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Repository for suggesting new lineages that should be added to the current scheme
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Indian BA.2 with S:S371Y and S:1202Q, ORF1a:768R (instead of BA.2 S:S371F) [50 seq, ~5-10% in India] #612

Closed corneliusroemer closed 2 years ago

corneliusroemer commented 2 years ago

Noticed this lineage as it was growing in Belgium and had an interesting mutation: BA.2 S:S371F has mutated further to S:371F (C22674 from T->A).

It seems most common in India, where it's been detected in a lot of states. Elsewhere, it's most common in Belgium at around 1%. But it's been detected in a lot of places.

Detections in India:

Location    Number of sequences Prevalence
Delhi           9   2.84%
Gujarat         1   0.111%
Haryana         6   5.608%
Punjab IN   1   100%
Rajasthan   1   0.035%
Tamil Nadu     23   1.638%
Telangana   1   0.109%
Uttar Pradesh   7   3.554%
India/TN-CDFD-W7-91/2022 | EPI_ISL_12354734 | 2022-04-20    
India/RJ-SMS-ICMR-INSACOG-TS-13631/2022 | EPI_ISL_12363060 | 2022-03-31

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_32723_8220b0.json?label=nuc%20mutations:C18086T

image

https://cov-spectrum.org/explore/India/AllSamples/Past3M/variants/international-comparison?aaMutations=S%3AS371Y%2CORF1a%3A768R%2CS%3A1202Q&pangoLineage=BA.2*&pangoLineage1=BA.2*&

InfrPopGen commented 2 years ago

Thanks for submitting. We've added lineage BA.2.43 with 25 newly designated sequences, and 0 updated designations. Defining mutation(s) A2568G (ORF1a:Q768R), T22674A (S:F371Y), G25166C (S:E1202Q).

FedeGueli commented 2 years ago

Hi @corneliusroemer i was noticing that nextclade (the nextclade option on covspectrum) dont recognize any BA.2.43 sequence, is this the right place to highlight this? https://cov-spectrum.org/explore/India/AllSamples/Past3M/variants?pangoLineage=BA.2.43*&pangoLineage1=BA.2.43*&