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Insight+ explores the new COVID-19 subvariant FLiRT, vaccine efficacy and concerns about the new outbreak of avian flu in Australia with Director of Infectious Diseases at Mater Hospital, Associate Professor Paul Griffin.
FLiRT: it’s a catchy name for a mutation of a virus that originally left a wake of devastation and destruction in its path, caused global lockdowns and was universally feared.
After working through the Greek alphabet to name variants of the coronavirus disease (COVID-19), we now have FLiRT. It sounds almost glib after what the world has been through. Are we taking the virus as seriously as we should? Associate Professor Paul Griffin says the virus doesn’t inspire fear like it used to after it was first detected on 25 January 2020.
“I think it’s clear that this far down the track from when this virus was first discovered…people’s perceptions have changed significantly, and it is much less feared.”
But he doesn’t believe there’s any link between this change in perception of the virus and its playful name.
“FLiRT is an abbreviation for the mutations in the spike protein that have given rise to the new subvariants that we are seeing cause an increase in COVID activity at the moment. More specifically it refers to amino acid changes in the spike protein, phenylalanine (F) to leucine (L), and arginine (R) to threonine (T),” Associate Professor Griffin said.
“This is not a new way of describing these changes but conveniently spells an easily recognisable word that has caught on.”
“We at times named variants after where they were originally found (eg, the UK variant otherwise known as alpha), we then transitioned to predominantly naming variants letters of the Greek alphabet and now we mostly talk about subvariants of Omicron, of which there are now well over 60,” he said.
“The subvariants are actually descendants of JN.1, sometimes referred to JN.1.* and including KP.1.1, KP.2, KP.3 and KW.1.1.”
Although it’s a unique name for a variant, its characteristics aren’t necessarily that unusual. However, it does have implications for vaccinations.
“What we are seeing is what has happened many times over, in that basically the virus has changed again, hence immunity derived from vaccination or past infection no longer provides as potent protection,” Associate Professor Griffin said.
Current vaccines that Australians have access to are not necessarily keeping up with new variants like FLiRT.
“The virus is currently changing faster than our vaccines are able to be updated. The WHO recommended updating vaccines to targeting JN.1 at the end of April but unfortunately these are not yet available,” Associate Professor Griffin said.
But that doesn’t mean people should not keep up with the available vaccines.
“My advice is for everyone to be up to date with vaccines according to their current eligibility, particularly given the rapid rise in cases and therefore risk in our country at the moment.”
While the FLiRT subvariants are not likely to be more dangerous than their predecessors, they could spread more easily.
“It is always challenging early after the detection of new subvariants to completely understand its properties. However, there is nothing at this stage to indicate the FliRT subvariants are any more dangerous.”
“When the virus changes, this can theoretically lead to a number of concerning properties including immune evasion but also potentially reduced performance of tests or antivirals although we haven’t really seen this yet,” Associate Professor Griffin said.
The reduced fear around the virus leads to a lack of testing, including of wastewater, making it harder to capture data on the virus and to see the bigger picture.
“Very unfortunately it is getting harder to understand what is happening with COVID-19 given reductions in surveillance and testing,” Associate Professor Griffin said.
“Reductions in people testing certainly means we have a reduced understanding of what is happening in terms of numbers of cases as well as what subvariants are causing them.”
“In Australia, many states have wound back wastewater testing, which is a really useful way to get a snapshot of both activity as well as what subvariants are circulating,” he said.
The lack of more severe variants of the disease shouldn’t lead people to think the battle with COVID-19 is over.
“The changes we see in the virus and the infection it causes are random so it is possible, although less likely for a few reasons, that one day a new subvariant may cause more severe disease. This is part of the reason why we can’t get complacent in terms of COVID-19.”
Concerns about bird flu
Australia’s first human case of avian influenza was reported this month, sparking huge culls of chickens on farms in Victoria where the outbreak began. Globally, the United States and Europe are looking at acquiring or making H5N1 bird flu vaccines.
Associate Professor Griffin finds the Highly Pathogenic Avian Influenza A (H5N1) (specifically Clade 2.3.4.4b) a little concerning but fortunately it is not currently being spread from person to person.
“Bird flu in itself isn’t new or concerning with avian influenza detected in poultry in Australia on nine previous occasions dating back to 1976,” Associate Professor Griffin said.
“Some of the concerning features of the current situation include how widespread the transmission is in birds and now the number of mammalian species involved.”
“While human cases have been reported, including a young, returned traveller in Australia, fortunately at this stage it does not seem able to be transmitted readily [from] person to person and the vast majority of cases have arisen via close contact with birds or infected mammalian species, particularly cows.”
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Circa 1950 came a polio epidemic with nightly news of mainly kids dead, dying (in iron lungs- did anyone survive them?) or maimed. (a separate story)
It ended, I thought with the Salk Vaccine (officially not approved but how could us kids be denied) (a separate story again). Then the “end of epidemic” was locked in by the oral sabin vaccine – a live virus with low pathogenic potential, but which conferred immunity.
It was later said that those of us with relatively grubby, rustic standards might already have been protected by sabin-like endemic viruses.
If that is so, having lived with chooks for years, which, in turn, had daily contact with untamed birds, might we also have had some immunity to bird-flu? How would we know?
Food for thought for (especially young) virologists / immunologists.
Rob Boughton raises the issue of comprehension and predictability with influential decision-makers within governments (Boughton, R. June 3, 2024, at 9.06 am). We might all be better off if we were to consider some fundamental principles concerning pandemic risk assessment.
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Having identified a potential risk, it is necessary to look at both the probability, and the impact if that risk were to occur, including its possible impact. iRisks are scored against both probability factors and the level of potential impact. The combined scores are used to give a measure of the overall risk posed. Risks can then be categorized as high, medium or low., with a strategy worked out accordingly. However, complexity, uncertainty, and ambiguity compound this process.
Complexity refers to the difficulty of identifying and quantifying causal links between a multitude of potential candidates and specific adverse effects. Resolving complexity requires deliberation among experts, the goal being to achieve a consensus on the definition and explanation of the phenomenon in question. Discourse among experts may reveal uncertainties and ambiguity associated with the profile of the risk in question. The debate on targeted prophylaxis is an example of complexity.
Uncertainty arises from components such as statistical variation, measurement errors, lack of knowledge, and indeterminacy. Uncertainty reduces the strength of confidence in the estimated cause-and-effect chain. For example, scientific uncertainty makes it impossible to attach a unique and reliable probability measure to the occurrence of an avian influenza pandemic.
Risks clouded in uncertainty may not lend themselves to conventional methods of risk management. Management strategies belonging to the precautionary approach are required. There is a need to add objectives that promise to enhance resilience and decrease vulnerability. Strategies based on resilience, for example, include specific measures of precaution, such as ALARA (as low as reasonably achievable) or BACT (best available control technology). There is a need to balance the possibilities for over- and under-protection based on uncertain data and ignorance. Here the stakeholders are asked to find a consensus on the extra margin of safety that they would be willing to invest in exchange for avoiding potentially catastrophic consequences.
Ambiguity refers to a situation of contested views about the desirability or severity of a given hazard. For instance, there is ambiguity as to the effectiveness of a vaccine, which depends on its efficacy, its quantity, and also the time of its availability. Arguably, ambiguity is resolved by discourse. Here the stakeholders are asked to find consensus on the dimensions of ambiguity that need to be addressed in the phase of data collection.
Complexity requires deliberation among experts who are aided in this process by access to appropriate data. And, knowledge generated by research and, data analysis and collection help to reduce uncertainty and resolve ambiguity thus helping to better inform risk managers in the future to develop more appropriate control strategies.
Pandemic risk assessment is a complicated task requiring the evaluation of a large number of variables in the context of uncertainty and ambiguity. Nevertheless, accurate evaluation of the risks to human health depends on obtaining as much specific data as possible. Data used for risk management decisions must be critically reviewed to identify significant gaps and deficiencies. Data informs the risk management process and helps resolve uncertainty and ambiguity.
Of course, the challenges will be to best define the specific mechanisms that are most significant in causing unacceptable risk so that resources can be applied in the areas that will produce the most benefit and, to break down the pandemic risk into its key component parts and then aggregate these risks to provide a balanced view of risks across the sector.
Successful and effective risk management requires a clear understanding of the risks and the implementation of appropriate control strategies. However, a global risk such as a pandemic is a risk that is difficult or impossible to assess quantitatively, yet understanding this risk is essential. The key to successful risk management is to focus on those risks that truly matter and ensure that the impact of these risks is understood and mitigated … no easy task when the issue is confounded by complexity, uncertainty, and ambiguity. However, to assess the probability and potential impact of an avian flu pandemic it is essential to have key data input into the risk management process.
Rob Boughton is not wrong in his thinking. Why on earth …. !
All the sensible ‘speak’ of variants and sub-variants of COVID-19 (i.e. SARS-CoV-2 virus.).
And, once again, more ‘speak’ surrounding ‘bird flu’ (i.e. Avian influenza).
Let us not forget that COVID-19, as the name suggests, is a Corona virus, whereas ‘bird flu’ belongs to the Type-A class influenza virus. Nothing new here.
Both COVID-19 and Avian influenza result in sudden acute respiratory illness and distress.
As much as we need to concentrate on finding the best vaccines (prophylatic and treatment), there is much work yet to be done on inventing appropriate vaccines for ‘bird flu’. What will be the success of Moderna’s developmental’ bird flu’ mRNA vaccine? Time will tell. Indeed. will time permit?
Perhaps the real concern with ‘bird flu’ is antigenic shift. Arguably, most strains resulting from antigenic will be dead-end strains. However, a few strains will have the potential to become pandemic viruses.
Nowadays, more than ever before, epidemiologic surveillance must become the priority of governments across the Globe. The same has to be said of virus identification despite the laborious processes involved such is involved, for example, with in-situ hybridization.
What of prevention? Here the debate presented by Dr. Griffin widens.
Doctor Griffin wites from the pint of view of treating infectious diseases. My concern, as public health practitioner
The imported human case of H5N1 did not spark the cull of Victorian chickens. That strain is H7N3 and is not a concern for humans at present. Why on earth the Victorian Health Department released the news of the historical H5N1 case on the same day as the news of the poultry cull broke is beyond comprehension and predictably caused the confusion that reigns even in a forum that should know better.