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I felt it may be helpful to provide an update on the new #COVID19 lineages in the UK and in SA that might both be more contagious than any #SARSCoV2 in circulation until recently. Those comments should be considered preliminary as the evidence available to me is still sketchy.
1/ https://twitter.com/virological_org/status/1340334403961180165
1/ https://twitter.com/virological_org/status/1340334403961180165
Both lineages have accumulated an unusually large number of mutations / deletions. A plausible explanation is a persistent infection in an immunocompromised patient. There is earlier evidence that such persistent infection leads to fast viral evolution.
2/ https://www.nejm.org/doi/full/10.1056/NEJMc2031364
2/ https://www.nejm.org/doi/full/10.1056/NEJMc2031364
All the mutations /deletions carried by the two strains have been observed before in other lineages. For example, both carry N501Y in the spike protein, a mutation that was first observed in Brazil in April and has remained at low frequency until recently.
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Individual mutations do not seem to affect transmission significantly. For example, the best studied candidate mutation for increased transmission, D614G, arose independently in different genetic lineages but only one of those increased in frequency.
4/ https://www.nature.com/articles/s41467-020-19818-2
4/ https://www.nature.com/articles/s41467-020-19818-2
Deletions might have a more important effect on transmission than mutations, but are more difficult to study. Most the genomic data is in the form of 'assembled genomes', with raw reads often not available. Deletions were sometimes miscalled /overlooked in genome assemblies.
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The UK / SA strains carry a series of deletions, in particular one at position 69/70 in the spike protein. While this deletion has been seen in other lineages before, it may play a role in transmission. Another deletion in the spike protein (144/145) might play a role.
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I can think of three main, non-mutually exclusive, preliminary hypotheses explaining the rise in frequency of the UK and SA lineages.
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1. The two lineages increased in frequency following a major founder effect. They were at the right time in the right place (i.e. major 'super spreader' event), and are not necessarily intrinsically more transmissible.
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2. Both lineages have acquired a combination of mutations and deletions not found together in the same genetic background before. In conjunction, some mutations / deletions make the lineage intrinsically more transmissible, for example by increasing viral load in the host.
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3. Both lineages may, at least in part, bypass immunisation caused by prior #SARSCoV2 infection (immune-escape). Despite not being more contagious, the lineages might have risen in frequency by infecting a larger pool of hosts (including a fraction of previously infected).
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Hypothesis 2 (intrinsically more contagious) feels most plausible given the available evidence. Though, the necessary data is not available to me at this stage for any formal assessment. Data from Denmark where the UK lineage is also widespread would be most useful.
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Additional evidence that feels essential is the relative disease severity caused by the new strains (which at this stage does not point to more severe symptoms), as well as the proportion of putative and confirmed reinfections caused by the new UK and SA lineages.
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