The Corona Virus Pandemic - the need for new models.

As the Corona virus spreads across the world, it has become apparent that we were not adequately prepared for a global pandemic. While limitations in preparation range from logistics (capacity of hospitals to handle infections, safety of health workers, supply of test kits etc) to human behaviour (correct hygiene practices, responsible actions in observing lock-down regulations etc) I wanted to particularly focus on the technical aspects of this limitation and that is the scientific models that inform our understanding of the natural world. A key motif in this inadequate preparation has been the challenges associated with testing kits. Two methods of testing have emerged (i) Tests that have relied on the identification and amplification of specific viral gene sequences by a technique called Polymerase Chain Reaction (PCR) and (ii) Tests that have relied on the identification of anitbodies against viral proteins. An article in the journal, Nature, has beautifully summarized the pros and cons associated with these tests (https://www.nature.com/articles/d41586-020-00827-6).

In my perspective, current tests all depend on a simple biochemistry principle called "the lock and key mechanism" (which has also been extended to an "induced fit" model). The idea behind this is that biological molecules called proteins behave - in a sense- much like larger machines. A simple example is a key that fits in a specific lock. As such a protein can only associate with a specific molecule. A consequence of this model is that molecules must physically interact and must be in a significantly high concentration to get a signal. For this reason, detection of viral particles only occurs after a particular "incubation" period when the concentration becomes significant (high enough for detection). The problem with this is that significant concentrations are a health hazard. By consequence, high concentrations for detection must arise from many rounds of replication and damage to the cellular composition. Symptoms may (or may not be showing at this stage). Clearly we must challenge existing paradigms that currently form the foundation of biochemistry and create new and more efficient technologies. To do this, we must actively reflect and research possible new models that may not be conventionally accepted. Basic research in scientific models that underpin our interpretation of data must not be ignored for more "exciting and trendy" work simply for the possibility of publishing in high end journals. The Covid-19 test kit scaling problem has less to do with logistics but more to do with our current models as bottlenecks (PCR takes at least two hours to complete due to its reaction chemistry and antibody based tests need high concentrations to yield results). Put simply, our current understanding of reaction chemistries is not enough to deal with the rate of infection on such a scale. We are simply not fast enough.

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