Here's the latest variant picture for the new "FLip" variant DV.7.1.

The leading countries reporting DV.7.1 are Spain (9%) and Israel (4%).

DV.7.1 is from the CH.1.1.* "Orthrus" clan; DV is an alias for CH.1.1.1.1. DV.7 added the Spike L858I mutation, then DV.7.1 added the adjacent L455F and F456L mutations, hence the "FLip" nickname.

Yunlong Cao explained the advantage of this pair of mutations here:
https://twitter.com/yunlong_cao/status/1687879512237993986?s=20

HT Raj Rajnarayanan (https://twitter.com/RajlabN) for the clever "FLip" tag.

Sample volumes from many countries are now very thin and patchy, leading to some variations.

#COVID19 #FLip #DV_7_1 #CH_1_1 #Orthrus

Here's the latest variant picture for New Zealand.

XBB.1.5.* "Kraken" (28%) has rebounded to overtake CH.1.1.* "Orthrus" (25%). XBB.1.16.* "Arcturus" (16%) and XBB.1.9.* "Hyperion" (19%) are still significant.

The new EG.5.* variant (5%) is present and growing, but is not significant yet.

The vigorous mix of variants implies increased immediate reinfection risks for those relying on immunity from a prior infection. Every variant is a minority of the recent samples.

The sample volumes seem representative up to July 10.

#COVID19 #NZ #XBB_1_5 #Kraken #CH_1_1 #Orthrus #XBB_1_16 #Arcturus #XBB_1_9 #Hyperion
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Here's the latest variant picture for New Zealand.

CH.1.1.* "Orthrus" (36%) rebounded to a leading position, in a close contest with XBB.1.16.* "Arcturus" (29%) and XBB.1.9.* "Hyperion" (29%).

The vigorous mix of variants implies increased immediate reinfection risks for those relying on immunity from a prior infection. Every variant is a minority of the recent samples.

The sample volumes seem representative up to June 22. Unfortunately, the update cycle for NZ seems to have fallen back to once a month. Any successful new variant will likely already be widespread by the time it appears in this data. More timely summarised frequencies are shared weekly (not via GISAID), but for a very limited set of variants.

#COVID19 #NZ #CH_1_1 #Orthrus #XBB_1_16 #Arcturus #XBB_1_9 #Hyperion
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Here's the latest variant picture for the Australian Capital Territory (ACT).

XBB.1.9.* "Hyperion" (29%) and CH.1.1.* "Orthrus" (29%) are battling for dominance.

XBB.1.16.* "Arcturus" (18%) and "Deltacron" XBC.* (13%) are still quite significant.

The chaotic mix of very different variants poses a raised immediate re-infection risk for anyone relying on natural immunity from a recent infection.

The sample volumes seem representative up to June 1.

#COVID19 #Australia #ACT #Canberra #FK_1_1 #CH_1_1 #Orthrus #XBB_1_16 #Arcturus @auscovid19

Here's the latest variant picture for Western Australia.

The XBC.* Deltacron variant clan (31%) appears to have surged to dominance, although recent samples are a bit patchy.

You could throw a blanket over XBB.1.16.* "Arcturus" (20%), XBB.1.9.* "Hyperion" (19%) and CH.1.1.* "Orthrus" (17%) variants.

XBB.1.5.* "Kraken" (9%) is still significant, along with XBB.2.3.* "Acrux" (9%).

The variant mix in WA continues to be uniquely chaotic, reflecting its situation as a global crossroads. Even WA residents who've been racking up regular reinfections are likely to meet new variants capable of overcoming their immunity. Four variants are at 17%+ frequency, with another two around 10%.

The sample volumes seem representative up to May 16.

#COVID19 #Australia #WA #Perth #XBC #Deltacron #XBB_1_9 #Hyperion #XBB_1_5 #Kraken #XBB_1_16 #Arcturus #CH_1_1 #Orthrus @auscovid19
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Here's the latest variant picture for the Australian Capital Territory (ACT).

XBB.1.9.* "Hyperion" (23%) has rebounded back to dominance.

There's been a recent surge from the last non-recombinant clan: CH.1.1.* "Orthrus" (18%).

The XBB.1.5.* "Kraken" clan (18%) is still significant.

XBB.1.16.* "Arcturus" (17%) is also quite prominent.

"Deltacron" XBC.* (16%) has been growing recently.

Be alert for conjunctivitis symptoms, particularly associated with the Arcturus variant.

The chaotic mix of very different variants poses a raised immediate re-infection risk for anyone relying on natural immunity from a recent infection.

The sample volumes seem representative up to May 17.

#COVID19 #Australia #ACT #Canberra #FK_1_1 #CH_1_1 #Orthrus #XBB_1_16 #Arcturus @auscovid19

Here's the latest variant picture for New Zealand. The sample volumes seem representative up to May 18.

XBB.1.16.* "Arcturus" (28%) has been growing steadily and now appears dominant, displacing CH.1.1.* "Orthrus" (23%).

Be alert for conjunctivitis symptoms, which seem more common with the "Arcturus" variant, although it's wave has likely peaked already by now.

XBB.1.5.* "Kraken" (19%) and XBB.1.9.* "Hyperion" (15%) are both significant.

XBB.2.3.* "Acrux" (9%) is starting to rise

The vigorous mix of variants implies increased immediate reinfection risks, for those relying on immunity from a prior infection.

#COVID19 #NZ #XBB_1_16 #Arcturus #CH_1_1 #Orthrus #XBB_2_3 #Acrux
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Here's the latest variant picture for the Australian Capital Territory (ACT).

There's been an unexpected surge from the last non-recombinant clan: CH.1.1.* "Orthrus" (28%).

XBB.1.16.* "Arcturus" (24%) is also very prominent.

"Deltacron" XBC.* (18%) has been growing recently.

XBB.1.9.* "Hyperion" (14%) has falled sharply from dominance.

The XBB.1.5.* "Kraken" clan (12%) has fallen but is still significant.

The chaotic mix of very different variants poses a raised immediate re-infection risk for anyone relying on natural immunity from a recent infection.

The sample volumes seem somewhat representative up to May 12.

#COVID19 #Australia #ACT #Canberra #CH_1_1 #Orthrus #XBB_1_16 #Arcturus @auscovid19

Here's the latest SARS-CoV-2 variant picture for New Zealand:

XBB.1.5 "Kraken" (36%) became dominant in early March.

It's main rival recently has been the resurgent CH.1.1 "Orthrus" (20%). This variant is hanging on impressively in NZ - in other countries where CH.1.1 was strong, it had faded below 10% by mid-February, as XBB.1.5 took over.

Newcomer XBB.1.9.1 "Hyperion" (7%) has been rising steadily.

XBF "Bythos" has faded below 5%.

Recent sample sizes are very solid and recent, up to March 11 (see grey column chart). However the cadence of updates appears to be roughly monthly, unfortunately.

#COVID19 #NZ #XBB_1_5 #CH_1_1 #Orthrus #Kraken #XBB_1_9_1 #Hyperion #XBF #Bythos
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Here's the latest variant picture for the United Kingdom:

The XBB.1.5 "Kraken" lineage (29%) is clearly dominant now, and is still rising. There's some slower growth from CH.1.1 "Orthrus" (15%). BQ.1.1 "Cerberus" has declined (9%).

Recent samples look representative, up to 3 February.

#COVID19 #UK #CH_1_1 #Orthrus #BQ_1_1 #Cerberus #XBB_1_5 #Kraken
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Here's the latest variant picture for the United Kingdom:

The XBB.1.5 "Kraken" lineage (9%) is rising rapidly, challenging the incumbents CH.1.1 "Orthrus" (20%) and BQ.1.1 "Cerebrus" (16%).

Recent samples look representative, up to 6 January.

#COVID19 #UK #CH_1_1 #Orthrus #BQ #Cerebrus #XBB_1_5 #Kraken
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Here's the latest variant picture for Hong Kong:

CH.1.1 "Orthrus" lineage (45%) appears to still be dominant, driving a wave of cases and deaths.

Recently it has been challenged by a sudden rise in the new BF.7.14 "Tarandos" lineage (36%). This is descended from the BA.5 lineage, and was first reported from China in November. I beleive this is the first significant spread of lineages out of China to other countries/territories. The sampling might not be random, e.g. targetting travellers from China.

BQ.1.1 "Cerberus" lineage (20-30%) is still present, but hasn't been dominant for some months now.

Recent samples look representative, up to 1 January.

#COVID19 #HongKong #CH_1_1 #Orthrus #BF_7_14 #Tarandos
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Here's the latest SARS-CoV-2 variant picture for New Zealand:

The BA.2.75.* clan lineages are now dominant at 52%. CH.1.1 "Orthrus" is the leading lineage in this clan at 32%. BR.2.1 (dominant in New South Wales) has slowly grown to 10%.

The X* recombinant lineages have been growing slowly. This includes the XBF "Bythos" lineage at 8%, which has showed strong growth in Victoria, Australia. There were only 2 samples reported for XBB.1.5 "Kraken" so far.

The BQ.* lineages (led by BQ.1.1 "Cerberus") are flat at around 22%.

The BA.5.* lineages continue to fade, down to 17% of recent samples. Recently infected Kiwis are 5:1 more likely to have caught one of the many new lineages.

It's hard to predict how this unprecendented scenario will play out. This particular combination seems unique to NZ.

Recent sample sizes are very solid and recent, up to Dec 19 (see grey column chart).

#COVID19 #NZ #CH_1_1 #BQ #XBF
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Here's the latest variant picture for Australia - the chaotic swarm of new lineages continue vying for dominance in each state:

There's continued recent growth from the BA.2.75.* lineages (41%). The BA.2.75.* clan includes the BR.2.1 (18%) and CH.1.1 "Orthrus" (4%) lineages, and many more. These are more prevalent in New South Wales and Tasmania (details below).

The X* clan of recombinant lineages includes the new XBF "Bythos" lineage, which is showing steady growth (22%) - mostly in Victoria (details below), but rising rapidly in most other states now.

Growth of the BQ.* lineages appears to have plateaued (21%). These seem far more prevalent in South Australia (details below), and are led by the BQ.1.1 "Cerberus" lineage (9%).

The BA.5.* lineages continue to fade, down to 12% of recent samples.

Recent sample sizes are smaller, but the daily sizes look representative up to 15 December (see grey column chart). Representative recent samples have been shared from most states, although WA and SA lag the others by about a week. Samples shared from the ACT stalled in November. Samples have not been shared from the NT for many months.

#COVID19 #Australia #BR_2_1 #CH_1_1 #BQ #XBF @auscovid19
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#CH_1_1 has already dislodged #BA_5 in Hong Kong.
Still no warning from the #WHO that this lineage is potentially close to #Delta :
- For its pathogenicity / fusogenecity.
- Because it doesn't give a f*** about vaccines.
Made in Europe...

Sharing this post again, since the #CH_1_1 lineage starts to be everywhere, especially in Europe
And that its sequence tells us it is potentially more dangerous since it shares a significant "fusogenic" portion with Delta lineage...
https://aus.social/@mike_honey_/109514781053014808

Here's the latest variant picture for Australia - an unprecedented chaotic swarm of new lineages are vying for dominance in each state:

There's continued recent growth from the BA.2.75.* lineages (40%). The BA.2.75.* clan includes the BR.2.1 (19%) and CH.1.1 "Orthrus" (5%) lineages, and many more. These are more prevalent in New South Wales and Tasmania (details below).

Growth of the BQ.* lineages appears to have plateaued (18%). These seem far more prevalent in South Australia (details below), and are led by the BQ.1.1 "Cerberus" lineage (4%).

The X* clan of recombinant lineages includes the new XBF "Bythos" lineage, which is showing steady growth (12%) - mostly in Victoria (details below), but rising rapidly in most other states now.

The BA.5.* lineages continue to fade, down to 18% of recent samples.

Recent sample sizes are smaller, but the daily sizes look representative up to 30 November (see grey column chart). Representative recent samples have been shared from most states - VIC lags about a week. Samples shared from the ACT resumed recently, but is now lagging by several weeks. Samples have not been shared from the NT for many months.

#COVID19 #Australia #BR_2_1 #CH_1_1 #BQ #XBF @auscovid19
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The new CH.1.1 "Orthrus" lineage appears to have sparked fresh waves across several European countries. Here are the European countries reporting significant growth in CH.1.1 samples.

The Netherlands is reporting the highest frequency (14%), followed by Ireland (11%), the UK (10%), Switzerland (6%), Sweden (4%) and Denmark (2%).

These countries all had significant BQ.* waves just a month or two earlier, so it seems prior immunity from BQ.* infections is not protective against CH.1.1? I'd be very interested some expert opinions on this.

The CH.1.1 lineage categorisation has yet to roll out to the GISAID database, so I'm approximating it here by searching for samples with the characteristic mutations - Spike F486S, Spike K444T, Spike L452R and Spike R346T (h/t https://mstdn.science/@corneliusroemer).

That method is currently catching ~1,050 sequences across Europe, since the start of November.

CH.1.1 is also driving the current waves in Hong Kong and New Zealand, and making a noteworthy contribution in South Australia.

The CH.1.1 lineage traces it's ancestry back to BA.2 (via BM.4.1.1), but has arrived at the same set of RBD mutations as BQ.1.1, as Moritz Gerstung shows on this thread.
https://twitter.com/MoritzGerstung/status/1593212033755131904

#COVID19 #Denmark #Ireland #Netherlands #Sweden #Switzerland #UK #CH_1_1 #Orthrus
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Here's the latest SARS-CoV-2 variant picture for New Zealand:

The BA.5.* lineages continue to fade, down to 37% of recent samples. Recently infected Kiwis are 2:1 more likely to have caught one of the many new lineages.

There's continued recent growth from the BA.2.75.* lineages (33%) - the leading challenger. The BA.2.75.* clan includes the CH.1.1 "Orthrus" lineage, and more (details below).

BQ.* lineages also grew steadily, but growth appears to have slowed recently (21%).

The X* lineages have been growing more slowly, and also seem flat recently (8%). The X* clan of recombinant lineages includes the new XBF "Bythos" lineage, which has showed strong growth in Victoria, Australia. XBB.1 "Gryphon" was dominant in Singapore, but has peaked in NZ at 3% so is not a significant factor.

It's hard to predict how this unprecendented scenario will play out. Perhaps natural immunity from CH.1.1 infections will suppress the rise of the other new lineages, or not. This particular combination seems unique to NZ.

Recent sample sizes are very solid and recent, up to Nov 28 (see grey column chart).

#COVID19 #NZ #CH_1_1 #BQ #XBF
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Here's the latest variant picture for the United Kingdom:

The BQ.* lineages (35%) are being challenged by the new CH.1.1 lineage (8%).

The CH.1.1 lineage traces it's ancestry back to BA.2 (via BM.4.1.1), but has arrived at the same set of RBD mutations as BQ.1.1, as Moritz Gerstung shows on this thread.
https://twitter.com/MoritzGerstung/status/1593212033755131904?s=20&t=sFVYR1-2cvqsc9D14-TAKg

CH.1.1 is driving the current waves in Hong Kong and New Zealand.

Recent samples look representative, up to 25 November.

#COVID19 #UK #CH_1_1 #BQ
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