The UK and South Africa are two countries where the transmission of the virus has escalated. Last week a highly transmissible new strain was identified as the source in the UK. Three days ago, the explanation of a marked upswing in cases in South Africa was also shown to be related to a new genetic variant of the Covid-19 virus. Indeed, in an unpleasant twist, two cases of this variant were also yesterday reported to the UK. The outbreak caused by these new variants will be much more challenging to control, both within these countries and beyond.
(I hadn’t intended blogging again before the holiday, but these new data are sufficiently concerning I thought readers would want some of this background!)
Some comments on terms!
- Mutation – a change in one of the genes of the virus as it multiplies
- Variant – as a consequence of one or more mutations, a different version of the virus appears with slightly different genes from the initial version
- Strain – often refers to when a particular variant becomes an important cause of some or all of the cases in a particular outbreak
Thus the new UK strain has some 23 separate mutations and this variant has become the dominant strain causing infection in much of this country
What do we know about the new South African strain?
- South Africa has seen a marked increase recently in the number of new cases of Covid-19
- Around 90% of new cases in that country are due to a new strain, based on a number of mutations
- As well as the 2 UK cases, the South African variant has now been found in Australia and Switzerland
- No doubt as other countries undertake the necessary complex genetic analysis this strain will also be identified in many other countries
Concern in younger people
- At the beginning of the epidemic less than 0.5% of cases in South Africa were in people under 30 (which may be related to who was being tested)
- In some South African provinces the peak age is now in the 15-19 year age group
- As with the new UK strain, the new South African one multiplies much more quickly than the previous common strains
- The problem is that those infected with these strains then produce much larger amounts of virus.
- Thus, the concern is young people infected with these strains have higher levels of virus than they did with the previous strain: the latter of which only rarely led to a severe illness.
- The greater viral load with the new strain could make them sicker
- Indeed, there are a few unconfirmed reports from South Africa, of young people with no pre-existing illnesses who became seriously ill with this strain
- It is too early to know how big these numbers are
How close are the South African and UK strains?
- Both strains are quite different variants
- Both however contain a number of mutations in the spike protein region, thought to be responsible for the increase in transmission
- Thus both the South African and the new UK strain carry the same ‘N501Y’ mutation in the spike protein
- It is likely that that these two variants have arisen spontaneously in different countries, but by chance both of them are particularly highly transmissible
- We may see other countries reporting on other highly transmissible strains
For the UK variant, is there any new analysis of its impact?
- In my post last week I thought it was highly likely that the UK strain would result in an increase in R
- The graph below, from an epidemiology modelling unit in Oxford shows that the transmission rate, R, is now well over 1.0
- It is fairly definite that the increase in R is because of the UK’s new strain (now called B117 or VUI-202012/0)
- What is interesting is that South Africa and the UK are two countries which, despite all the current lockdowns and mitigations, have two of the highest estimated R values in the world
- UK R=1.26
- South Africa R=1.33
- As a comparison the estimates for other high prevalence countries are lower
- USA R= 1.03
- France R = 1.06
- Italy R = 0.88
Conclusions about these new strains remain the same
- New strains occurring during a pandemic are not unusual
- The fact that these strains are more likely to transmit infection does not mean that the infection is more serious, but this will need to be monitored
- Most experts also still expect the new vaccines to be effective, as the antibodies generated by these vaccines should still ‘work’ against even the mutant forms of the spike protein
- As I mentioned last week, if necessary new vaccines can be made very easily against a new strain
- Indeed, one sensible suggestion this week was that even if the vaccines turn out to be less effective against any new strain, that wouldn’t necessarily be a big problem
- Given what is known about the effectiveness and safety of existing vaccines, it may be possible for regulators to approve slightly modified new vaccines without the need for additional lengthy trials
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