Researchers are getting some unusual results from a study of sewage waste as they attempt to decipher the origin of some COVID variants.
Researchers are getting some unusual results from a study of sewage waste as they attempt to decipher the origin of some COVID variants.
Though the mutations of note share many similarities with Omicron, they have not as yet appeared in human patients — or at least have survived undetected in sequencing. They don’t currently appear to present any extra risk to humans.
Some scientists suspect these ‘cryptic lineages’ may come from virus-infected animals, possibly the city’s enormous population of rats that skitter around the metropolis, or from cats or dogs.
In a paper published today in Nature Communications and reported in the New York Times , the scientists say these viral fragments may lead to the emergence of new variants resistant to naturally acquired or vaccine-induced immunity.
Because wastewater samples contain an amalgam of lineages — so called because they are of common descent from a known virus — the report says it is not possible to reconstruct individual genomes using standard methods. About twice a month since June 2020 they have been sequencing SARS-CoV-2 RNA isolated from the raw influent in all 14 city wastewater treatment plants. In January 2021, the Times writes, they began doing targeted sequencing of the samples, focusing on parts of the gene for the virus’s all-important spike protein.
Eventually, they saw that even these cryptic lineages had mutated in that time.
The researchers found that these lineages appeared repeatedly at just a handful of the 14 treatment plants, but won’t divulge their locations. Most polymorphisms remained within their own sewershed, but one location’s traces were found in a neighbouring treatment plant’s wastewater.
Four treatment plants were singled out for more detailed study. Each of the lineages found in them contained at least five polymorphisms, and one showed 16. Some contained similarities to Omicron and several showed resistance to some antibodies.
Consideration was also given to population movement in the city. The researchers were challenged by the fact that New Yorkers, and any variants they may have been carrying, generally move widely throughout the city — although numbers were far reduced from pre-lockdown periods.
But having been able to pin it down to a very small area of the sewershed suggests to the authors that it is not a contagious human pathogen.
John Dennehy, a virologist at Queens College in New York and an author of the paper, speculated that the sequences could be coming from people who are confined to long-term health care facilities in just a few areas of the city. But he has not been able to prove it.
Alternatively, the researchers noted, the cryptic lineages may exist in areas of the body standard swabbing tests aren’t covering. It’s possible these lineages “predominantly replicate in gut epithelial cells and are not present in the nasopharynx….”
Many scientists theorize that Omicron emerged from an immunocompromised patient and, indeed, people who have compromised immune systems may have more difficulty fighting off the virus, giving it more opportunities to mutate.
This is a very promiscuous virus
Virologist Marc Johnson
As the wastewater sources have been narrowed down to a certain few locations, University of Missouri virologist Marc Johnson is of the mind that the sequences are coming from animals — likely a few specific populations with territorial bounds. Supporting his theory is that in May and June of 2021, when the number of human COVID-19 cases in New York City was low, more of the odd lineages showed up in the viral RNA in wastewater, suggesting that they may have come from a non-human source.
The researchers initially considered that the source might be squirrels, skunks, dogs, cats and rats. “This is a very promiscuous virus,” Johnson told the Times. “It can infect all kinds of species.”
The wastewater again yielded more information, as the animals leave behind other genetic traces of themselves. Johnson created pseudoviruses with the same mutations as in the cryptic lineages. With them, he was able to infect both mouse and rat cells. While the original version of the SARS-CoV-2 virus does not appear able to infect rodents, some variants, such as Beta, can.
But, so far, there have been no signs of the virus in blood and fecal samples from local rats.
“Maybe we’re not hitting the right animals,” Dennehy said.
It has been shown that humans can pass the virus to animals, and the concern is that it may mutate there and emerge to reinfect humans.
But no evidence indicates that the virus is circulating in wild rats, and in any event it is not known how humans could have infected them.
The team is looking to other states for potential clarification on the cryptic lineages’ origins. So far, similar results have been found by scientists studying wastewater at University of California, Berkeley.
They also analyzed data “from nearly 5,000 other wastewater samples globally spanning 2020–2021, including 172 samples from New York state,” the report states. “Of all samples, only seven, all from N.Y. state sewersheds, had sequences resembling the lineages we described.”
“Nothing makes perfect sense,” Johnson said, “but we will know eventually.”
Former senior civil servant and diplomat Norman Spector shared a fascinating article with me this weekend from the Ottawa Citizen.
A family physician in the national capital, Dr. Nili Kaplan-Myrth, hoped to conduct mass vaccinations for people who want a fourth dose of COVID-19 but don’t qualify under Ontario’s rules.
She reportedly wanted to create a large outdoor “jabalooza” clinic but health officials refused to provide her with vaccines.
Ontario restricts access to fourth shots of COVID-19 vaccines to those who are 60 years of age or older.
Next door in Quebec, people can get fourth shots if they are 18 and older.
“I am receiving lots of individual requests for help,” Kaplan-Myrth tweeted on Sunday (June 26). “I can’t give you the vaccine at this time, but hands up (and DM) if you as plaintiffs want to bring this to court as a group. Would require a litigation team.”
There’s a tremendous amount of scientific data showing that COVID-19 vaccines lessen the severity of COVID-19. They reduce the likelihood of dying or being hospitalized from the disease.
However, COVID-19 vaccine effectiveness wanes over time. This is why Kaplan-Myrth is such a strong advocate for booster shots. She believes that these boosters are particularly important when so many people are not wearing masks indoors.
Keep in mind that COVID-19 initially presents as a respiratory infection.
In some cases, however, it causes serious brain injuries and cardiovascular problems. It’s especially dangerous for the immunocompromised, who are at higher risk of suffering severe COVID-19.
That’s because the virus that causes COVID-19 not only damages blood vessels and triggers blood clots, but also disrupts the immune system. Researchers have even linked immune dysfunction to serious brain injuries, which is explained in the video below.
In the face of all of this, B.C. continues adopting a hard line on the distribution of fourth vaccine doses.
This is the case even after Global News B.C. reporter Richard Zussman revealed that 226,000 doses intended for the vaccine-hesitant will expire at the end of July.
In B.C., you have to be 70 years of age or older and have gone six months since a previous COVID-19 vaccination to qualify for a fourth dose.
There are exceptions: Indigenous people, for example, can get a fourth dose if they’re 55 or older.
Below, you can read other exceptions listed by the B.C. Centre for Disease Control for those between the ages of 60 and 69.
However, when the Georgia Straight asked the Ministry of Health about who qualified for a fourth COVID-19 vaccination, it did not include what’s written after the letter “d”: “Caregiver of a frail elderly or moderately to severely immunosuppressed person”.
So it remains unclear in B.C. if a person between 60 and 69 who is a caregiver for either a frail elderly person or a moderately to severely immunosuppressed person is able to receive a fourth COVID-19 vaccination.
Yet it seems pretty clear from the exemptions above that if you are a cancer survivor or have kidney disease or have heart disease or have multiple sclerosis or have had a transplant and you’re under 70 in B.C., you will not qualify for a fourth COVID-19 vaccination under existing rules.
Why is B.C. being more restrictive with COVID-19 booster shots than Ontario, Quebec, Saskatchewan (where you only need to be 50-plus), as well as the entire United States?
Health Minister Adrian Dix needs to come clean on that.
What possible justification is there for withholding a fourth COVID-19 shot for British Columbians under 70, especially the immune-compromised, when 226,000 vaccine doses are set to expire next month?
Why is Dix so convinced that he knows better than the governments of Ontario, Quebec, and Saskatchewan?
We don’t know the answer.
That’s in part because our pusillanimous B.C. Liberal MLAs refuse to hold the provincial NDP government accountable for its COVID-19 policies.
Some on social media are speculating that the booster shots are being withheld as part of a population-level experiment—conducted without the people’s consent—on the efficacy of delaying second booster shots.
Dix and provincial health officer Dr. Bonnie Henry, through their actions, are giving oxygen to this hypothesis.
Who knows? There might even be a scientific justification for withholding booster shots.
But in the absence of evidence provided by the B.C. government, the health minister must get in front of a microphone on Monday (June 27) and provide a coherent explanation.
Failure to do so will only fuel more suspicion about the motives behind the government’s policy.
Perhaps it’s worth noting that in January 2021, Science published a study involving 188 people, which offered a glimmer of hope.
It showed that more than 95 percent of those who had recovered from COVID-19 had immune systems demonstrating “durable” memories of the virus, lasting up to eight months.
This prompted speculation on the National Institutes of Health website that the immune systems of those who are vaccinated would have lasting memories of the virus.
But a study of 188 people is insufficient as the basis for an entire provincewide policy.
Some might wonder if the government isn’t making fourth doses of COVID-19 vaccines available to those under 70 because of the cost of distribution or due to the labour shortage in the health-care sector.
Others might suspect it’s because the B.C. government thinks everyone is going to get COVID-19 anyway, so why bother?
If that’s the real reason, it’s a monumental disservice to those with compromised immunity. This should demand a response from Human Rights Commissioner Kasari Govender that goes well beyond writing a letter to Henry. Like by holding a public inquiry under section 47.15 of the B.C. Human Rights Code.
In the meantime, show us the evidence, Minister Dix, for why so many British Columbians are being denied a fourth COVID-19 vaccination.
And if you’re unwilling to do that, then please step aside so another health minister can do this in your place.
They are finally here! Vaccinations against COVID-19 were at last approved for the youngest people ages 6 months to 5 years old. Studies in children have been done showing definite protective benefits and no major adverse reactions occurring. The first step was the FDA approval after an advisory panel deliberated the week of June 13 — only 2 days — to vote unanimously to recommend authorization, stating the benefits outweigh any risks for young kids.
The CDC signed off on the vaccines June 18 with another unanimous vote. The two vaccines consist of the Pfizer mRNA version in adults, but a much-reduced dose of 3 micrograms instead of 30 micrograms, given in three doses to induce a high level of antibodies equivalent to young adults. The first two doses are spaced three weeks apart, and the third at least two months later. The study found only 10 COVID cases in the three-dose group and seven in the placebo group for an efficacy of 80%. The study included only a small number of patients. Most of the infectious disease and pediatrician experts cautioned not to lose sight of the fact that the vaccines were saving children’s lives.
The Moderna mRNA vaccine is the same as the adult one but only a quarter of the dose at 25 micrograms in a two-dose series given four weeks apart. Both this and the Pfizer vaccine achieved the same levels of immunity that have protected young adults against severe disease. None of the developed COVID vaccines have achieved the ideal of elimination of the infection. But they have saved many lives.
In children, the risk from COVID is very real, even though hospitalization and deaths are lower than in adults. In children ages 1-4, COVID is the fifth leading cause of death. One source that looked at the period from January 2020 through May 2022 said 202 kids in this age group died from COVID. Another source quoted 480 kids dead from COVID. That’s more deaths per year than hepatitis, meningitis, rotavirus, and other common infectious diseases each caused before routine vaccinations for them were recommended. And the risk wasn’t limited to any particular group. More than half of the youngsters hospitalized due to COVID had no underlying conditions.
These vaccines have proven to be some of the safest of any for adults. In the preliminary studies in this age group the adverse reactions/side effects were mostly mild and short lived, much like those in adults, and similar to those from other vaccines. The main one was pain and redness or tenderness at the injection site. There might be some irritability, fatigue, or sleepiness, loss of appetite, headache, abdominal pain or discomfort, mild diarrhea, vomiting. But everyone got better quickly! Fevers were uncommon and mild in the participants. Those can be treated with acetaminophen.
A pediatric infectious disease specialist at Children’s Hospital, Denver, Colo., said it’s important to keep in mind that COVID-19 is now one of the vaccine-preventable diseases with the highest mortality rate. Hospitalization rates for children with COVID were five times higher during the recent wave than the worst previous points of the pandemic. Katherine Poehling, director of pediatric population health at Wake forest School of Medicine, said, “I am struck by these numbers. I’m also concerned there’s a real underappreciation of the potential severity.” FDA commissioner Robert Califf said, “Any death of a child is tragic, and should be prevented if possible.”
It’s a guarantee that, if a respiratory germ gets into a home, it gets into everyone living there. It may not take hold in each individual to create what we call disease for a host of reasons, but the microbe made the rounds, positive test or not. That includes every kid kissing you or sharing food with you.
The COVID variants currently crawling down our craws are killing fewer Americans daily than during any other period except the summer of 2021. But the country is now recording 10 times as many cases as it was at that time, indicating that a smaller number of cases are causing deaths. But COVID is still killing an average of 314 people a day. These darling little Petri (not “peach tree”) dishes we parents and grandparents love to hug and kiss can be vectors of so many viruses. The vaccines are a tool to help prevent that spread and contagion. It’s an incomplete tool, but it’s part of a larger effort to stop infections, along with hand washing, etc.
Maybe you could liken it to a fork among our eating utensils. We could eat most everything on the plate with that fork, but a knife and spoon sure help us to divide and down the delectables we can’t spear. The vaccines are essentially safe and a valuable tool. One preventable child’s death is one too many. Get your tot shot!
Dr. Bures, a semi-retired dermatologist, since 1978 has worked Winona, La Crosse, Viroqua and Red Wing. He also plays clarinet in the Winona Municipal Band and a couple dixieland groups. And he does enjoy a good pun.
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A vial of the Moderna COVID-19 vaccine for children six months through five years old is seen, June 21, 2022. /AP
There is now a second COVID-19 option for kids aged six to 17 in the U.S.
The U.S. Centers for Disease Control and Prevention (CDC) on Friday announced it is recommending Moderna shots as an option for school-age kids and teens. This group has been able to get shots made by Pfizer since last year.
CDC sets the federal government’s vaccine guidance for U.S. doctors and their patients.
Last week, the Food and Drug Administration authorized the shots – full-strength doses for children ages 12 to 17 and half-strength for those six to 11. The doses are to be given about a month apart. An expert advisory panel this week voted unanimously to recommend that CDC endorse the Moderna shots, too.
Moderna officials have said they expect to later offer a booster to all kids aged six to 17.
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