So, a rural county may look to Chicago for guidance, but not for similarities. But if they can compare themselves to another rural county, they might be able to find more and more programs like themselves,” she said.

“Those are the places where having everything compiled in a CDC location allows us to explore the possibility for expanding partnership outside of just one state with the similarities around county size and jurisdiction size and population type and infrastructure set-up.”

Covid-19 wastewater surveillance is promising tool, but critical ...

CNN —

Covid-19 surveillance is at a crossroads in the United States. With at-home tests now outnumbering those done in laboratories, official case counts are more incomplete than ever as the nation – and world – faces down increasingly transmissible coronavirus variants.

Wastewater surveillance is poised to fill in the gaps and help avoid the threats that an invisible wave of the virus could bring. This surveillance can help identify trends in transmission a week or two earlier than clinical testing, giving public health leaders the chance to focus messaging and resources. It can be used as a tool to sequence the virus and find new variants sooner, too.

But eagerness to use this tool is stifled by uncertainty about exactly how to do so, along with a lack of resources and support to learn.

Testing sewage for virus particles can provide early warning signs of increased transmission in a community, capturing even those who have asymptomatic infections or aren’t being tested.

Since the US Centers for Disease Control and Prevention launched the National Wastewater Surveillance System in September 2020, hundreds of sites have come online, with potential to expand even more. The CDC has funding for the program through 2025, and the National Association of County and City Health Officials says interest among its members has grown significantly over the past two years.

But few communities have been able to translate that interest into a sustainable practice or concrete actions to manage the pandemic.

Although 38% of local public health agencies have monitored wastewater at some point during the pandemic, only 21% plan to continue after the pandemic wanes, according to a recent report.

Public health agencies ranked wastewater surveillance as the least influential factor in pandemic management, and only about half have used it to inform decision-making.

The report represents findings from a survey of more than 200 public health officials across the country that was conducted between November and January.

“The thing about wastewater data is that it is inherently messy,” said Megan Diamond, who leads wastewater work for the Rockefeller Foundation’s Covid-19 Response & Recovery team. The Rockefeller Foundation conducted the survey, along with the Pandemic Prevention Institute and Mathematica.

A government watchdog report from April said wastewater surveillance has “enormous potential” to be a key public health tool in the US but noted that some aspects of the science need “further development.”

Sewage samples can be diluted by rainwater or industrial discharge and can be contaminated by things like animal waste, for example.

“As a result, you get a lot of uncertainty, and uncertainty is not the word that you want to present to an epidemiologist. It’s scary. It means you have to make a lot of assumptions, or you have to explore a new science during a pandemic,” Diamond said.

Wastewater surveillance is not a new public health tool, but it was far from mainstream before Covid-19.

Public health agencies were most likely to implement wastewater surveillance programs if they had the support of expert advocates, according to the survey of public health leaders. But about a quarter said there is no clear agency leading this work, and about half said they didn’t have the resources or capacity to do it themselves.

“There’s this whole rally in visibility around wastewater surveillance, and then the guys on the ground, the people who are actually leading the work are like, ‘Yeah, this is not sustainable for us,’ ” Diamond said.

The CDC’s launch of the national wastewater program has helped some, the survey found.

But it has not come without its own challenges. It took the CDC about a year and a half to work through how to best standardize and present the data it had been collecting into a national dashboard, a testament to how complicated the data can be.

The agency first stood up the national dashboard in February, presenting only one data point on the relative change in virus levels at each site over the past 15 days. It recently updated the dashboard to include another data point on how the current level of virus detection compares with other points in the pandemic.

But last month’s report from the Government Accountability Office noted that more remains to be done.

The watchdog agency called out “a lack of national coordination and standardized methods” that challenge broader adoption and complicate efforts to interpret the data and use it to drive public health interventions.

It’s also unclear how cost-effective wastewater surveillance is, according to the report. The GAO says wastewater surveillance can be “particularly useful when clinical testing is resource constrained” but otherwise raises questions about when it makes sense to use it.

Clinical testing may not be constrained in the US right now, but it is underutilized in favor of at-home tests that remain unreported or no testing at all.

Current trends in the data are clear: Virus levels have been rising in most surveillance sites in the US for weeks. And at the end of last week, more than a third of surveillance sites had detected levels that were higher than most historical levels, according to CDC data.

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Despite the challenges that remain, the benefits of wastewater surveillance shouldn’t be ignored, Diamond says.

“I don’t think we should not be held back by lack of consensus around standardization in the data, because it may never come,” she said.

Coronavirus: As BA.2 subvariant of Omicron rises, lab studies point ...

CNN —

The BA.2 virus – a subvariant of the Omicron coronavirus variant – isn’t just spreading faster than its distant cousin, it may also cause more severe disease and appears capable of thwarting some of the key weapons we have against Covid-19, new research suggests.

New lab experiments from Japan show that BA.2 may have features that make it as capable of causing serious illness as older variants of Covid-19, including Delta.

And like Omicron, it appears to largely escape the immunity created by vaccines. A booster shot restores protection, making illness after infection about 74% less likely.

BA.2 is also resistant to some treatments, including sotrovimab, the monoclonal antibody that’s currently being used against Omicron.

The findings were posted Wednesday as a preprint study on the bioRxiv server, before peer review. Normally, before a study is published in medical journal, it is scrutinized by independent experts. Preprints allow research to be shared more quickly, but they are posted before that additional layer of review.

“It might be, from a human’s perspective, a worse virus than BA.1 and might be able to transmit better and cause worse disease,” says Dr. Daniel Rhoads, section head of microbiology at the Cleveland Clinic in Ohio. Rhoads reviewed the study but was not involved in the research.

The US Centers for Disease Control and Prevention is keeping close watch on BA.2, said its director, Dr. Rochelle Walensky.

“There is no evidence that the BA.2 lineage is more severe than the BA.1 lineage. CDC continues to monitor variants that are circulating both domestically and internationally,” she said Friday. “We will continue to monitor emerging data on disease severity in humans and findings from papers like this conducted in laboratory settings.”

BA.2 is highly mutated compared with the original Covid-causing virus that emerged in Wuhan, China. It also has dozens of gene changes that are different from the original Omicron strain, making it as distinct from the most recent pandemic virus as the Alpha, Beta, Gamma and Delta variants were from each other.

Kei Sato, a researcher at the University of Tokyo who conducted the study, argues that these findings prove that BA.2 should not be considered a type of Omicron and that it needs to be more closely monitored.

“As you may know, BA.2 is called ‘stealth Omicron,’ ” Sato told CNN. That’s because it doesn’t show up on PCR tests as an S-gene target failure, the way Omicron does. Labs therefore have to take an extra step and sequence the virus to find this variant.

“Establishing a method to detect BA.2 specifically would be the first thing” many countries need to do, he says.

“It looks like we might be looking at a new Greek letter here,” agreed Deborah Fuller, a virologist at the University of Washington School of Medicine, who reviewed the study but was not part of the research.

Mixed real-world data on subvariant’s severity

BA.2 has been estimated to be about 30% more contagious than Omicron, according to the World Health Organization. It has been detected in 74 countries and 47 US states.

The US Centers for Disease Control and Prevention estimates that about 4% of Americans with Covid-19 now have infections caused by BA.2, but many other parts of the world have more experience with this variant. It has become dominant in at least 10 other countries: Bangladesh, Brunei, China, Denmark, Guam, India, Montenegro, Nepal, Pakistan and the Philippines, according to World Health Organization’s weekly epidemiological report.

However, there’s mixed evidence on the severity of BA.2 in the real world. Hospitalizations continue to decline in countries where BA.2 has gained a foothold, like South Africa and the UK. But in Denmark, where BA.2 has become the leading cause of infections, hospitalizations and deaths are rising, according to WHO.

Resistant to monoclonal antibody treatments

The new study found that BA.2 can copy itself in cells more quickly than BA.1, the original version of Omicron. It’s also more adept at causing cells to stick together. This allows the virus to create larger clumps of cells, called syncytia, than BA.1. That’s concerning because these clumps then become factories for churning out more copies of the virus. Delta was also good at creating syncytia, which is thought to be one reason it was so destructive to the lungs.

When the researchers infected hamsters with BA.2 and BA.1, the animals infected with BA.2 got sicker and had worse lung function. In tissues samples, the lungs of BA.2-infected hamsters had more damage than those infected by BA.1.

Similar to the original Omicron, BA.2 was capable of breaking through antibodies in the blood of people who’d been vaccinated against Covid-19. It was also resistant to the antibodies of people who’d been infected with Covid-19 early in the pandemic, including Alpha and Delta. And BA.2 was almost completely resistant to some monoclonal antibody treatments.

But there was a bright spot: Antibodies in the blood of people who’d recently had Omicron also seemed to have some protection against BA.2, especially if they’d also been vaccinated.

And that raises an important point, Fuller says. Even though BA.2 seems more contagious and pathogenic than Omicron, it may not wind up causing a more devastating wave of Covid-19 infections.

“One of the caveats that we have to think about as we get new variants that might seem more dangerous is the fact that there’s two sides to the story,” Fuller says.

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The virus matters, she says, but as its would-be hosts, so do we.

“Our immune system is evolving as well. And so that’s pushing back on things,” she said.

Right now, she says, we’re in a race against the virus, and the key question is, who’s in the lead?

“What we will ultimately want is to have the host be ahead of the virus. In other words, our immunity, be a step ahead of the next variant that comes out, and I don’t know that we’re quite there yet,” she said.

For that reason, Fuller says, she feels like it’s not quite time for communities to lift mask mandates.

“Before this thing came out, we were about 10 feet away from the finish line,” she said. “Taking off the masks now is not a good idea. It’s just going to extend it. Let’s get to the finish line.”

Coronavirus wastewater data, CDC guidelines can give mixed ...

CNN —

The federal government has taken clear steps toward a new phase of the Covid-19 pandemic in recent weeks: The Biden administration released the National Covid-19 Preparedness Plan, and new guidelines from the US Centers for Disease Control and Prevention dropped masking recommendations for most of the country.

As many Americans try to move on from the height of the pandemic and as testing wanes, detecting coronavirus levels in wastewater offers an alternative to monitoring community spread.

The CDC captures wastewater data for about 650 sewersheds, representing about a quarter of the US population. For most of those sites, the amount of virus detected has dropped over the past two weeks.

But for some, the amount of virus has spiked – up at least 1,000% compared with 15 days earlier.

For local leaders, an early warning sign such as this might prompt a renewed emphasis on prevention measures. But with the vast majority of the country now living in areas considered to have a low or medium “community level” of Covid-19, this surveillance data may conflict with what CDC guidelines suggest.

In June, wastewater surveillance in North Carolina detected elevated levels of the coronavirus in a local community. A news release went out, reminding residents to “stay vigilant” and encouraging continued mask use.

The surveillance most likely alerted officials about rising levels of infection days faster than more traditional measures like testing numbers.

“Especially with a virus as quick and contagious as this one is, those few days really matter,” said Kody Kinsley, secretary of the North Carolina Department of Health and Human Services. “So our first reaction has been to use it as an early warning system, through public communication.”

But under the new CDC guidelines, most of the places that have had a recent spike in the amount of virus detected in the wastewater are in counties where indoor masking is no longer recommended.

Of 28 sites that had a 1,000% increase over the past 15 days, only four are in counties considered to have a “high” community level, where indoor masking is still universally recommended as of Wednesday. More than half are in counties with a “low” community level, where there is no recommendation for masking at all.

Though previously driven solely by local case rates, the CDC’s new masking guidelines now prominently factor in hospital admissions and hospital capacity. Some critics have argued that they stray too far from measures aimed at Covid-19 prevention, such as minimizing coronavirus transmission.

The CDC continues to monitor community spread, and at a briefing last week, CDC Director Dr. Rochelle Walensky touted strategies that “can better anticipate a rise in cases” and alert people in real time, including wastewater surveillance.

“For SARS-CoV-2, wastewater can detect an increase in cases four to six days before we might see these cases show up through a rise in positive tests,” she said.

The CDC says wastewater data is meant to complement other surveillance tools. When wastewater levels are low, a small uptick can seem like a dramatic increase, said Brian Katzowitz, a health communication specialist with the CDC. But it best informs public health decision-making when used in harmony with other metrics.

Although wastewater data is not formally part of the CDC’s new guidelines, the public health response to rising levels would be very similar to those taken if trends head in the wrong direction with other metrics, said Amy Kirby, program lead for the National Wastewater Surveillance System – including encouraged masking, social distancing and vaccination.

It offers “situational awareness” and gives communities “time to prepare and make sure they have all the resources that they need,” she said.

The CDC has been collecting wastewater data from some sites for more than a year but first made the data public a month ago.

Kirby said the agency first wanted to have “enough coverage at the national level that it was meaningful to share.” And it took some time to figure out how to best visualize the data, as sewage systems often serve neighborhoods that cross county lines.

About 250 sites representing an additional 30 million people have been added since the national dashboard was launched, and new sites continue to be added.

The federal dashboard presents levels of coronavirus detected in sewersheds in terms of the percent change over the past 15 days.

A watershed serving about 116,000 people in St. Louis County, Missouri, was one of the 28 on the CDC dashboard that recently saw more than a 1,000% increase in virus levels. But for Dr. Mati Hlatshwayo Davis, director of the St. Louis City Department of Health, data in this format isn’t always useful without an understanding of the baseline levels.

“Our baseline is currently so low that some of the percentages that are being reporting are not as reflective of the current situation,” she said, especially when viewed in the context of other metrics.

“The federal data is certainly not something we’re using to make day-to-day decisions,” she said, but it is still something they monitor. “If we see huge increases here, the first thing we’re going to do is go [to the CDC dashboard] and see if that’s consistent nationally. But we’ve never been in a position where something has happened here that wasn’t reflected in the national picture.”

As at-home Covid-19 tests become more common – or as demand for testing drops off – wastewater offers a much more reliable and consistent surveillance alternative.

Wastewater epidemiology is “inclusive and representative,” said Newsha Ghaeli, president and co-founder of Biobot Analytics, a company focused on tracking coronavirus in sewage.

” ‘Everybody has a voice in our sewer systems’ is a line we like to say at the company,” she said. It encompasses people who might be missed in other clinical data, including those without health insurance who may avoid going to the doctor and those who don’t have the resources to get tested or don’t feel like doing it, in an anonymized sample.

It’s also scalable, Ghaeli said, which is critical for the nation’s chronically under-resourced public health system. It’s much more affordable to test a wastewater system that serves 100 million people than to clinically test each individual, she said.

Wastewater treatment facilities stepped up early to move the work forward, while public health departments were a little bit slower, she said – and funding played a big part. “What we found was that funding mechanisms within the public health world were more rigid than budgets are within wastewater treatment.”

Many early adopters of wastewater surveillance were jump-started by partnerships with research institutions, such as North Carolina’s with the University of North Carolina.

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Wastewater data may not play a formal role in federal guidance right now, but making the data public removes a hurdle for it to continue to play a part in the conversation.

“Having the CDC step in and highlight the need for this national database is, of course, tremendously valuable for understanding where we’re at with Covid-19 right now,” Ghaeli said.

“But I also think it’s tremendously valuable because it is essentially demonstrating to the country that we need this as a fundamental piece of our pandemic surveillance infrastructure. We are going to have another public health crisis – it might not be as severe as Covid-19 – but we are going to have public health emergencies as a society, and so wastewater [epidemiology] being established today can really help us in the future.”

Health department finds COVID omicron variant in Missouri ...

The Missouri Department of Health and Senior Services has found the omicron coronavirus variant in wastewater samples across Missouri, including Columbia.

Sequencing tests identified the first presence of the omicron variant in Missouri from two sets of sewershed samples collected Dec. 7-8 in Jackson County and Buchanan County.

Columbia's results come from samples taken Dec. 20.

According to DHSS, the omicron variant is "likely present among the population" of the areas in which it is found in wastewater samples.

"Our robust program for monitoring COVID-19 through sewershed sampling provides us with reliable information regarding the presence of the virus and its variants,” said DHSS Director Donald Kauerauf in a statement. “The existence of the omicron variant is becoming much more prevalent each week, making the actions of COVID-19 individual testing, vaccination and other mitigation measures more important as we already face the threat of the delta variant and an increase in flu cases."

More than half of the statewide samples taken Dec. 20 tested positive for the omicron variant. Other areas that tested positive include three Kansas City facilities (Blue River, Westside, and Birmingham), seven St. Louis facilities (Lemay, Grand Glaize, Coldwater Creek, Bissell Point, Fenton, Lower Meramec and Missouri River), five St. Charles County facilities (St. Peters Spencer Creek, Duckett Creek Sewer District WWTF #1, Duckett Creek Sewer District WWTF #2, O'Fallon and Wentzville), Branson (Cooper Creek and Compton Drive), Interim Saline Creek Regional, Troy Southeast, Farmington East, Perryville Southeast, Springfield, St. Joseph, Atherton, Cape Girardeau, Nixa, West Plains, Washington, Oak Grove, Crystal City and Joplin Turkey Creek.

More:Boone County COVID-19 vaccine tracker: 59% of people fully vaccinated

Omicron present in Boone County

Sequencing testing results of wastewater samples are updated weekly in the state's COVID-19 Sewershed Surveillance Project tracker.

The first confirmed case in Missouri of the omicron variant was discovered in St. Louis earlier this month.

Columbia/Boone County Public Health and Human Services receives information about variants from both the Sewershed Surveillance Project and when the state conducts additional lab testing on positive cases, spokesperson Sara Humm wrote in an email.

"We have received information from both methods that omicron has been detected in Boone County," Humm wrote Tuesday.

The sewershed project indicates omicron has not yet become the area's dominant strain.

"Variants other than omicron remain dominant, and delta is likely most of that," Humm wrote.

More:Uncounted: Inaccurate death certificates across the country hide the true toll of COVID-19

CDC shortens recommended isolation period

The news comes as the CDC shortens its recommended isolation and quarantine period for those who test positive for COVID-19 in any of its forms.

According to the new guidelines, those infected with the virus are recommended only to isolate for five days if they are asymptomatic at that point. The previous recommendation was for 10 days of isolation.

"The change is motivated by science demonstrating that the majority of SARS-CoV-2 transmission occurs early in the course of illness, generally in the 1-2 days prior to onset of symptoms and the 2-3 days after. Therefore, people who test positive should isolate for 5 days and, if asymptomatic at that time, they may leave isolation if they can continue to mask for 5 days to minimize the risk of infecting others," read a Tuesday statement from the CDC.

Additionally, the CDC updated its recommended quarantine period for those exposed to COVID-19. For people who are unvaccinated or are more than six months out from their second mRNA dose (or more than two months after the J&J vaccine) and not yet boosted, CDC now recommends quarantine for five days followed by strict mask use for an additional five days. Individuals who have received their booster shot do not need to quarantine following an exposure but should wear a mask for 10 days after the exposure.

“The omicron variant is spreading quickly and has the potential to impact all facets of our society. CDC’s updated recommendations for isolation and quarantine balance what we know about the spread of the virus and the protection provided by vaccination and booster doses," said CDC Director Rochelle Walensky. "These updates ensure people can safely continue their daily lives. Prevention is our best option: get vaccinated, get boosted, wear a mask in public indoor settings in areas of substantial and high community transmission, and take a test before you gather.”

Health recommendations ahead of New Year's Eve

Humm recommends celebrating the new year responsibly.

"Whenever folks from various households gather for an extended period of time in an indoor space, the risk of transmission is higher," she wrote. "It is possible that we'll see an influx of positive COVID cases in the next couple of weeks, but it's hard to be able to predict the future of what might happen."

The department recommends following CDC guidelines when going out, including:

Getting vaccinated,

Wearing a mask when inside public places,

Social distancing,

Washing hands often and

Staying home when sick.

"If folks are hosting events at their home or another facility, we recommend that they communicate with the attendees about chosen guidelines before the event so everyone is on the same page about what is expected," Humm added.

The local health department has a list of testing options at como.gov/coronavirus.

"We recommend that folks check hours and appointment availability (if required by the location) before going to a location that does testing," Humm wrote.

Free test kits are also available through a state program. More information can be found online at health.mo.gov.

What rising Covid-19 infections in the UK and Europe could mean ...

CNN —

Two weeks after the United Kingdom dropped its last remaining Covid-19 mitigation measure – a requirement that people who test positive for the virus isolate for five days – the country is seeing cases and hospitalizations climb once again.

Covid-19 cases were up 48% in the UK last week compared with the week before. Hospitalizations were up 17% over the same period.

The country’s daily case rate – about 55,000 a day – is still less than a third of the Omicron peak, but cases are rising as fast as they were falling just two weeks earlier, when the country removed pandemic-related restrictions.

Daily cases are also rising in more than half of the countries in the European Union. They’ve jumped 48% in the Netherlands and 20% in Germany over the past week, according to data from Johns Hopkins University. But daily cases in Germany had yet to drop below pre-Omicron levels, and the Netherlands hadn’t seen cases fall as much as they did in the UK.

The situation in Europe has the attention of public health officials for two reasons: First, the UK offers a preview of what may play out in the United States, and second, something unusual seems to be happening. In previous waves, increases in Covid hospitalizations lagged behind jumps in cases by about 10 days to two weeks. Now, in the UK, cases and hospitalizations seem to be rising in tandem, something that has experts stumped.

“So we’re obviously keenly interested in what’s going on with that,” Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, told CNN.

Fauci said he’s spoken with his UK counterparts, and they have pegged the rise to a combination three factors. In order of contribution, Fauci said, these are:

The BA.2 variant, which is more transmissible than the original Omicron

The opening of society, with people mingling more indoors without masks

Waning immunity from vaccination or prior infection

In a technical briefing Friday, the UK Health Security Agency said BA.2 had an 80% higher relative growth rate than the original Omicron strain, though it does not seem more likely to lead to hospitalization.

Given that BA.2 doesn’t seem to be causing more severe disease – at least not in the highly vaccinated British population – it’s not clear why hospitalizations are ticking up.

“The issue with hospitalization is a little bit more puzzling, because although the hospitalizations are going up, it is very clear their use of ICU beds has not increased,” Fauci said. “So are the numbers of hospitalizations a real reflection of Covid cases, or is there a difficulty deciphering between people coming into the hospital with Covid or because of Covid?”

The US, like the UK, has lifted most mitigation measures as Covid-19 infections have fallen. Two weeks ago, the US Centers for Disease Control and Prevention changed how it measures Covid-19 impact in communities. The new metric – which relies on hospitalizations and hospital capacity in addition to cases – did away with masking recommendations for most parts of the country. States and schools have followed suit, lifting indoor masking requirements.

READ: Your top Covid questions, answered

“Without a doubt, opening up society and having people mingle indoors is clearly something that is a contributor, as well as overall waning immunity, which means we’ve really got to stay heads-up and keep our eye on the pattern here,” Fauci said. “So that’s the reason why we’re watching this very carefully.”

Michael Osterholm, who directs the Center for Infectious Disease Research and Policy at the University of Minnesota, told CNN, “it’s like a weather alert. Right now, the skies are sunny and bright, and we hope they stay that way. But we could have some bad weather by evening, and we just don’t know.”

What will BA.2 do in the US?

BA.2 has been growing steadily in the US. Last week, the CDC estimated it was causing about 12% of new Covid-19 cases here.

Meanwhile, BA.2 now accounts for more than 50% of cases in the UK and several other European countries.

“The tipping point seems to be right around 50%,” said Keri Althoff, an epidemiologist at Johns Hopkins Bloomberg School of Public Health. “That’s when we really start to see that variant flex its power in the population” as far as showing its severity.

Althoff said although the UK may provide a glimpse of the future, there are key differences that will affect how BA.2 plays out in the United States.

In the UK, 86% of eligible people are fully vaccinated, and 67% are boosted, compared with 69% of those eligible vaccinated and 50% boosted in the US.

“What we see happening in the UK is going to be perhaps a better story than what we should be expecting here,” Althoff said.

In the Netherlands, it took about a month for BA.2 to overpower BA.1, she noted. If the same timeline occurs in the US, that will mean the variant is taking off just as the immunity generated by winter’s Omicron infections will be waning.

“I’m concerned about that,” Althoff said. “But we were in a similar situation last spring, where we really got hopeful that things were going to settle down, and we got a little bit of a summer, and then we got walloped by Delta.”

It will be important for people to understand they may be able to take their masks off for a few weeks, Althoff said, but they might also need to go back to wearing them regularly if cases spike.

“We could see another wave of illness at our hospitals,” she said.

Althoff will also be closely watching wastewater data over the next few weeks.

“Wastewater surveillance is an incredible advancement in how we can monitor SARS-CoV-2 and what it’s doing in the population without needing, really, any input from people,” she said. “Keeping our eye on wastewater surveillance is an important tool to understand where the virus is going and if it’s increasing in terms of infection.”

Preparing for the next wave

Protection against the next variant has to start with vaccination.

“We absolutely have to continue to find people who are unvaccinated and get them vaccinated,” Althoff said.

Fauci agreed that vaccination rates could be better in all age groups but said current numbers are especially bad for kids. Data collected by the CDC show about 28% of children ages 5 to 11 are fully vaccinated, while 58% of kids ages 12 to 17 have had two doses of a Covid-19 vaccine.

Even though the youngest children, those under 5, can’t yet be vaccinated, recent studies have shown young kids are less likely to catch Covid-19 when they’re surrounded by vaccinated older children and adults.

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“So the way you protect them is to surround the children, to the extent possible, with people who are vaccinated and boosted so that you have somewhat a veil of protection around them,” Fauci said.

It will also be important to continue to be flexible.

“The important thing in this massive experiment where we’re dropping all masking and restrictions is we have to stay diligent in terms of monitoring of it and testing and be prepared to possibly reverse a lot of the relaxing of these restrictions,” said Deborah Fuller, a microbiologist at the University of Washington.

“We can’t let our guard down, because the message that people get when they say ‘we’re lifting restrictions’ is the pandemic is over. And it’s not,” she said.

Brenda Goodman Deidre Mcphillips
Brenda Goodman
Deidre Mcphillips

BA.2, where are you? Dominant strain hasn't shown signs of starting ...

CNN —

Maybe BA.2 really is the “stealth variant.”

The Omicron subvariant caused as many as 3 in 4 cases of Covid-19 in the United States last week, according to the latest genomic surveillance from the US Centers for Disease Control and Prevention, but so far, there are no signs of a looming surge in the US.

Even as BA.2 has become dominant, overall numbers of cases are still decreasing, says Dr. Jessica Justman, an epidemiologist at Columbia University’s Mailman School of Public Health.

“This is a clear example of how these two trends are not necessarily tied together,” she says.

If things stay quiet, as some models predict, it will mark the first time a viral strain has taken over in the US without causing an increase in Covid-19 cases.

That’s different from what’s happening in the UK, some European countries and parts of Canada, where the arrival of BA.2 coincided with a new wave of cases and hospitalizations.

Andy Pekosz, who studies viruses at Johns Hopkins University, says the new wave of cases in Europe may have more to do with timing than any features of BA.2.

“What you’re seeing in Europe may be resulting from the fact that they lifted their restrictions early, not so much that it’s BA.2 that’s there,” he says.

Pekosz says many European countries dropped some precautions when there was already lot of virus circulating. He says cases in the US were coming down faster and fell farther before BA.2 outgrew its Omicron cousin here.

“When you start at a low place, it takes a lot longer to build up a high number of cases,” he says.

It also suggests that the US may not be entirely out of the woods with BA.2 since Spring Break and the Easter and Passover holidays will mean more travel and more mixing of people from different parts of the country.

Little sign of rising infections

Why the US isn’t seeing the same increases in new infections with BA.2 as countries in Europe did continues to be an open question.

One theory is that we’re no longer seeing positive cases show up in testing. The data collected by the CDC and state health departments about positive tests is generated by laboratories; it doesn’t count the tests people take at home.

And there’s been a “dramatic shift” toward at-home testing in the US, says Mara Aspinall, a professor at Arizona State University who has been estimating home and lab testing volumes.

In January and February, she says, there were roughly 1 million to 1.5 million Covid-19 laboratory tests being recorded each day – but 6 million to 8 million at-home tests available. A case detected by an at-home test doesn’t typically get reported unless it is later confirmed by a lab test.

“I think there’s no question there’s underreporting of positive cases,” Aspinall said. She believes this is, in part, why the CDC has shifted its pandemic measures to focus on hospitalizations and hospital capacity, and pivoted its surveillance to wastewater, which measures infection levels even when people aren’t getting tested.

Watching wastewater

Even in wastewater, though, there’s not a lot to see.

Zooming in on areas of the country that are seeing more BA.2 transmission, like New York, wastewater has been only modestly affected.

“It’s still low when we look at absolute raw numbers of viral copies in wastewater,” said David Larson, an associate professor of public health at Syracuse University who helped create the state’s wastewater dashboard.

“We’re not at the level of the Omicron [BA.1] surge, but it’s increasing, and community spread is present, and transmission is still high,” Larson said.

With more virus being transmitted, Larson says, officials could see cases go up, but he’s not sure. It will depend on how sick people get from their infections.

“Cases measure access to treatment and access to testing,” he said. “So it’s hard to say what cases will do.”

San Francisco is also seeing signs that BA.2 may be making a move, but it hasn’t been a major one.

Dr. Peter Chin-Hong, an infectious disease specialist at the University of California, San Francisco, says the Bay Area has been one of the most cautious parts of the country throughout the pandemic. There are even some schools that are still closed because they’re unwilling to tolerate the risk.

He was surprised to see San Francisco County recently take the top spot for its seven-day average of new cases on the California Department of Public Health’s Covid Dashboard.

“I had to rub my eyes,” Chin-Hong said. “I look at these trends pretty much every day, and SF used to be amongst the lowest, and now it’s amongst the highest” in terms of new cases. Test positivity is inching up, too.

But the increases he’s seeing are small ones. “They’re teetering on the point of going up and like trying to boost forward,” he said.

Chin-Hong says San Francisco is “super immune” right now, with one of the highest vaccination rates in the country and an antibody boost from recent wave of infections from Omicron’s BA.1 version.

At the hospital where he works, things are quiet in terms of Covid-19.

It reminds him of what happened in Denmark and South Africa with BA.2, “which was basically nothing. No explosions of cases, no lives lost.”

That won’t stop people from feeling anxious, he said. As cases rise, people will stay home and will keep their kids home from school.

He says the anxiety comes from two things: PTSD from previous surges and a measure of freedom that they don’t want to give up.

And though he’s not ready to sound the all-clear, he thinks things may be better than people are expecting this time around.

Are we failing upward?

If BA.2 does go quietly, it may be because the US did such a poor job of stopping transmission of Omicron and the variants that came before it, that we have failed upward, bungling our way to a high level of immune protection.

BA.1 and BA 1.1 ran rampant in the US over the winter, as people abandoned mask wearing and largely resumed their holiday plans.

“That spike was just massive. It was like nothing we’ve seen before,” says Mariana Matus, president and CEO of Biobot Analytics, a company that that’s been testing wastewater for local counties and other sewersheds across the US since 2020.

Matus says Omicron and Delta swept through the population in a matter of weeks, while BA.2 has been creeping up for a few months.

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“It’s been going very, very slowly, and so far, we haven’t seen an impact on the level of disease,” she said.

Matus points to Ontario, which is seeing a larger viral load in its wastewater levels, indicating more infections. That province’s Omicron peak with BA.1 a few months ago was not as high as the one in the US and may not have left as much immunity in its wake.

“That data, to me, would say that, you know, they had a smaller Omicron wave, and now [BA.2 is] picking up,” she said.

The latest CDC estimate is that 95% of Americans have some level of immunity, either through infection or from vaccination. About 43% of Americans are thought to have antibodies from infection.

This immunity came at a high price: The US remains a world leader in Covid-19 deaths with more than 980,000, according to data from Johns Hopkins University.

Remembering this makes any respite from Covid-19 over the next few weeks somewhat bittersweet. It may also be brief, as the world waits to see what other surprises the virus has in store.

How worried should we be about the new 'stealth' Omicron? | CNN

CNN —

A new subvariant of Omicron is spreading rapidly in some parts of the world. This spinoff from the original Omicron variant, called BA.2, has been found in at least 49 countries, including the United States. In some countries, like Denmark, BA.2 has already surpassed the original Omicron (BA.1) as the dominant variant.

Because it doesn’t cause a certain signature on lab tests called an s-gene target failure, it can look like other coronavirus variants on a first screen. That has some calling it “the stealth variant.”

How worried should we about this “stealth” Omicron? Are vaccinated people still protected? What about those who recently had Covid-19—could they be reinfected? And can tests pick up this subvariant?

For answers to these and other questions, I spoke with CNN Medical Analyst Dr. Leana Wen. Wen is an emergency physician and professor of health policy and management at the George Washington University Milken Institute School of Public Health. She is also the author of “Lifelines: A Doctor’s Journey in the Fight for Public Health.”

CNN: Should we be worried about this new Omicron subvariant?

Dr. Leana Wen: We should be cautious and monitor new information as it comes out, but we shouldn’t worry.

Here’s what we know about BA.2. Given how quickly it has spread and even displaced the very contagious original Omicron variant, known as BA.1, in some places, this new subvariant appears to have an even higher rate of growth. There’s no evidence that it causes more severe disease than the original Omicron, which has been associated with milder illness than previous variants like Delta.

Preliminary studies from the United Kingdom also show that people vaccinated and boosted are as well-protected against BA.2 as BA.1. That’s very important, because it means that those vaccinated and boosted are unlikely to become severely ill if infected with this new version of Omicron.

CNN: If you’re diagnosed with Covid-19, how would you know if you have the original Omicron variant versus this one?

Wen: Most people do not find out what variant they are infected with, because that takes special technology called sequencing that takes place in certain labs. Right now, the original Omicron BA.1 still accounts for over 99% of new infections in the US, so if you are diagnosed with Covid-19, chances are, that’s what you have.

A healthcare worker places solution droplets into a rapid antigen Covid-19 test at a Reliant Health Services testing site in Hawthorne, California, on January 18. Patrick T. Fallon/AFP/Getty Images

CNN: If someone recently had Omicron, could they get reinfected with the new variant?

Wen: It’s unlikely. Recent infection, especially in combination with prior vaccination, protects against reinfection. We don’t know how long that immune protection will last. Given how similar BA.1 and BA.2 are to each other, it stands to reason that someone who just had Covid-19, and therefore most likely had BA.1, is not going to contract BA.2 in the near future.

CNN: Will the new Omicron-specific booster work against BA.2?

Wen: Pfizer and Moderna have announced that they are both testing vaccines against Omicron. Since both BA.1 and BA.2 are subvariants under Omicron, it’s expected that the vaccine would probably be effective against both.

However, we will not know until the clinical trials are complete just how effective the new Omicron-specific booster is, compared to the vaccine and booster that we have already been using. No one should wait for an Omicron-specific booster if they are already eligible to be boosted. If you are five months out from two doses of Pfizer or Moderna, or two months out from the one-dose Johnson & Johnson vaccine, you should get a booster now.

CNN: What could happen if BA.2 becomes dominant in the US?

Wen: This is certainly a possibility, as it has occurred in other countries. A more transmissible variant means that it displaces previous variants.

The best-case scenario is that we have enough people protected here in the US due to vaccination and recent infection that BA.2 does not cause a substantial rise in cases. We could continue on the track to experiencing a lull in case numbers over the spring and summer. Another scenario is that BA.2 blunts the sharp drop in cases that we are seeing, and we end up having a more prolonged fourth wave than we would have with BA.1 alone.

In either situation, the key is to keep monitoring whether vaccination and boosters continue to protect against severe illness from BA.1 and BA.2. If so, that means vaccines are successful—that’s what vaccines were designed to do, to keep us out of the hospital and to prevent severe illness and death.

CNN: Does “stealth” mean that the new subvariant isn’t picked up on tests?

Wen: No, there’s no evidence to suggest that BA.2 isn’t detectable with laboratory PCR or at-home antigen tests.

CNN: What’s your advice for protecting myself and my family from this subvariant?

Wen: There are many people who want to continue taking precautions to keep from getting infected with Covid-19: those who are immunocompromised, for example, or others who are medically frail and therefore still vulnerable to severe outcomes despite being vaccinated. There are families with young children under 5 who are not yet eligible for the vaccine, although it looks like that could be coming.

Another contagious virus means that people who want to avoid getting Covid-19 have to continue taking precautions. The most important is indoor masking, and quality of mask really matters. The best mask is a well-fitting, comfortable one that you can consistently wear and is a certified N95, KN95 or KF94.

Wear these masks anytime you are indoors around people of unknown vaccination status. While coronavirus infection numbers are high in your community, you may want to take additional precautions—for example, asking everyone outside your household to get a rapid test prior to gathering with you indoors.

CNN: Will this be the last variant we see?

Wen: Almost certainly not. New variants are popping up all the time, because that’s what viruses do: They mutate when they replicate. Whether a new variant causes global concern depends on if it’s more contagious, more virulent or if it can override prior immunity. This is why real-time surveillance is so important, and it’s also why vaccination is key. The more population immunity we have, the less viruses will spread and mutate, and the quicker we can all emerge from this pandemic.

Sewage systems near Miami, St. Petersburg, Pensacola show COVID

The Centers for Disease Control and Prevention effectively lifted indoor masking recommendations this week for all of Florida's counties even as parts of the state are detecting spikes of coronavirus levels in their sewage.

Until Thursday, CDC officials classified 10 of Florida's 67 counties as places where COVID-19 poses a high threat to hospitals, and therefore recommended residents wear masks indoors. Now that those counties — clustered near Alachua County and bordering Georgia — have been downgraded to medium-risk areas, no Floridians live in a county where federal health experts recommend indoor masking.

But some sewage systems in Florida detected an increase of the coronavirus' genetic fragments in their wastewater systems between Feb. 28 and March 14, the CDC reports.

COVID data in Florida:Florida to update COVID-19 data less frequently than all other states

Spring break 2022: Florida reports 10,000 COVID cases, 863 newly reported deaths in a week

Test results from Escambia County, home to Pensacola, revealed increases in viral particles. Three samples from Miami-Dade County showed the same thing. So did one of two samples from Pinellas County, home to St. Petersburg.

Two of three samples from Orange County, home to Orlando, showed declines in viral fragments. A sampling from Brevard County, home to Cape Canaveral, also showed a decrease.

The CDC cannot distinguish between the coronavirus' omicron variant and one of its subvariants, BA.2, CDC spokeswoman Jasmine Reed said Friday by email. "We are currently looking into these efforts and will update the surveillance system as appropriate," she said.

Boston company that tests sewage nationally reports mixed results

Boston-based laboratory Biobot, which collects and tests sewage from across the nation, reports mixed results.

BA.2 particles constituted one-third of coronavirus fragments in Seminole County sewage Biobot examined Wednesday. But it found no trace of the subvariant in a sample from Hillsborough County, home to Tampa.

BA.2 is known as "stealth omicron" because of how tough it is for regular COVID-19 polymerase chain reaction (PCR) tests to detect and distinguish from the delta variant.

Sewage test results can detect the spread of the coronavirus in a community faster than swab testing in part because it takes a shorter time to process the results. None of the six Florida counties Biobot gets samples from show a recent spike in viral fragment levels.

Florida health officials have cut COVID-19 reporting to every week, from weekly. Their previous data release was March 11. The next will come March 25.

To figure out how widespread and dangerous COVID-19 currently is in Florida, statistics seekers must piece together data from federal websites and other sources. Those numbers, collected from the state Health Department, can be as old as several days or a week by the time they're published.

Eighth week in a row that Florida death count has hovered above 500 per week

Florida's death toll sits at 72,592 residents, data collected Thursday by the CDC shows. That's a 732-person increase from what state health officials reported March 11.

It is the eighth week in a row the weekly statewide fatality count has hovered above 500. During the delta variant-driven coronavirus surge last summer, weekly deaths stayed above that number for 14 weeks straight.

The respiratory disease is hitting a swath of the Panhandle around Tallahassee harder than the rest of Florida.

Madison County, on the state's northern border with Georgia, recorded Florida's highest death rate in the 30 days ending Thursday — about one in 1,000 residents. A total of 21 fatalities were logged there, which is a high sum for the rural county of about 19,000 people.

Just 46% of eligible Madison County residents ages 5 and older have received at least two shots of the Moderna or Pfizer vaccines, or one shot of the single-dose Johnson & Johnson formula, federal data shows.

Florida saw smallest 1-week increase in cases since Thanksgiving week

Florida's total case count increased by 8,005 from March 11 through Thursday, the smallest one-week hike since Thanksgiving week, a comparison of CDC and state data shows. The state has logged 5,832,733 infections over the course of the pandemic, the CDC reported Thursday.

An average of just under 2.4% of tests statewide had come back positive in the week ended Monday, according to the latest results the CDC collected from Florida. That's the lowest level recorded by the federal agency.

Meanwhile, Florida is still tending to more COVID-positive patients than before the omicron mutation engulfed the state. Hospitals statewide are taking care of 1,135 COVID-positive patients, the U.S. Health and Human Services Department reported Friday. That number was 994 on Dec. 1.

Hospitals nationwide have about one-third as many patients as they did Dec. 1. Other large states, such as California, New York and Texas, report fewer patients compared to pre-omicron. The same is true for states such as Pennsylvania, West Virginia and Maine, where around one in five residents are ages 65 or older.

Florida health officials have offered no explanation for why state hospitalizations have been worse than other states. Nor have they offered plans on how to tackle the issue.

While COVID-positive hospitalizations nearly tripled nationwide during the omicron wave, Florida hospitalizations surged more than 11-fold.

Meanwhile, vaccinations continue to crawl at a slow pace statewide.

The CDC estimates that about 5.5 million people across Florida have received booster shots, the strongest protection against the omicron variant.

But state health officials usually report lower counts. Just over 5 million had gotten boosters as of March 11.

The CDC also says just over 16.8 million people statewide have gotten at least one shot, much higher than the 15.4 million state health officials reported March 11.

The CDC counts some people state health officials might not, such as military personnel stationed in Florida.

Chris Persaud is The Palm Beach Post's data reporter. Email him at cpersaud@pbpost.com.