Coronavirus statistical update: New variants greatest threat to defeating Covid-19

As the vaccination campaign continues to spread protection against Covid-19 over an increasing proportion of the population, the greatest threat to defeating the coronavirus lies in new variants which render current vaccines less effective. Nearly a dozen significant new variants have been identified, the latest being the Indian. Text by Nick Terdre, research and graphics by Russell Hall.

The vaccination campaign remains the primary weapon to overcoming the coronavirus infection. Speaking in the Commons on 19 April, health secretary Matt Hancock gave an upbeat account of its progress, reporting that cases, hospitalisations and deaths have been reduced to September levels, “we are on track to offer a vaccine to all adults by the end of July” and uptake of vaccines has been “astonishingly high.”

But, he warned, “The biggest risk to our progress here in the UK is a new variant that the vaccine does not work as well against.” (He appears not to have been speaking of any particular new variant.)

Once all adults have had their prescribed two doses, the plan is to give everyone a booster shot – existing vaccines tweaked or new vaccines specifically designed to combat new variants.

All the vaccines currently in use have been developed specifically to activate and strengthen the body’s immune system against the form of Covid-19 which was prevalent in the early stages of the pandemic.

But like any living organism, the coronavirus constantly adapts or mutates as it reproduces. While most mutations make no practical difference, there will inevitably be some that do – and by virtue of proving less vulnerable to the effect of the vaccines, they equally inevitably have the potential to thrive.

Kent variant

The most prevalent form of Covid-19 in the UK today is the Kent variant, also known by its lineage designation B.1.1.7, which first came to public attention when it drove the rapid rise in infections in December which helped prompt the second lockdown. Other variants also began emerging – notably the South African and two in Brazil.

New variants or strains of Covid-19 are identified by using genome sequencing to monitor changes in the genome of the virus over time – an ability in which the UK is genuinely a world leader. Significant versions are classified in two categories: variants of concern (VOCs) and variants under investigation (VUIs).

VOCs are associated with increased transmissibility, increased virulence and/or a decrease in the effectiveness of vaccination or other forms of treatment. VUIs are variants which are put under monitoring as they show the potential to become VOCs.

Some variants include the E484K mutation in the virus spike protein that has been shown to reduce the efficacy of current vaccines by evading antibody neutralisation.

There are currently 11 new variants on the health authorities’ watch-list – four VOCs and seven VUIs. The latest addition is the Indian variant, B.1.617.1, which has just been classified as a VUI. According to Hancock, 103 cases have been detected, but more recent data from the Covid-19 Genomics UK Consortium (who process the samples) put the total at 222 up to 17 April. The vast majority of cases had links to international travel, but some were traced to community transmission.

Red list

This variant may be associated with the soaring infection rates in India, which led prime minister Boris Johnson to cancel a trip there and to India being placed on the red list of travel destinations. However, there is insufficient evidence as yet to establish a link – the surge may also be the result of a lengthy period of lax precautions and significant underestimation of the prevalence of infections.

The first cases of travellers arriving from India infected with the Indian variant occurred in the week beginning 15 March. By early April they had overtaken the number of arrivals with the Kent variant.

According to one expert, Dr Jeffrey Barrett, director of the Covid-19 genomics initiative at the Wellcome Sanger Institute, since this variant was known in India late last year, “…if it is driving the wave…it has taken several months to get to this point which would suggest it’s probably less transmissible than the Kent B.1.1.7 variant.”

According to the COVID-19 Genomics UK Consortium, in the 28 days to 17 April the Kent VOC made up 97.85% of cases sampled. This has spawned its own variant with the E484K mutation, also known as the Bristol variant, which made up 0.07% of cases sampled in the same period.

The South African variant, B.1.351, which is also classified as a VOC, made up 0.57%. The fourth VOC is P.1, a Brazilian variant first identified in Japanese travellers returning from Manaus,  which made up 0.07%.

Among four prevalent new variants, the South African and the Indian have been detected with most new cases, though numbers are small.

The other Brazilian variant is P.2, a VIU linked to 0.01% of cases, though no new ones in the 28 days to 17 April.

VUI B.1.525, first detected in England, has 0.09% of cases linked to it (0.16% in the 28 days to 17 April) and VUI B1.1.318, the origin of which has not been established, 0.03% of cases (0.13% in the same period).

Of VOCs, only the Kent strain has been detected in East Sussex. Two VUIs have been found in the county – one case of P.2 and six of B.1.525. Both have the E.484K mutation.

Surge testing

To minimise the risk of new variants establishing a foothold, the authorities have introduced surge testing, intensive testing in the neighbourhood where cases have been detected. There is no special treatment – new cases are asked to self-isolate to reduce the risk of spread, and their contacts are traced.

A cluster of cases of the South African variant was found last week in south London, predominantly in Lambeth, Wandsworth and Southwark. Surge testing has been introduced in these areas, including for the first time across whole boroughs in the case of Wandsworth and Lambeth, where 19 mobile testing units have been deployed and test kits distributed to housing estates, secondary schools, places of worship and workplaces, Hancock told the Commons.

Such testing is voluntary  and may well be avoided by those who fear being asked to self-isolate as they cannot afford it. Government assistance has been criticised as inadequate and even the much-vaunted one-off grant of £500 is said to be difficult to access.

Leaving aside the Kent variant, which as said is now the dominant form of Covid-19 in this country, of the 40,127 UK genomically sequenced cases with a specimen date in the 28 days to 16 April the other variants of interest were linked to only 585 cases – 279 to the other three VOCs and 306 to the seven VUIs.

So the strategy seems to be keeping a lid on their spread so far, though this is not the moment to relax precautions, as the example of India tragically shows.

 

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