The longer a virus such as SARS-CoV-2 is “allowed” to spend in its new host (us!), the more likely it becomes that it can accumulate mutations some of which will give the virus a competitive edge. It can be thought of as Darwinian evolution in rapid…
(real-) time. With more infections, there are more viral replication cycles and more chances for random mutations to arise; selection then takes place in which, virions typically more transmissible will become the dominant new clones; the fitter virions (selective advantage and survival), then give rise to the new dominant strain.
There have been a few “popular” mutations and new SARS-CoV-2 strains emerging during this pandemic. The initial D14G and mink cluster-5 mutations were popularised but were relatively benign. The UK (Kent) alpha variant was the first variant which truly had an impact with respect to transmissibility and hospitalization. The beta variant first identified in South Africa is still highly active and recent reports are suggesting that it driving a surge in Seychelles, where ~70% of the population is fully vaccinated. Amongst other mutations a key mutation in the beta variant (which we will revisit below), is the K417N mutation in the spike protein (the part that binds to ACE2 receptors on host cells. The gamma variant (previously known as P1), is the one causing problems in Brazil and South America.
Currently, most attention has been focussed on the delta variant; the variant first identified in India which caused the second “devastating” wave in that country. The delta variant is thought to be 60% more transmissible that the alpha variant and has essentially now taken over in the UK and is expected to become the dominant variant in the US in the coming months; it is now reported to be in 85 countries and although not yet definitive, is thought to be associated with more serious disease (particularly in unvaccinated people). Thankfully, it appears that major vaccines, Pfizer/BioNTech, Moderna, and AstraZeneca are effective with only small drops in efficacy. There are serious concerns for countries in which vaccination rates remain low.
To highlight the evolutionary process, a delta plus, variant has now emerged (first identified in Nepal), which also highly transmissible. The variant has not yet been formally classified a variant of concern but has appeared in 11 countries as of today (197 cases). Not much is known about this variant however, an interesting feature is that it has “independently” acquired the K417N mutation observed in the beta variant; convergent evolution! This is a strong example of adaptation and highlights the “fitness” to the virus imparted by this specific mutation.
Given the seriousness of the delta variant, the UK is delaying reopening by four weeks in attempt to curtail the spread and to hopefully, vaccinate a higher proportion of the population (currently ~50% fully vaccinated). As shown in the photo taken at Melbourne Central (top), during Melbourne’s latest lockdown 4.0, lockdowns are necessary but not pretty. The photo was taken on a Friday night after work, at time where it should be peak hour… usually lots (too many), people! The UK is doing the right thing and closer to home, parts of Sydney gone into lockdown; as of today (22 new cases reported with confirmed “delta” cases).
Delta is not mucking around; luckily vaccines are effective against variant, but as we can see by the continuous evolution, illustrated by the delta plus, SARS-CoV-2, will not go away easily.
Until next time …