There are a few signs that the COVID pandemic is waning in the U.S., with this January 2023 being less severe than January 2022. Cases, hospitalizations and deaths are all slightly dropping, according to data from the Centers for Disease Control and Prevention. But our baselines have shifted, changing our definition of normal. These metrics, especially deaths, are still much higher than we've tolerated historically. And while things aren't as bad as they were a year ago, as we've seen many, many times throughout the pandemic, it has a way of roaring back when we drop our guard.
Experts are especially concerned with the virus jumping from humans to animals and then back again, each time presenting new opportunities for novel mutations in different creatures. And many experts are worried that we aren't doing enough to monitor the situation, meaning a nasty and surprising new variant could emerge from this viral game of human-to-animal-to-human ping-pong.
"This back-and-forth transmission is also called 'ping pong zoonosis' or 'zooanthroponosis' too, as in the case of a circulating SARS-CoV-2 variants like BQ.1.1 or BF.7 getting passed on from humans to mammals."
Certainly, things have changed a lot since the initial 2020 outbreak. We have excellent vaccines for the virus and we know that high-quality masks are effective at mitigating the spread. We also have many drugs and therapies to fight SARS-CoV-2, the virus that causes COVID.
But, as viruses do, SARS-CoV-2 keeps mutating. Viruses are pathogenic microorganisms that may or may not be alive (scientists still actively debate this question). When they infect us, they hijack the genetic code of our cells to make copies of themselves. These viral Xeroxes can be kind of sloppy and the mistakes can either make the virus more destructive or less. This is normal and even expected.
The less concerning viruses tend to fizzle out. But the more concerning variants — think alpha, delta or the many off-shoots of omicron — can spread global illness, disability and death. As immunity wanes — also a normal and expected problem with coronaviruses — slightly different variants of the virus can evade our bodily defenses and whatever therapies we throw at it, though vaccines remain effective against severe illness and death.
Experts have been carefully monitoring for problematic mutations since SARS-CoV-2 was first sequenced in January 2020. A new paper in the journal Nature Reviews Microbiology attempts to summarize some of these recent changes and help public health experts attempt to handle them.
It won't be easy. The authors, which include Prof. David Robertson, a virologist at the University of Glasgow, detail the many ways in which the has virus mutated to evade our immunity, both from vaccines and recovering from sickness. (Getting a shot in this case is less likely to prevent you from getting sick, but vaccines still broadly protect against dying and hospitalization.) There are a couple of "unpredictable implications," they observe, that are especially concerning.
The first is the virus could spread from humans to animals and back again. The second is that we're not doing enough to monitor for these mutations by doing less sequencing, which is a method of studying the contrasting genetic makeup of organisms — sort of playing a very complex, tiny version of spot-the-difference.
"There are many countries with low sequencing capacity, or places with previously good surveillance that are decreasing or phasing out sequencing altogether," Robertson and his colleagues wrote. "This is troublesome as a lack of genomic surveillance will mean future variants will be detected much later or could be circulating at low levels before eventual detection. There is, thus, a need for widespread and equitable surveillance coverage to rapidly detect potential new [variants of concern] among these individuals and communities before they spread more widely."
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When a virus jumps from animals to humans, it's called zoonosis, from the Greek zōon "animal" and nosos "disease." So far, there isn't much evidence that animals are spreading COVID to us, even though we've done it to them multiple times. (Of course, the prevailing theory on SARS-CoV-2's origin is that it came from bats.) Once COVID went global, humans shared it with deer, dogs, hamsters, zoo animals and many other mammalian species. But no creature has absorbed more virus from us than mink, a species in the weasel family which are farmed for their fur.
Dr. Rajendram Rajnarayanan, an assistant dean of research and associate professor at the New York Institute of Technology campus in Jonesboro, Arkansas, has been following these reverse zoonotic transfers for a while. He's counted 133 cases in cats, 323 in deer and 1,320 in mink. In general, mink farms are a bad idea, with some also spreading avian flu recently.
Animal reservoirs are why smallpox was able to be eradicated in the '80s through a global vaccination campaign — because, quite simply, there aren't any animal reservoirs for smallpox.
"This back-and-forth transmission is also called 'ping pong zoonosis' or 'zooanthroponosis' too, as in the case of a circulating SARS-CoV-2 variants like BQ.1.1 or BF.7 getting passed on from humans to mammals," Rajnarayanan told Salon in an email. When this happens, it creates a "reservoir" for the virus, a place for it to always hide and potentially spring back. We see this with the occasional bubonic plague outbreak, which is caused by the bacteria Yersinia pestis and lives in wild rodents like groundhogs. Thankfully, while plague killed millions in the Middle Ages, today it is treatable with antibiotics.
We aren't always so lucky. To use one example, the H1N1 influenza virus that caused the 2009 pandemic is sometimes called a "quadruple reassortant" virus, because segments of the virus originated from humans, birds and two species of pigs, North American and Eurasian. This is an example of reverse zoonosis that the CDC estimates killed more than half a million people globally.
Animal reservoirs are why smallpox was able to be eradicated in the '80s through a global vaccination campaign — because, quite simply, there aren't any animal reservoirs for smallpox. Animals can't spread smallpox, therefore they can't hold onto it and give it to us. That's not the case with COVID or other viruses, like Ebola or mpox. As with bubonic plague, it is unlikely we'll ever totally eradicate any virus, bacteria or pathogen that naturally occurs in animals.
"Animal reservoirs also keep a lineage in circulation and potentially reintroduce it back into circulation at an opportune moment," Rajnarayanan said.
"Just as many pathogens can move from non-humans to humans, some can also move from humans to non-humans," Dr. T. Ryan Gregory, an evolutionary and genome biologist at the University of Guelph in Canada, told Salon in an email. "The result could be that even if we manage to eliminate the pathogen from human populations, it could show up again later and cause an outbreak by jumping back into humans from another species. [Additionally], if a pathogen is circulating in another species, then it will be evolving under the conditions of that species' immunity, which is likely to be different from ours. This could result in a variant that is quite different and against which we would not have strong immunity if it moved back to humans."
As we approach the third anniversary of COVID stay-at-home orders and the initial (justified) panic of the pandemic, so many people are so exhausted they've declared that the pandemic is over. On January 17th, Rep. Brett Guthrie (R-KY) introduced the "Pandemic is Over Act," a bill sponsored by more than a dozen other House Republicans, with the aim of overturning the public health emergency Americans entered in spring 2020. But President Joseph Biden said essentially the same thing a few months ago, though his quote that the pandemic is "over" was mostly taken out of context.
Yet, the pandemic is not over. Not only are thousands of people still dying per week, China is currently undergoing one of its worst outbreaks yet, with an estimated 80 percent of the population (some 1.12 billion people) getting infected in the latest wave. Each infection is a new opportunity for the virus to mutate into something our defenses will struggle against. While there's no guarantee China's outbreak will create huge problems for the rest of the world, we did see omicron and delta emerge from similar waves in South Africa and India respectively.
Meanwhile, as the Nature Reviews Microbiology paper noted, many countries are dialing back the surveillance precisely when we should be monitoring for new variants to emerge, from animals or otherwise. Right now, we have about 700 sub-lineages from omicron, according to Rajnarayanan, which is sometimes called a "variant soup." It's worth noting that climate change is a big reason for all the recent pandemics and viral illnesses are predicted to worsen as the planet warms.
"Variant evolution is becoming increasingly complex, and it is as important as ever to detect, characterize, and track variants as they evolve and spread," Gregory said. "Wastewater is especially useful in identifying the presence of 'cryptic' variants, meaning ones that are not in wide circulation but are still potentially important."
Unfortunately, some conspiracy theorists want to blame this whole mess on vaccines, even though that's not how vaccination works. While immunity from either vaccines or past infection do create an important selective pressure, according to Gregory, it is overwhelmingly infections that are driving variant evolution.
"Ultimately, it's having a lot of virus circulating, mutating, and being subject to natural selection that is the biggest issue," Gregory said. "That's why mitigation is also important. Vaccines do a good job at preventing severe acute illness, but they aren't stopping transmission and thus we need other measures. Fortunately, the ones we have available such as wearing high quality (N95) masks, ventilation, air filtration, and reducing indoor crowd sizes are all variant-proof."