Mutants, variants and strains: How muddled thinking help shift the blame

The fourth COVID-19 peak has arrived. That should give us a pause to reflect whether the recurring peaks could have been predicted. Thankfully, modellers seem to have abandoned the field, so we are not being entertained anymore. But could the epidemiologists and infectious disease experts have predicted the pandemic's course, which is now into the second year? 

Modelling with wrong statistics

Infection modelling could have adopted a better statistical basis, having known that superspreaders are crucial. During the peak infection in any country, more than 80% of cases are usually reported from two or three cities. In those specific cities, two or three localities contribute most of the infections. Yet the role of supers spreaders, who are these people, how the episode happens, and other aspects remain in the fringes of modelling and public health management efforts. The need for power laws, not bell curves, has not fully sunk in the world of modelling intelligentsia. 

Muddled thinking underlies all muddled messaging we have seen in the past year. We were told early last year that wearing masks is a health risk. Hand-washing and deep surface cleaning were recommended as the only precaution, apart from social distancing. Even in January 2020, it was recognized that most coronavirus transmissions happen silently. Late into 2020, we were asked to wear masks. By the end of 2020, wearing two masks, one over the other, become wisdom. We should apparently wear masks even after getting two vaccine jabs.

Conflation is not science

Mutants, variants and strains are the current victims of muddled thinking. News media can be excused for confusing these terms. But public health officials also seem to use these terms with cheerful abandon without understanding what they mean. Mutants become variants and then strains. Then they become the most recent cause for increased spread. They "could" make vaccines ineffective, we are told.

Mutations do not happen at an organism level. They happen at the genetic level, and it takes place all the time when DNA or RNA copies itself. Sometimes other factors such as ionizing radiation or chemicals can cause mutations in the genetic code. We can have mutated genetic code everywhere, which is practically what we have in each individual in any species, including humans. But each individual is not a mutant, though our DNA invariably has mutations, some of which could be heritable. Similarly, we can have mutant viral genetic code without essentially having a mutant virus.

Base rates indicate that most mutations do not make any changes in the biological makeup of an organism. In a few cases, mutations are harmful, and the natural section will tend to weed them out. Only in a rare instance, a single mutation can make a significant biological change, which is also not deleterious, so that it could be carried over to future generations. Rarer still will be a mutation that could have positive benefits, an evolutionary advantage to the organism. As all changes are heritable in a virus, they will carry forward if the changes are not harmful. 

As a large number of mutations accumulate, a variant emerges. I am not sure how many mutations are needed to announce a new variant has just appeared. The threshold for determining a variant seems to be arbitrary. The infamous B.1.1.7 coronavirus variant of the UK has 17 mutations. 

In virology, only when a variant causes a distinct change in the host's biological behaviour is called a strain. In the instance of SARS-CoV-2, no such change in biological behaviour in the host, i.e., the human host, has been observed. There is no hard evidence that the mutations in the spike protein had made the variant more effective in latching to a cell and thus becoming more transmissible. True, absence of evidence is not the evidence of absence. But the evidence should come from laboratory experiments, not from the logic of correlating it to spikes in infections. 

Stability and instability in the genome

Micro biologists study the genetic code of a virus and infer how fast mutations are accumulating, therefore how fast new strains are likely to emerge. In the case of SARS-CoV-2, changes are prolonged, and so new strains emerging in a short period is unlikely but not impossible. When vaccine development started early last year, this genome's stability was seen favouring a future vaccine's success. Large scale vaccine efficacy studies continue to affirm this observation. To date, the efficacy rates of different vaccines in repeated trials are not changing much. 

So, mutants, variants and strains are not the same. Some SARS-CoV-2 variants are reported, none of them so far qualify to be a strain. A variant does not have changed biological behaviour in the host. Hence, a variant can't usually be more infectious than the parent. The same applies to fatality rates in infected people. A variant cannot be more fatal. 

Speaking of fatality rates, it will be good to understand a phenomenon called "passage". The transmission of a virus strain through several generations in an environment usually makes it less virulent but sometimes more virulent. Sometimes, a virus starts as less virulent and can become more virulent after a few generations of passage. The reverse can also be true. Usually, a virus stain can be weakened or 'attenuated' by passing it through a different host. As a virus strain becomes more adapted to a different species, that strain will become less adapted to the original host, thus decreasing virulence to the original host. Such virus is often called attenuated strains as they do have altered biological behaviour.

Variants and the "founder effect"

We see a new Covid-19 peak. It is muddled thinking to bring in new variants to explain the peak. At a minimum, a new "strain" should have been evoked to keep the science proper. Supers spreading events will continue to fuel new peaks. A particular variant may be associated with a peak due to what is known as the "founder effect." It happens when a new cluster is established by a tiny number of individuals from a larger cluster. Due to the founder effect, the new cluster may be distinctively different from the parent cluster. 

Remember, correlation does not imply causation. It is the cum hoc ergo propter hoc ('with this, therefore because of this) fallacy. One super spreading event can cause a spike in a community, and we don't need a variant to explain it. And if it is proven that a variant is the cause of a spike, it is not a variant anymore - it is a new strain. The fact that the most reputed sources are sticking to the word "variant" means that hard evidence for a "strain" is not yet there.

Fuelling vaccine hesitancy 

Vaccines continue to work as ever, whether these are mutants, variants or strains. There is no hard evidence on the diminishing efficacy of vaccines. True, vaccine efficacy does not prove or disprove new strains. However, no other evidence exists for a new strain or that a new strain is more infectious. In science, experimental data can not be replaced with "maybe," "could be," "highly likely," and similar scenarios. Muddled thinking can only fuel vaccine hesitancy.

Shift the blame

"Psychologically and politically we would much rather assume that the cause of a problem is "out there," rather than "in here." It's almost irresistible to blame something or someone else, to shift responsibility away from ourselves, and to look for the control knob, the product, the pill, the technical fix that will make a problem go away." - Donella Meadows, Thinking in Systems (2008)

Public health science has the responsibility to prevent infectious diseases. If the infection could not be prevented, it should be controlled by the tools at our disposal. Sadly, the only tool we used with much vigour was quarantine - practised from at least the 6th century when plagues become common. While quarantines are justified in the initial phase, muddled thinking prevents us from taking advantage of other tools, including vaccines.  

Muddled thinking prevents us from understanding the progression of the pandemic and take practical steps to contain it. Instead, we are trying to shift the blame on elusive mutants, variants and strains.