In recent days a new variant has been proposed - a recombinant of BR.2.1 "Cerastes" and XBF "Bythos". The earliest sample reported so far was from Victoria, in mid-January. All the samples globally have been found in Australia - covering New South Wales, Queensland and South Australia.

Recombinant variants typically arise when an immune-compromised patient is infected with multple variants at once. The more often that happens, and the longer the co-infection, the more chances of recombinant variants being formed and spreading to the broader population.

As recombinant variants have become more common, they are involved in more of these scenarios. This gives the virus a multiplier in it's constant search to find new, more evasive combinations.

I'm searching for those samples here by looking for samples with the Spike F486P and NS8 S82T mutations. There are 10 so far, rising to around 1.5% frequency for Australia. There's now very limited genomic sequencing data shared from other states besides NSW, so this could be going undetected elsewhere.

#COVID19 #Australia #XBF #Bythos #BR_2_1 #Cerastes @auscovid19
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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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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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Here's the latest variant picture for Australia:

The BA.5.* lineages continue to fade, down to 30% of recent samples.

There's continued recent growth from the BA.2.75.* lineages (27%) - the leading challenger. The BA.2.75.* clan includes the BR.2.1 (10%) and BN.1.3 (6%) lineages, and many more. These are more prevalent in New South Wales (details below).

BQ.* lineages also continue to grow steadily (23%). These seem far more prevalent in South Australia (details below), and are led by the BQ.1.1 "Cerberus" lineage (9%).

Growth of the X* lineages accelerated recently (18%). The X* clan of recombinant lineages includes the new XBF lineage, which is showing strong growth (12%) - mostly in Victoria (details below).

Recent sample sizes are smaller, but the daily sizes look representative up to Nov 23 (see grey column chart). Representative recent samples have been shared from most states - VIC lags about a week and recent samples from WA are very thin. Samples were shared from the ACT recently, but lag by a couple of weeks. Samples have not been shared from the NT for many months.

#COVID19 #Australia #BR_2_1 #BQ #XBF @auscovid19
🧵

Here's the latest variant picture for Australia:

The BA.5.* lineages continue to fade, down to 34% of recent samples. Recently infected Australians are about 2:1 more likely to have caught one of the many new lineages.

There's continued recent growth from the BA.2.75.* lineages (30%) - the leading challenger. The BA.2.75.* clan includes the BR.2.1 and BN.1.3 lineages, and many more. These are more prevalent in New South Wales (details below).

BQ.* lineages also continue to grow steadily (23%). These seem far more prevalent in South Australia (details below).

The X* lineages were growing more slowly, and recentl fell slightly to (8%). The X* clan of recombinant lineages includes the new XBF lineage, which is showing strong growth - mostly in Victoria (details below).

Recent sample sizes are smaller, but the daily sizes look representative up to Nov 15 (see grey column chart). Representative recent samples have been shared from most states - VIC lags about a week and recent samples from WA are very thin. Samples were shared from the ACT recently, but lag by a couple of weeks. Samples have not been shared from the NT for many months.

#COVID19 #Australia #BR_2_1 #BQ #XBF @auscovid19
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