I think the least disruptive way to control #SARSCoV2 is to act early, focus on high transmission settings, masks, and Test-Trace-Isolate-Quarantine to keep Re below 1. But with rising cases, this strategy looks less and less plausible in many parts of Europe.
[1/7]
This could be a prelude to what I fear will be a difficult winter. Controlling #COVID19 will require combinations of tighter measures with difficult trade-offs and serious societal, health, and economic implications.
The old are much more likely to suffer or die from #COVID19, while the young bear the lion share of the cost of restrictions.
Previous and current generations benefited from burning fossil fuels, while the young will suffer most from the climate crisis.
[4/7]
Instead of ballooning the stock market and propping up moribund industries, I feel strongly that any economic stimulus needs to be targeted at providing opportunities for future generations and at protecting the climate.
A firm commitment to address the challenges of the future, along with clear communication of #COVID19 risks and transmission patterns, would go a long way to convince society as a whole to control the virus and make a short-term sacrifice worthwhile.
[6/7]
On the other hand, shaming particular groups for spreading the virus is completely unacceptable. Blame and stigmatization have consistently hampered control of many other infectious diseases, #COVID19 is no different.
[7/7]
PS: I am no longer as young as in my profile pic.
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Within each variant, diversity and divergence increase linearly with time. The rate of synonymous evolution is around 6 changes per year in all variants, while the non-synonymous rate varies from variant to variant.
2/N
In this graph, each dot/square marks the emergence of a variant in time and distance from the root. The line starting at the dot shows the subsequent within variant evolution.
Non-synonymous evolution within variants is much slower than the overall rate of change.
Poxviruses have low evolutionary rates of around one mutation per genome per year. The #monkeypox sequences associated with the recent outbreak, however, differ by about 40 mutations from viruses sequenced 4 years ago. [1/5]
Since 2017, the lineage leading to the recent samples has a peculiar mutation pattern where almost all mutations are G->A or C->T. Furthermore, they almost all occur in specific sequence contexts as Andrew Rambaut discusses here:
We have mapped the fraction of all mutations that are either G->A or C->T and the fraction of them that occur in the specific context (G followed by A for G->A, T preceding C for C->T mutations) onto the tree. [3/5]
Reference genomes don't capture all genetic diversity. This is particularly true for bacteria, where one strain can have 100s kilobases a close relative lacks. This is often summarized by gene-by-gene 'bean-bag' pan-genome analysis.
But genome structure matters! 1/
Nick @n_b_noll has developed a PanPraph for scalable construction of pan-genome graphs from closely related bacterial genomes or plasmids. 2/
The algorithm is based on iteratively growing compatible regions of the trees and removing "blocking" clades that reassorted by optimizing an objective function by simulated annealing. 2/
Within hosts, positions that are initially in a non-consensus state change much faster than consensus positions. This acceleration is particularly pronounced at 2nd positions in codons, that are typically more conserved than 3rd positions. 2/
When tracking the frequency of mutations after they reached a certain frequency window (say 40-60%), reversions to consensus continue to increase in frequency, while that of other mutations is flat or decreases. Hence these reversions are positive selected on average. 3/
The δ variant has caused devastating outbreaks in South Asia and has recently become dominant in the UK, displacing the very transmissible variant α. Various lines of evidence point towards an even higher transmissibility of δ.
But there are some puzzling aspects. [1/5]
As others have pointed out, the δ variant is diverse with a common ancestor at some point last summer. Many genotypes spread across the world, not just one particular lineage as you would expect if a more transmissible variant suddenly started to spread. [2/5]
Outside the UK, the rise of δ has been much slower.
While δ has been consistently detected across Europe since early April, its frequency remained steady at a few percent in May. (linear scale on the left, logit scale on the right) [3/5]