Do Not Underestimate The Consequences Of SARS-CoV-2 Escape: The Omicron Example

(Posted on Thursday, February 17, 2022)

From the outset of the Covid pandemic, the extent to which the virus SARS-CoV-2 might vary was seriously underestimated. We all recall when leading national and international healthcare authorities assured us that because the virus had a “proofreading” activity, it was unlikely that the fundamental characteristics of the virus would change.

The history of the pandemic—the story of the Omicron family of viruses in particular—has shown just how misguided such early optimism was. Some of us were more cautious. We warned that coronavirus infections typically return year after year to reinfect populations infected just the year before. Such is the case for the four human cold-causing coronaviruses that sweep the globe every year. Such is also the case for chronic infection of long-lived bats, cats, and many other species.

Coronaviruses seem uniquely well-adapted to reinfecting immunocompetent adults infected just a few months prior. That is why I was dismayed by the early assurances that we would quickly reach “herd immunity” (a term I intensely dislike), and we would need to worry no more. A few of us warned that not only was the concept of “herd immunity” flawed but deadly dangerous to countries that embraced it. Sadly the idea of “herd immunity” lives on, many suggesting that the Omicron is a blessing in disguise and that the virus will now infect so many we can now relegate Covid to the status of a disease like influenza with which we can live.

I argue it is unwise to dismiss the potential of the disaster that may come about with a future virus variant that combines the transmissible characteristics of Omicron with the lethality of SARS and MERS. Is such a scenario guaranteed? By no means. Is such a scenario within the realm of the possible? Absolutely. Each of us may assign a probability to such a catastrophe. I place the odds at about fifteen percent over the next few years. I am sure that is one of the most pessimistic estimates. Given what we know today, no one can, in good faith, place the odds at zero.

Three Dimensions of Virus Variation that Determine Pandemic Severity

Transmission: How contagious is the virus? How likely is it that a person with the infection will transmit it to others? The Omicron family shows displays a dramatic increase in transmission from earlier variants, demonstrating how SARS-CoV-2 may rapidly alter infectivity via variation.  

Immune Evasion: Will the virus evade neutralizing antibodies raised by prior infection or vaccination? The Omicron variants are far more immune evasive than previous variants, capable of infecting most of those previously infected or vaccinated.

Virulence: How virulent is the infection? How many people infected will fall seriously ill or die? Mercifully, the Omicron variants are less virulent than their immediate predecessor, the Delta variant. However, the very fact that the virulence of SARS-CoV-2 does vary should be cause for concern if not alarm.

Protection Against Severe Disease and Death

There is some positive news. Vaccination is extraordinarily effective in protecting against severe illness and death for most. Moreover, for many protection outlasts the transient protection against infection offered by neutralizing antibodies

The biggest question in predicting how serious the pandemic will become is how long protection against the severe disease a death may last. A second question still outstanding is to what good fortune we owe such protection.

Scientists and doctors are working around the clock to unravel both questions. One answer—how long such protection lasts—will only come with time. We have hints but no definitive answer to the second question of exactly how, once vaccinated, our bodies protect us from severe disease. Recent studies show that long-term protection from Omicron may not be universal. Up to 20% of those previously infected, vaccinated, or both fail to mount strong CD8+ T-cell responses to the Omicron Spike protein required to protect against hospitalization and death. SARS-CoV-2 variants have the potential to escape both antibody and T-cell immunity. Until we know how widespread such resistance may arise, we wonder whether the following variant may overpower even our most robust defenses.

Determinants of Virus Variation

So now on to the fundamental properties of the virus that determine transmission, immune evasion, and virulence.

Transmission 

Multiple virus characteristics influence the transmission of SARS-CoV-2. These include:

Peak Virus Particle Concentration

The peak concentration and location of virus particles in an infected person are important determinants of transmission. The sheer number of virus particles in nasal secretions is amazing, varying at the peak from 100 million to ten billion or more. SARS-CoV-2 is also shed in urine and feces.

Variants differ in the concentration of shed virus by orders of magnitude. The peak concentration of the Delta within nasal fluids is about one thousand times higher than that of earlier SARS-CoV-2 variants. However, a high viral load is not in and of itself a guarantee of greater transmission. Yes, Delta is about twice as transmissible as earlier variants, but Omicron is twice as transmissible as Delta without increasing peak viral loads. We still have more to learn.

Speed and Duration of Virus Growth

Variants differ in how rapidly they reach peak concentration. They also differ in the number of days a person remains infectious. Omicron replicates much faster than does Delta. In cell culture, recent data shows that Delta and Omicron follow similar trajectories with respect to the kinetics of infection, the peak viral load, and the time to viral clearance in naive and well-vaccinated individuals.

Stability

The stability of the released virus particle in aerosols, droplets, and surfaces will influence transmission. Recent evidence suggests that Omicron virus particles remain infectious longer than earlier variants. The longer the virus lives once released, the likelier it may infect another. There are reports that infectious virus particles may hang in the air for over half an hour in enclosed spaces.

Receptor Avidity

Once released, the virus must attach itself to the surface of an infected cell. The primary site of binding of SARS-CoV-2 is a surface protein called ACE2. The receptor is present on the surface of some cells that line nasal passages, upper and lower airways, and the lung.

SARS-CoV-2 variants differ in how tightly they bind the receptor. Some of the earlier variants bound ACE2 much more weakly than later variants such as Delta. Omicron binds to ACE2 more tightly than the earliest variants but less tightly than Delta.

Can SARS-CoV-2 virions become more avid than those naturally observed? Laboratory experiments demonstrate that the association of the virus to the cell can become tighter several hundredfolds, raising troubling possibilities. I should mention that there is evidence that ACE2 binding is not the only means by which SARS-CoV-2 attaches and enters cells.

Cell Entry

One of the most surprising characteristics of the Omicron viruses is the mode of entry. The original Wuhan variant, and all prior SARS-CoV-2 variants, enter cells via fusion of the virus and cell membranes. This is not so for the Omicron viruses. After attachment, the virus particles are surrounded by the cell membrane and transported to the interior. The virus then bursts through this enclosure to enter the cell, called endosomal entry. Endosomal entry is the most unanticipated feature of Omicron.

By itself, the endosomal entry does not account for all the unusual properties of Omicron. SARS-CoV-1, the cause of the SARS epidemic, enters cells via the endosomal route yet is far less transmissible and far more lethal than are any of the SAR-CoV-2 variants.

The takeaway from these observations is that SARS-CoV-2 can alter fundamental characteristics relevant to transmission. We have yet to understand the full range and disease implications of such changes.

Replication Rate

The rate at which a virus replicates once it enters the cells is determined by many factors, some of which we understand, most of which remain opaque. My conservative estimate is that the rate of replication is determined by the concerted action of at least twenty-five of the thirty viral proteins and their interactions with literally hundreds of cellular proteins and RNAs. It will require generations of dedicated work by scientists to understand the replication process in sufficient detail to predict the course of viral evolution.

Experiments to date allow us to variation in replication through a glass darkly. One of the earliest variants noted is a single nucleotide change in the 5’ translated region, changing from a C to a U at nucleotide 241. The change occurs at the tip of a conserved stem-loop structure. This single base change increases the rate of virus replication in laboratory experiments. Moreover, changes in a small set of amino acids of the viral nucleocapsid proteins (N), at positions 199 to 205, increase the virus’s replication rate in culture by over a hundredfold. Such significant changes in a fundamental virus trait, such as replication rate altered by such a slight change in the genome sequence, one nucleotide of 30,000, should give us an appreciation for the power of tiny changes in the genome to affect major changes the pandemic. For comparison, Omicron variants contain least of more than seventy nucleotide changes when compared to the original Wuhan isolates.

The takeaway from these observations is that SARS-CoV-2 can alter fundamental characteristics relevant to transmission. We have yet to understand the full range and disease implications of such changes. We should remain humble but observant.

Immune Evasion

SARS-CoV-2’s ability to evade protraction from an infection acquired by prior infection or vaccination has come as an unpleasant shock. That should not have been the case. As mentioned, we know that the cold-causing coronaviruses infect the global population every year regardless of prior exposure. In that respect, they resemble the influenza viruses. Decades of research have taught us that such viruses deploy several tactics to evade our immune defenses. The concentration of protective antibodies raised either by natural infection or vaccination capable of neutralizing wane with time. Continued protection relies on the rapidly mobilizing antibodies that recognize the invading virus.

We recognize two primary means by which viruses can thwart the memory response:

The first is antigenic variation. Influenza viruses—and as we now know, coronaviruses also—alter the virus’s exterior to avoid recognition by the antibodies made to earlier versions of the virus. These viruses are practically invisible to the earlier antibodies. Despite these changes, the virus retains key properties such as binding and entering cells. As Omicron infections demonstrate, such altered virus can sweep through an entire population regardless of prior infection vaccination status.

A virus may also outrace the memory response. The production of high levels of protective antibodies by memory cells requires that they recognize the presence of an invader and proliferate in sufficient numbers to produce enough protective antibodies to make a difference. Two to four days may pass before antibodies reach the required level. Both influenza and SARS-CoV-2 replicate so rapidly that those infected may become infectious within one to one in a half days from exposure. In other words, the virus may enter and exit before the memory response kicks in.

Omicron is case-in-point on both accounts. The Spike protein of SARS-CoV-2 is the major target for neutralizing antibodies. The Spike proteins variants contain thirty-six amino acid changes. These mutations reduce the ability of vaccine-induced antibodies to recognize the virus by more than thirtyfold, even after double vaccination followed by a booster. Moreover, protection by current vaccines or prior infection falls dramatically over the ensuing months leaving the population, vaccinated or not, susceptible to Omicron infection.

We have yet to understand the extent of possible antigenic variation fully. I am not optimistic that we will ever reach the point where SARS-CoV-2 has reached the limit of possible variation. Witness the decades-long success of coronavirus infections n humans and the millennia-long success of the virus in other species, most notably bats.

I am much more optimistic regarding the power of our immune system to protect us from severe disease and death once infected. The best evidence is that T-cell, not B-cell, is the immunity that offers us such protection. The good news is that, at least for now, we have observed only limited variation in the ability of the virus to evade recognition by memory T-cells. However, the observation that CD8+ T-cell recognition of the Omicron Spike protein is diminished in 20% of those multiply vaccinated may be a warning of dangers to come.

Virulence

My greatest fear of a variant that has the transmission characteristics of Omicron and the lethality of SARS or MERS. Remember that SARS killed about four percent of those under fifty and about forty-five percent of those over sixty-five. MERS killed and still kills about one-third of all those it infects. We remain in the uncomfortable position of not knowing how to account for the striking differences in the pathogenic impact of the viruses. Optimists point to the four cold-causing coronaviruses that, except in rare cases, cause cold-like symptoms. Pessimists highlight the lethality of SAR-CoV-1 and MERS.

The history of viruses is replete with examples in which the change of one or a few nucleotides of amino acids convert a mild disease into almost uniformly lethal. Two of the best examples come from studies of coronavirus. The closest being studies of a SARS-1.

Nieto-Torres et al. adapted a lethal variant of SARS-CoV-1 to grow in mice. To attenuate the virus for vaccine use, they introduced single point mutations into the envelope protein (E) at two different positions. Both are located within the hydrophobic amino-terminal region ion channel pore-forming sequence. Both mutations inactivate the ion channel activity. One of the mutations is a change from asparagine to arginine at position 15, the other valine to phenylalanine at position 25. Both mutants are viable and infect mice. Both resulted in no or at most very mild disease.

The first conclusion is that a single amino acid change in the E protein can attenuate pathogenicity without destroying virus viability.

Repeated passage of both mutants in culture resulted in rapidly growing revertants. Mice infected with the revertant virus die quickly. Surprisingly the revertants retain the original mutations but contain second site amino acid changes within the short hydrophobic region that restore ion channel activity. The revertant mutations occur at different sites within the hydrophobic channel. All restore ion channel activity.

The second conclusion from these experiments is that a single amino acid change with the E protein hydrophobic channel can transform a nonpathogenic strain of SARS-1 into highly lethal in mice.

The E proteins of SARS-CoV-1 and SARS-CoV-2 are similar. Omicron contains a mutation in a conserved amino acid immediately amino adjacent to the transmembrane region, a threonine to isoleucine substitution at position 9. Might the T9I mutation contribute to the reduced virulent of Omicron? Might a second site revertant transform SARS-CoV-2 into a virus with lethality characteristic of the SARS-1 variant? Frightening to contemplate.

The second example is found in feline coronaviruses. One variant causes only mild disease in kittens. However, a change in three amino acids in the membrane-associated S2 protein transforms the virus into uniformly lethal to adult animals. Mutations in this area of the feline coronavirus Spike may also increase macrophage tropism, as well as alter the mode of entry from fusion to endosomal, as seen with the Omicron variant. I note that the Omicron variants carry 7-9 amino acid changes in S2 protein compared to the Wuhan strain. Some of these mutations likely contribute to the preferred endosomal route of viral entry. Might these Omicron variants affect Omicron pathogenesis as well?

Conclusion 

The take-home message is that highly lethal variants of coronavirus can and do exist. Some of these variants differ only slightly from one another, sometimes by as little as a single amino acid change. It is not farfetched to imagine such changes arising in SARS-CoV-2. After genomes differ from those of the Wuhan parent by more than 50 changes, not including small deletions and insertions, while we hope for the best, we must prepare for the worst. Our recent experience with Omicron teaches us that most countries are are unprepared to contain a highly contagious virus. While our vaccines provide significant protection against severe disease and death against current variants, we are unsure how long that protection will last. We cannot be certain to remain protected against whatever nature may devise.

Our future will depend on the success of continued research, drug and vaccine development, and our willingness to institute effective mitigation measures.

Read the full article on Forbes.