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We Now Face an Army of COVID Viruses

The pandemic has not ended. It is evolving, with big implications. Here are six.

Andrew Nikiforuk 30 Jan

Tyee contributing editor Andrew Nikiforuk is an award-winning journalist whose books and articles focus on epidemics, the energy industry, nature and more.

“There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”  — The Origin of Species, Charles Darwin

What began as an airborne pandemic driven by a single virus has become a viral cloud roiling around the globe thanks to public policies that have allowed unfettered transmission.

As a consequence the pandemic now represents different threats in different regions for different classes of people at different times. The wealthy elite attending Davos may be protected by tests and clean air machines, but the rest of us face contrasting realities.

Some virologists have argued that people shouldn’t be concerned by these evolutionary doings, and that the messy world of Omicron subvariants is better left to the experts.

But that’s a patronizing attitude. The pandemic affects us all, demanding citizens make decisions individually and together. So the point is not to be complacent or alarmed, but curious and attentive. We have entered an epoch of biological volatility and the risks this entails demand constant vigilance.

Here are six observations on viral evolution and how it may shape our lives in this, the fourth year of the pandemic.

1. One virus has become many.

We no longer face one viral foe or a single variant such as Delta. Omicron has produced four lineages of genetically diverse descendants morphing into an ever-growing swarm of 700 subvariants referenced by a confusing jungle of numbers and letters. What was once a single violin has become a complex and expanding orchestra with no discernable conductor. Even virologists now have trouble keeping track of where the variants are coming from, and what their different mutations mean.

Our actions, or inactions, are driving this evolution. Current policies allow unimpeded transmission. And in that context, vaccines and anti-viral treatments, despite their obvious life preserving benefits, have created conditions under which the virus is evolving rapidly.

Some variants have become immune evasive. Others have become more transmissible or adept at binding to human cells. Many mutations have rendered antibody treatments totally ineffective. A study showing the descendants of BA.2 and BA.5 have become more pathogenic. There is no shortage of new variation thanks to a high mutation rate, and variants continue to beget new descendants in an ever-expanding viral family tree.

By naming the latest subvariant XBB. 1.5 "Kraken" after a legendary squid-like sea monster, the Canadian evolutionary biologist T. Ryan Gregory has done the world a small favour. People tend to pay attention to things we name and that name served as a reminder that this new viral swarm is mutating at an accelerating pace. One star has become a viral nebula.

2. The new COVID soup is a unique experiment in evolution.

As leaders have shifted to the position that masks and tests are matter of personal choice rather than collective self-preservation, they have implicitly silenced a vital message to the citizenry about how pandemics actually come to an end. It is this: less transmission means fewer mutations; fewer mutations means less variation, the fuel of evolution. Reducing infections, then, puts the brakes on viral evolution.

The combined actions of “letting the virus rip” in a population with varying degrees of protective and waning immunity created by vaccines or previous infections “has led to unprecedented increase in viral diversification in 2022,” as one group of researchers explained in a recent paper published in the International Journal of Molecular Sciences.

“The scale at which SARS-CoV-2 has spun off new variants and lineages appears unprecedented in modern virology history,” conclude the researchers. (Humans are but a footnote in viral history.) And those 700 Omicron subvariants are converging towards evasion of human immunity.

Welcome to our current pandemic paradox. About two-thirds of the world have been vaccinated. These vaccines can prevent death and disease, but not infection. They reduce the risk of long COVID, but only provide partial protection against it. The effectiveness of many vaccines are now waning in many jurisdictions against more immune-evasive variants.

At the same time people’s vaccine hesitancy has sharply increased, despite research that shows bivalent boosters save lives.

So the many subvariant descendants of SARS-CoV-2 have no trouble finding human hosts. As they replicate, they mutate and behave as Darwin would have predicted. Evolutionary pressure on the virus selects variants that can escape drugs or vaccine-prompted immunity in addition to immunity elicited by prior infections.

In the Molecular Sciences paper, the researchers conclude that letting the virus rip and pursuing a vaccine-only approach to the pandemic has “produced a remarkable natural experiment in viral evolution for which we cannot discern its conclusion.”

Meanwhile the genomic surveillance of these multiplying subvariants is decreasing around the world. That means less transparency and fewer early warnings about more dangerous variants.

3. What were viral peaks are now a constant rising sea of infections with high and low tides.

The pandemic no longer resembles an elegant graph composed of peaks, valleys and occasional lulls in infection, death and disability. The new viral swarm, as evolutionary biologist Gregory has cogently explained in interviews, is producing not one or two waves but a sustained succession of waves, including four last year in Canada and five in the U.K.  

In other words the pandemic has gone from an acute emergency (sudden death and clogged hospitals) to an ongoing chronic reality (chronic disease and clogged hospitals plus waves of excess deaths).

Gregory asks: What are the consequences of a rising sea of infections as opposed to tsunamis? And answers: “Sustained pressure on health-care systems with no major lulls anymore. In fact, the lows over the past Omicron year exceed the peak during Delta.”

Result: Canada experienced its worst death and hospitalization rate for the virus in 2022.

Christina Pagel, a British scientist, recently described the same phenomenon in the U.K. “So 2022 was a year when the virus ran free with five waves, over 135,000 hospital admissions, 33,000 deaths and more than 650,000 new people with long COVID. Hardly the end of the pandemic. This has certainly contributed to NHS crisis & people leaving employment.”

Australian infectious disease expert Brendan Crabb has documented the same impact in his country: rising excess deaths, overwhelmed hospitals and continuous infections.

Sustained levels of infection mean chronic dysfunction: clogged hospitals, declining life expectancies, slow ambulance service, sick-ridden schools, the menace of long COVID and the loss of grey matter.

4. One pandemic has morphed into regional epidemics.

The pandemic no longer presents one face to the world because it has become a multi-headed hydra. As a consequence it behaves differently in different regions. While one subvariant like Kraken may triumph in the U.S., another variant Orthrus may take possession of the U.K.

Meanwhile a collection of other variants including BF.7 are conquering China as it abandons most pandemic defenses in the name of the global economy and progress. A handful of subvariants likely will kill more than a million people in China this spring in what can only be described as a humanitarian catastrophe.

Diversification in variants also means deaths may be going down in some countries but rising in others at any given time. Sweden, which took a laissez-faire approach to the virus with few protections, is now recording its highest pandemic death rates: about 300 a week. Swedish newspapers are largely yawning.

Japan once boasted the lowest infection and COVID death rate in the world despite an aging population. But more transmissible subvariants have fuelled Japan’s seventh wave and its highest death rate — nearly 520 day. Since December COVID has dispatched more than 10,000 Japanese citizens. The majority have been over the age of 60. Nearly 40 per cent of Japan’s population is over the age of 65.

One Indian specialist explained the situation: “These new subvariants are bypassing the vaccine/booster immunity so far achieved in the populations. Therefore, a fresh COVID-19 pandemic is emerging the world over with new medical challenges.”

5. Reinfections rarely happened. Now they are commonplace.

Ever since the appearance of Omicron and its multiplying lineages, researchers have reported a dramatic change in the pandemic. Reinfections, once a rare thing, have taken off.

Factors accounting for this change are the reduction of measures that reduced transmission such as masks in crowded spaces and staying home while sick, combined with the evolution of immune-evasive subvariants.

As a result people in Australia have been infected as many as five times in a year. Public health authorities there have warned that reinfection can occur as early as 28 days after the first.

The Canadian government now says that reinfections can occur within 20 to 60 days.

This increase in reinfection rate has helped to fuel a major disabling event in the general population: long COVID. About one in ten infections lead to this debilitating condition, which mostly affects working adults, and especially women.  

Long COVID targets multiple organs including the brain and heart and presents with vascular and clotting abnormalities. It is currently not treatable. Researchers don’t know why the virus can reduce healthy and athletic adults into patients who can barely walk or complete a thought.  

There is reason to worry that COVID’s new viral soup might make subvariants more likely to cause long COVID.

A preprint study, not yet peer reviewed, offered this finding: “Long COVID diagnoses also occurred much closer to the index date following both initial or first reinfection in the Omicron BA epoch as compared to earlier Delta and Omicron epochs. The rate of long COVID diagnoses has been increasing for reinfections in more recent variants.”

Last year a Nature study established that reinfections, whether mild or acute, are not benign. The study, which drew upon health data from a large population of U.S. veterans, found that people with reinfections “were twice as likely to die and three times more likely to be hospitalized than those with no reinfection.” The risk of developing lung problems, strokes, an irregular heartbeat, gut problems and brain damage all increased in people with repeat infections compared to those who had only been infected once.

U.S. epidemiologist Ziyad Al-Aly, the lead author of the Nature study, recently said that COVID “is teaching us that there is a clear line between infections and chronic disease.” The multiplication of subvariants and the rise in reinfections have also changed the complexity of the pandemic.

In recent comprehensive review of long COVID, researchers lead by U.S. scientist Eric Topol noted vaccines only reduce the risk of long COVID by 14 to 41 per cent.

There are also critical differences between variants according to the U.K. government.

The debilitating condition appeared to be more common with Delta among the double vaccinated than with Omicron BA.1. But the odds of developing long COVID in the triple vaccinated increased with Omicron BA.2. As evolutions continue, as Topol’s study noted, “The different SARS-CoV-2 variants and level of [and time since] vaccination may impact the development of long COVID.”

Another area of research to keep a close eye on is tracking what effect COVID has on the immune system’s strength in dealing with subsequent infections in both adults and children.

After China’s government let rip Omicron subvariants, reinfections became common and often worse than the first infection. Radio Free Asia recently reported that health-care workers were encountering “a very large number of reinfections in out-of-town areas, due to the damage done to the immune system by the first infection with COVID-19."

6. We can do more to blunt the evolutionary threat of COVID subvariants.

So the pandemic is not over. Viruses, one of the most abundant entities on this planet, don’t stand still. They mutate. They shift. They adapt.

The more a virus transmits, the more opportunities it can exploit to change its shape and character. Infections and repeated infections where random mutation and non-random natural selection lead to variants better adapted to the environment in which the viruses survive and reproduce — namely us.

We can do better at recognizing this reality and collectively respond to save lives and limit constant waves of infection. We can:

Such public discourse must acknowledge hard truths about the risks of repeated infection, long COVID and uncertainties about the changing burden of disease.

From where we stand today, viral evolution, which is never linear, can pursue many futures, as evolutionary biologist Gregory has written. 

An immunocompromised host could produce a variant capable of launching another major wave like the original Omicron.

Animal reservoirs could add something surprising or nasty to the evolutionary party, too.

China’s explosion of infections in 1.4 billion people could generate its own bold new variant.

Two viruses with wildly different parents could recombine in human hosts and also alter the pandemic.

Or one of Omicron’s four lineages could evolve in a different direction altogether. 

In any case the pandemic will continue to evolve.

Will our response?  [Tyee]

Read more: Health, Coronavirus

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