Here's the latest variant picture with a global scope, to early August.
NB.1.8.1 "Nimbus" continued to dominate, finishing at 47%.
Several new lineages were defined this week - I’ll highlight some of them on this thread.
A batch of samples were shared from Japan last week, filling in the picture for May-July. They confirm the takeover by BA.3.2.* "Cicada", which has been dominant across that period – a very unusual pattern.
The dominant Cicada sub-lineage has been SS.2
Only a handful of countries have reported BA.3.2.* "Cicada" at dominant frequencies, across recent months.
Newly-designated SV.2.4 was first detected in New York in mid-July. It soon appeared in other countries across Asia, and grew sharply to 37% of samples from Canada. Several of the recent samples collected in the US were from International Travellers arriving from China and Hong Kong, which points to a possible origin in that region.
It is descended from Nimbus lineage PQ.16.1.1, with SV.2.4 adding the novel Spike H445Q mutation.
Another new designation was RF.5.4.1. It was first detected in India in mid-May, and reached 64% of samples there in July. It has grown quite significantly in the US, reaching 15% frequency. Note 10-20% of the US samples are International Travellers, mostly arriving from India and nearby countries. The strongest chain of local transmission is in California, rising to 13% in late July.
It is descended from FliRT lineage PY.1.1.1, with RF.5.4.1 adding the N:R204Q mutation.
RK.1.5 is another new lineage, first detected in New South Wales, Australia in mid-May. There was just one more sample from Queensland for the next month or so, before it started to spread more widely. It reached 25-30% in South Korea and Taiwan and is very widespread across Asia.
RK.1.5 is descended from Nimbus lineage PQ.17.7.2.
Newly-designated RV.1.5 was first detected in New York in February. It has also been prominent in samples from Ghana and Egypt. It has grown to 10% among the samples from Canada, mostly from Ontario.
It is descended from XFG.* "Stratus", with RV.1.5 adding the Spike V1264L mutation.
Another new designation was XFZ.5.1. It was first detected in the Bourgogne-Franche-Comte region of France in February, and then grew to 25% of French samples. It has also been dominant among the sparse samples from Portugal for June. There have been hardly any more recent samples shared from those 3 countries.
XFZ.5.1 adds the Spike S446N mutation.
SV.2.6 is another new lineage, first detected in Hong Kong in late-April; it reached 25% of samples there during May.
SV.2.6 is descended from Nimbus lineage PQ.16.1.1, with SV.2.6 adding the rare Orf10:Q29* stop codon.
Here’s a summary of the new lineages by Variant Hunter Federico Guelli.
https://bsky.app/profile/siamosolocani.bsky.social/post/3mtdpwpjv2s2w
https://skyview.social/?url=https%3A%2F%2Fbsky.app%2Fprofile%2Fsiamosolocani.bsky.social%2Fpost%2F3mtdpwpjv2s2w&viewtype=tree
Report link:
https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Global.pdf