It is probably still highly effective against severe outcomes and death. But the protection against infection will decline over time. There are +5 new spike mutations from LP.8.1 (current vaccine) to SF.1, plus +1 more for the proposed new lineage. OTOH there are still ~60 spike mutations matched.

Here are the leading detailed lineages. SF.1 has been driving the Nimbus rebound in NZ. SF.1 added the ORF3a:S40P mutation to PQ.43.1.1. 🧵

Here's the latest variant picture for New Zealand, to early July. BA.3.2.* "Cicada" was been dominant during June, but fell to finish at 26%. NB.1.8.1 "Nimbus" rebounded to 53% in early July. #COVID19 #SARSCoV2 #NZ 🧵

Here are the leading detailed lineages, with RK.1 dominant. 🧵

Here's the latest variant picture for Australia, to the end of June. NB.1.8.1.* "Nimbus" remained dominant, but fell to 45%. #COVID19 #SARSCoV2 #Australia 🧵

Australia has displaced the US in producing the highest volume of samples recently. Also Singapore has leap-frogged Canada. 🧵

Here's the latest mutation picture from the global clinical samples, zoomed into the bottom-left quadrant. D420N is moving to the centre as it becomes more "mainstream" with SV.* and RK.1.*. It’s still a long way NW of the split line, so still growing. 🧵

The TA.1 lineage adds the Spike Q613H mutation onto XFG.14.8.1, and has been reported with a very broad geographical distribution. 3 of the samples shared from the US were International Travellers arriving from Nigeria. 🧵

Here are the leading detailed lineages, with SV.1.* and RK.1.* prominent. 🧵

Here's the latest variant picture with a global scope, to the end of June. NB.1.8.1 "Nimbus" continued to dominate, growing to 47%. XFG.* "Stratus" fell to 25%. 🧵

Here's what I'm getting at the lineage level for NSW. The picture had been dominated by RK.1 (NB.1.8.1.* Nimbus), but there was an interesting late surge in the new QF.7.2 (XFG.* Stratus), featuring the Spike I197V mutation.

Here's the latest variant picture for Australia, to late June. NB.1.8.1.* "Nimbus" remained dominant, finishing at 60%. BA.3.2.* "Cicada" was roughly flat at 23%. #COVID19 #SARSCoV2 #Australia 🧵

XHB is a newly defined recombinant of PY.1.1 and RV.1.1.1 (descended from XFG.23.1.3). The first samples were collected in France and then the Netherlands, in March. 2 more samples were recently collected in French Guiana. 🧵

Here’s map of the JN.1.* + FLiRT samples for the 6 weeks up to June 21. Singapore has been the global hotspot, with samples also reported from across Asia, North America and Oceania. 🧵

Here are the leading sub-lineages of JN.1.* + FLiRT, with the recent growth driven by the RF.5.* branch. 🧵

Here's the latest variant picture with a global scope, to late June. NB.1.8.1 "Nimbus" was roughly flat at 50%. JN.1.* + FLiRT (led by RF.5.*) grew to take over second spot from XFG.* "Stratus" at 18%. 🧵

The "small multiples" view of deaths by DRC Health Zone highlights sharp recent growth in Nizi and also Mangala. 🧵

I recently integrated the data series for Cumulative Confirmed Deaths. It’s interesting that Mongbalu health zone has reported the most deaths, despite a lower level of cases than Bunia – perhaps representing differences in care and treatment capacity or underreporting. 🧵

Bunia remains the leading Health Zone in terms of cases. The growth appears to have slowed somewhat in Rwampara. Cases have been growing rapidly in Nizi, since the start of July. 🧵

Here’s the latest picture of the Bundibugyo Ebola outbreak in the DRC, up to June 8 (SitRep 55). Confirmed cases have continued growing at a roughly steady pace. The total by Health Zone is 1,789, with 3 cases unassigned. 🧵

XHA is a newly defined recombinant of TB.2 (descended from XFG.5.1.7) and RV.1.1.1 (descended from XFG.23.1.3). A further sample was shared from South Africa, collected in April (before the previously-reported samples). 🧵

Here's the latest variant picture with a global scope, to mid-June. NB.1.8.1 "Nimbus" grew slightly to 54%. XFG.* "Stratus" fell further to 16%. BA.3.2.* "Cicada" was roughly flat at 15%. 🧵

An amazing scenario of convergent evolution Fede! S:D420N continues to star in the "fresh and blazing" sub-quadrant of my mutation scatter (from recent GISAID clinical samples, globally).

The genomic sequencing data from Thailand is still super thin and patchy. But it looks increasingly like the culprits are the new JN.1.* + FLiRT sub-lineages: RF.5.*. RF.5. features the Spike K478T (reversion) mutation. Those lineages are also common among International Travellers into the US.

For the US, XFJ.* (including RW.1.1.*) showed a growth advantage of 4.4% per day (31% per week) over XFG.*, which predicts a crossover in early June (the data routinely lags). 🧵

Here's the latest variant picture for the United States, to early June. XFG.* "Stratus" remained dominant but fell sharply to 39%. XFJ.* (led by RW.1.1.*) finished at 18%. JN.1.* + FLiRT (led by RF.5.*, mostly from International Travellers) finished at 18%. #COVID19 #SARSCoV2 #USA 🧵

There’s no significant jump associated with that takeover in the wastewater signals reported at poops.nz, apart from in Dunedin, Otago. The level there is the highest since August 2025. 🧵

Here's the latest variant picture for New Zealand, to mid-June. BA.3.2.* "Cicada" grew sharply to dominance at 67%. NB.1.8.1 "Nimbus" fell sharply to 22%. #COVID19 #SARSCoV2 #NZ 🧵

The recent samples have been dominated by New South Wales and South Australia. 🧵

RK.1 has reportedly been most successful in New South Wales, reaching 68% of samples. 🧵