It’s been nine months since I’ve blogged so today you’re getting my lunchtime musings on the new variant
B.1.1.529 Omicron and some actions we could be doing on the Island to ensure we’re prepared for it.
Yesterday (25th November 2021) the South African government were open and transparent with the world and let us all know they had detected a new variant with a significantly large number of new mutations circulating in several areas of South Africa.
- Why is the scientific community taking so much notice of this new variant compared to the many others which are still occurring throughout the world?
- How could that affect the Isle of Man over the next few months?
- What is the current status of our defences against vaccine-escaping variants on the Island, given the current strategy is entirely vaccine based?
It’s not so much that the new variant carries so many new mutations that makes us scientists sit up and listen. It’s the data that is showing that it is more transmissible than Delta, the current variant dominating UK infections, and the data which suggests it may reduce response to COVID19 treatments. The data also shows it may be capable of immune escape i.e. it can get past the vaccinations or significantly reduce the effectiveness of the vaccinations.
The data from SA also suggests that
B.1.1.529 Omicron may be rapidly outcompeting Delta to become the dominant variant there. When COVID has radically changed like this in the past – for example when Alpha first emerged in Kent – the first theory is one of emergence from an immunocompromised patient with a chronic infection which gave the virus an opportunity to mutate further. In this scenario the patient goes on to infect people with their new variant. The second theory is one where testing and genomic surveillance is low and, as such, transmission without testing and surveillance naturally leads to a “blind spot” which when genomic surveillance is finally carried out shines a light on previously untracked infections.
Having looked at many ssRNA viral genome assemblies and phylogenies in my career I’m inclined to think that
B.1.1.529 Omicron may have originated with the first theory given the branch lengths on the tree. As with anything in science, if I see more data then my opinion might change.
While this variant has emerged from an area where there is low vaccination coverage it’s not yet known how it will fare in a country with high vaccination coverage. Given the large number of mutations across the
B.1.1.529 Omicron genome there is a strong suspicion that it will cause infection in vaccinated people. Time will tell but it’s better to be safe rather than sorry and this is why countries are reacting by closing their borders to travellers from affected countries.
What’s the current status on the Isle of Man?
There are a number of changes which have been made over the last six months under the political “living with COVID” banner which mean that we are dangerously susceptible to the effects of a new variant like
The “living with COVID” rhetoric has led to virtually no mitigations being in place other than vaccination. The strategy should always have been “vaccination plus masks” but the messaging of the vaccination campaign has led to our population discarding masks as a mitigation method. This is one of the primary reasons for our current case rate.
Adding to the lack of mitigations is a level of complacency in testing methods and strategies which leaves us wide open to the risks posed by new variants like
- Gold standard PCR testing has been restricted in favour of less sensitive LFDs and subsequently PCR has been wound down to negligible levels.
- The hospital is now using LFDs for admissions instead of PCR, opening up the possibility of COVID transmission within the hospital given the big difference in false negative rate between the two types of test.
- The second PCR test that the path lab are using to determine variant (instead of genomic sequencing) is substandard and not fit for purpose.
- The detection PCR tests in use by the path lab do not detect one of the proxies that can be used to identify positive samples from lineages such as B.1.1.529.
What does this mean in lay terms? We’re not detecting the cases we do have, we’re not testing enough with decent methods, we can’t detect new variants, we specifically can’t detect
B.1.1.529 Omicron on-Island with the PCR tests in use, and the hospital is at risk of an outbreak on the wards.
B.1.1.529 Omicron were to be introduced then it could rapidly replace Delta as the primary variant on the Island and if the immune escape data turns out to be proven then it would affect the effectiveness of the current vaccinations. This would lead to sicker people, more deaths and more risk of overwhelmed health services. If this were to occur it would require significant mitigations be put in place until one of the vaccines – likely one of the mRNA ones – could be amended to cover this variant and be distributed throughout the population as a booster. This is why the UK government immediately put SA on the red list, which is not without it’s ethical considerations, as the openness and transparency shown by SA was rewarded with border closures from the rest of the world (but that’s another post for another time).
What can the Isle of Man do to prepare for the arrival of
B.1.1.529 Omicron or other new variants?
There are a number of issues that need to be urgently addressed if we are to be prepared for new variants of concern such as
B.1.1.529 Omicron hitting our shores.
Number 1: The low uptake of booster vaccinations needs to be addressed immediately
I’m not sure how eight months ago we were perfectly able to know who needed vaccinating and coordinate appropriate appointments but now we are not able to coordinate booster vaccinations in the same way. Remember, we spent almost half a million pounds on vaccination hubs, yet our booster take-up is very poor. Recent research is showing that the booster at six months is key to protecting ourselves from serious illness with Delta. That suggests it will be just as important for new variants. If we can’t roll out boosters rapidly and successfully how will we cope with an
B.1.1.529 Omicron specific booster if needed quickly? We can’t lock down unvaccinated/unboosted people until the DHSC gets around to vaccinating the population against a new variant. Nor should we accept any deaths while the good ship DHSC takes a leisurely slow turn.
RECOMMENDATION 1: We should not be complacent in the face of
B.1.1.529 Omicron. There needs to be responsibility and accountability within the DHSC for increasing our booster levels up from 37% to >80% of the population as fast as possible.
Number 2: If the DHSC won’t fund PCR testing properly then we need to be using LFD tests which are sensitive enough to detect infection in infected people
I am hearing an increasing number of reports of symptomatic people testing negative with the government-issued lateral flow tests who are testing positive with other brands of lateral flow test a few minutes later. The same patients are also subsequently testing positive with PCR.
LFDs are only useful if they work and are as specific and sensitive as they need to be for the application they’re being used for. Assuming that all brands of LFD are the same is a fallacy (as is thinking all PCR tests are the same).
RECOMMENDATION 2: Immediate review into the on-Island laboratory testing carried out to determine the best LFD to roll out for public use. Did our own testing show that the selected LFD is sensitive enough to detect an acceptable number of positive cases to use it as a PCR replacement? If not, why not?
Number 3: Re-introduction of PCR as the COVID screening test for hospital admissions
This one is about as obvious as it gets. We do not want Nobles hospital to be another Abbotswood. If LFDs are testing negative in positive patients in the community then it is only a matter of time before it happens on the wards and isn’t caught for a few days. “Nosocomial infection of COVID” (i.e. the patient got infected in hospital) isn’t a phrase anyone should be hearing on the Island. PCR is used for detection of other pathogens in hospitals so why are we OK with NOT using it for the one pathogen which is currently of interest? Money shouldn’t be making these decisions but if that’s the way it has to be then think of it this way: PCR is cheap but extended hospitalisation from a nosocomial COVID infection is expensive. Just like that age-old 2020 phrase “testing is cheaper than a lockdown”.
RECOMMENDATION 3: Reintroduction of PCR testing for hospital admissions.
I have already recommended, through the EAG, that the variant-detecting PCR in use at the path lab should be stopped (chocolate teapot came to mind) and I could write an actual book on why genomic sequencing is going to be key with the variant detection and why masks are the most effective mitigation for reducing spread and thus case numbers.
However, I can see the brick wall and I’d like my forehead to still be intact going forward.
In conclusion, the Isle of Man needs to start preparing for
B.1.1.529 Omicron coming to our shores, sooner rather than later. We can’t keep relying on the UK to do the work for us. We shouldn’t be work-shy in doing our own Island-specific contingency planning for things needed in the face of a vaccine evading variant like ramping up PCR testing to thousands per day, assessing testing methods to make sure they work for the application we want to use them for, and vaccinating as much as possible.
Unfortunately if the world does the right thing with
B.1.1.529 Omicron and controls its spread then the vocal minority of naysayers will say that scientists were “scaremongering”. I’d rather we were accused of that, having done the right thing and have it work, than being responsible for not doing anything and watching the case rate and death rate increase.
One thing to be sure of with this virus (and variant) is that it’s better to be safe than sorry.