Here's the latest picture for the new BA.2.75 sub-lineage (nickname: "Centaurus") - an evolutionary jump from BA.2.

It has most commonly been detected in India, showing extremely rapid growth to 18% of recent samples.

It is also spreading rapidly to other countries.
🧵
As that classification has yet to flow out to the GISAID database, I'm approximating it by searching for the defining Spike K147E and W152R mutations.

Note the Frequency is calculated for each country independently, compared to all the recent samples sequenced in that country.
Here's the growth of "BA.2.75" in the states of India. Most of the 31 samples shown have been reported from Maharashtra (Mumbai).

Samples sizes for India are shown in the grey column chart across the bottom.
For India, "BA.2.75" has a very high growth advantage of 16% per day over all BA.2.* lineages, which predicts a recent crossover.
Here's the latest variant picture for India. BA.5 had begun rising, but might already be suppressed by BA.2.75.
For context, here's a dataviz on India's recent cases, deaths, testing, vaccinations and protections.

Daily cases have been below 3,000 for months, but recently started rising as high as 18,000, but still only 1/100K population.
Interactive mutation matching dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/sar…

Genomic sequencing dataviz here:
github.com/Mike-Honey/cov…

COVID stats dataviz here:
github.com/Mike-Honey/cov…

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More from @Mike_Honey_

Jul 2
Here's the latest variant picture for Portugal.

BA.5.1 (Spike L452R mutation, others) rose steadily to take over from BA.2 in mid-May, and has continued to rise to ~90% of recent samples.

Portugal was the first country where BA.5.* became dominant.
🧵
For context, here's a dataviz on Portugal's recent cases, deaths, testing, vaccinations and protections.

During May, reported daily case rates rose to ~270/100K.

Death rates also rose to ~47/10M, the highest since early Feb.

Cases and deaths have receded to the pre-BA.5 level
Portugal's experience with BA.5 should be indicative for the many other countries with similar immunity profiles that are entering their BA.5 wave.
Read 4 tweets
Jul 1
Here's my first effort at tracking the new BA.2.75 sub-lineage. This is attracting a lot of interest as it has an impressive list of mutations, and appears to be an evolutionary jump from BA.2.

It has most commonly been detected in India, showing rapid growth.
🧵
As that classification has yet to flow out to the GISAID database, I'm approximating it by searching for the defining Spike K147E and W152R mutations.

Note the Frequency is calculated for each country independently, compared to all the recent samples sequenced in that country.
I'll refresh this every few days to track the spread of BA.2.75, and dive into the locations for some countries when there is enough data for informative time-series charts.
Read 7 tweets
Jun 30
Here's the latest variant picture for Germany.

BA.5 (Spike L452R mutation, others) has won the race to replace BA.2, beating out BA.2.12.1 and BA.4.

BA.5 has risen to 41% of recent samples.
🧵 ImageImage
This chart shows the rise of the 3 new lineages in Germany.

BA.5 has dominated from the outset. Image
@Unusual_Times highlighted the unusually high proportion of BA.5 samples from Germany with the N:E136D mutation - approaching 20% frequency.

This was recently classified as BA.5.3.1, but that has not flowed out to the GISAID database yet. ImageImage
Read 6 tweets
Jun 30
Here are the latest covid stats for Australia, covering the last 8 weeks.

The trends for cases were declining but have begun to rise again.

Hospitalised is currently the highest across that period.

States and territories below.
🧵 Image
In New South Wales, cases are rising and hospitalised and deaths are at a high for the 8-week period. Image
In Victoria, cases and hospitalised are rising again.

PCR tests are declining steadily - under 1/3rd of the recent peak.

The crude Case Fatality Rate is still the highest nationally. Image
Read 10 tweets
Jun 28
Here's the latest variant picture for the Philippines.

BA.5 (Spike L452R mutation, others) has won the race to replace BA.2, beating out BA.2.12.1 and BA.4.

BA.5 has risen to 42% of recent samples.
🧵 ImageImage
This chart shows the rise of the 3 new lineages in the Philippines.

BA.2.12.1 took an early lead, but the growth rate of BA.5 is more rapid. Image
For context, here's a dataviz on the Philippines' recent cases, deaths, testing, vaccinations and protections.

Daily cases have begun rising noticeably with BA.5, but still only at 1/100K (around 800 cases).

"Fully vaccinated" (boosted within 120 days) has declined to 4%. Image
Read 5 tweets
Jun 28
Here's the latest variant picture for Indonesia.

BA.5 (Spike L452R mutation, others) has won the race to replace BA.2, beating out BA.2.12.1 and BA.4.

BA.5 has risen to 46% of recent samples.
🧵
This chart shows the rise of the 3 new lineages in Indonesia.

BA.5 has grown very rapidly since it was introduced.
For context, here's a dataviz on Indonesia's recent cases, deaths, testing, vaccinations and protections.

Daily cases have begun rising noticeably with BA.5, but still only at 1/100K (around 2,000 cases).

"Fully vaccinated" (boosted within 120 days) has risen to 14%.
Read 5 tweets

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