Covid Scotland: Herd immunity and the threat from New York's 'son of BA.2' variant

Unlike earlier in the pandemic, when they were a “lag indicator”, hospital cases now track much more closely the patterns of disease in the community because such a high proportion are patients who test positive incidentally (or catch the virus in hospital) as opposed to becoming unwell with Covid - a process that tended to take around seven to 14 days from infection.

All this has happened despite no new restrictions being introduced and evidence that behaviour is becoming less cautious - not more.

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According to analysis for the Scottish Government, average daily contacts increased by 19 per cent, to five, between March 23 and April 6 (although this is still well short of the eight-per-day average pre-pandemic), with average contacts in the workplace increasing by 55% as working-from-home requirements ease.

The ‘R number’ is also estimated to be back below one, signalling a shrinking epidemic.

Although it is too early to evaluate any impact of downgrading facemasks in Scotland from law to guidance on Easter Monday, it is clear that far fewer people are wearing them indoors (compliance in Scotland previously exceeded 80%).

However, England dropped mask laws back in January did not see an associated surge.

Hospital admissions for patients with Covid are in steady decline (Source: Pubic Health Scotland)

Adam Kucharski, a mathematician and professor of infectious disease epidemiology at the London School of Hygiene and Tropical Medicine, tweeted earlier this month - in response to similar patterns occurring UK-wide - that “if infections are peaking without new control measures or substantial behaviour change, something must explain the patterns”.

The best explanation, he suggested, was herd immunity, where this is defined as “sufficient immunity within a population to push R below one in absence of other control measures”.

In short, levels of population immunity accumulated through vaccination and natural infections mean the virus is running out of susceptible new hosts: nearly 80% of adults in Scotland have been boosted and ONS figures suggest over a million Scots may have been infected with Omicron or its BA.2 cousin since the beginning of the year alone.

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Neither offers a 100% immunity barrier against the virus but, for now, there is enough collective protection against infection to tip the scales in our favour.

Daily life in Scotland (outside of the NHS) is now the closest it has ever been to pre-pandemic normality, but - as Prof Kucharski also noted - even if we have, technically, reached herd immunity that “doesn’t mean infections will continue to decline indefinitely”.

Bear in mind how quickly we swung from a decline in the Omicron wave in late January to a sudden increase driven by the arrival of the even more infectious BA.2 variant from mid-February.

A combination of waning immunity and the emergence of new variants - either more transmissible, more virulent or, in a worse-case scenario, both - remain the biggest threats to the current status quo, and to NHS remobilisation.

PCR community testing hubs will close across Scotland tomorrow

There are already some on the horizon.

In England, 1,179 cases of a potentially faster-spreading Omicron “XE” variant - a hybrid form of BA.1 and BA.2 - had been detected as of April 8, mostly in the south and east of the country.

The strain was first sequenced in the UK back in January but has also been detected in Thailand.

The World Health Organisation estimates that it may have a 10% growth advantage over BA.2 - meaning it is even more transmissible again - but the UK Health Security Agency cautions that it is too early to draw conclusions. Overall, it remains a fraction of total Covid cases.

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Such "recombinant" viruses are not unusual, and are not necessarily more worrisome.

While recombination can enable viruses to evolve more quickly and significantly compared to the random mutations thrown up during replication errors - for example, enabling them to acquire resistance to drugs or increased infectiousness - recombination can also end up producing strains that are not significantly different from their parent.

The XF and XD strains (colloquially dubbed ‘Deltacron’ because they combined parts of Delta and Omicron) led to fears of a variant combining Omicron’s transmissibility with Delta’s higher lethality.

To date, however, it appears to have had little impact - perhaps because it cannot outcompete BA.2’s sheer transmissibility.

Potentially the most alarming variant currently on the horizon is the “son of BA.2” strain (its official designation is BA.2.12.1), which was first identified in the US in February and now accounts for 20% of the country’s cases.

The BA.2.12.1 strain has spread rapidly in districts across the New York State region since February (Source: New York State Department of Public Health)

It has gone from making up 3% of all new cases in New York state in February to 58% across New York, New Jersey and Connecticut combined, according to data released by the US Centres for Disease Control on Tuesday.

It is still early days, but preliminary estimates suggest that ‘son of BA.2’ spreads faster than its predecessors and could be better at dodging the immune system’s antibodies.

This is coming at a time when the World Health Organisation warns it is "increasingly blind to patterns of transmission and evolution” of Covid-19 as countries around the world - including the UK -wind down testing.

Community-based PCR testing hubs will close in Scotland from tomorrow, meaning that far fewer Covid samples will be collected, not to mention genomically sequenced, from now on.

Anyone with possible symptoms is encouraged to self-isolate, but self-isolation support grants will also end along with access to free lateral flow kits for close contacts of a positive case.

So, are we at “herd immunity”? For now, perhaps. But Covid probably still has some curveballs to throw.