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Mike Honey

@Mike_Honey_

Sep 23

8 tweets
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Here's the latest variant picture for the recently-designated BA.2.3.20 lineage, nickname "Basilisk". It has been rising sharply in Singapore, over 5% of recent samples. It has also been reported in some other countries, but at frequencies below 1%. 🧵

The BA.2.3.20 categorisation has yet to roll out to the GISAID database, so I'm approximating it here by searching for samples with the characteristic BA.2.3.20 mutations - NSP2 T547I and NSP3 I896T (h/t @Cornelius Roemer). That method is currently catching around 60 sequences.

For Singapore, BA.2.3.20 has a growth advantage of 8% per day over all BA.5.* lineages, which predicts a crossover in early October. The clustering of points along the trend line is a bit loose, so lower confidence in that prediction.

However for Singapore, BA.2.3.20 has a growth advantage of under 1% per day over all BA.2.75.* lineages (nickname "Centaurus" plus child lineages). BA.2.75.* is now the dominant grouping in Singapore.

Here's the high-level variant picture for Singapore. BA.2.75.* lineages recently took over dominance from BA.5.* lineages. The BA.2.3.30 lineages above are included in the BA.2.* grouping, which recently began growing as well.

Cases had been falling steadily in Singapore, but that trend reversed in early September, and they climbed again to a rate of around 40/100K daily cases. That change coincided with the rise in frequency of BA.2.75.* and BA.2.* to around 20-40%.

Interactive genomic sequencing dataviz, code, acknowledgements and more info here: github.com/Mike-Honey/cov… Mutation matching dataviz here: github.com/Mike-Honey/sar…

On this thread, @Ryan Hisner (first to spot this one) described BA.2.3.20 in some detail, explaining it's rare 2-nucleotide mutation: twitter.com/LongDesertTrai…

Ryan Hisner

@LongDesertTrain

Sep 01View on Twitter

Today I discovered an extraordinary microlineage of BA.2.3. What makes it extraordinary? A colossal genetic saltation (10 spike mutations) combined with striking geographic spread for a very small number of sequences (just 4 so far). 1/25 github.com/cov-lineages/p…

Description Sub-lineage of: BA.2.3 Earliest sequence: 2022-8-15, USA, California — EPI_ISL_14744358 Most recent sequence: 2022-8-24, Singapore — EPI_ISL_14727166 Countries circulating: Singapore (2...

github.com/cov-lineages/p…

BA.2.3 Sublineage with 10 highly convergent S1 mutations (5 seqs, 3xSingapore, 1xAustralia, 1xUSA)...

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Mike Honey

@Mike_Honey_

Data Visualisation and Data Integration specialist - Melbourne, Australia

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