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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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First XBB.1.4 sublineage gained S:F486P and Orf1a:V3595F (NSP6_V26F) - 80 Seqs - 70% of Prevalence in Federal District Brazil in May #2031

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

I propose for a rapid review this sublineage pre proposed originally here: https://github.com/sars-cov-2-variants/lineage-proposals/issues/96

The input to find this was an anomaly spotted by a twitter account https://twitter.com/mrmickme/status/1661192927916466176?s=20. The fact is that this sublineage was systematically misassigned by Nextclade to XBB.1.5.63 so that resulted in a sudden spike in prevalence in Brazil. Hence i started digging inding on covspectrum the increasing share of a NSP6 mutation and that rang a bell for me. Checking then the tree directly from CovSpectrum it was immediately clear that i had in front of me something of unprecedented : the first XBB.1.4 sublineage carrying the world dominant mutation S:F486P.

After tracking it a bit on the preproposal page this went on growing hence the immediate transfer to this page, also considering the high prevalence in the Federal District in Brazil.

Lineage:

Defining mutations: XBB.1.4>> T26160C > C7639T > Orf1a:V3595F( G11048T = NSP6_V26F), A20553G > S:F486P (T23018C)

Gisaid query: C7639T , G11048T, A20553G ,T23018C

First Sample: hCoV-19/Brazil/DF-LACENDF-530041388/2023 EPI_ISL_17008513 collected on 2023-02-05

Tree: Schermata 2023-06-02 alle 02 54 07 Schermata 2023-06-02 alle 02 54 33 Schermata 2023-06-02 alle 02 54 59 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1e2bb_93d040.json?label=id:node_6737304

Countries: : 67 out 76 samples of this lineage have been collected in Brazil Schermata 2023-06-02 alle 02 55 52

Prevalence:(Brazil ) 22 out 35 samples collected in the Federal District after May 1 (it was 18 /33 in April) 10 out of 44 samples collected in Goias after April 1 4 out of 34 in Maceio during May

Advantage: If i set #Collection42 maintained by @alurqu with this lineage as baselinefrom March ahead in Brazil there is no lineage that could compete (but be aware that XBB.1.5.70 is very likely underestimated in the chart) ![Schermata 2023-06-02 alle 02 56 28](https://github.com/cov-lineages/ pango-designation/assets/87669813/16e3f8a5-3241-4195-823c-d89b1c983d97) https://cov-spectrum.org/collections/42?country=Brazil

Samples: EPI_ISL_17008513, EPI_ISL_17008515, EPI_ISL_17008523-17008524, EPI_ISL_17127141, EPI_ISL_17127143, EPI_ISL_17127153-17127154, EPI_ISL_17367962-17367963, EPI_ISL_17430470, EPI_ISL_17535830, EPI_ISL_17535836, EPI_ISL_17535839-17535841, EPI_ISL_17535845-17535846, EPI_ISL_17544968-17544969, EPI_ISL_17589400, EPI_ISL_17589759, EPI_ISL_17593021, EPI_ISL_17602539, EPI_ISL_17602543, EPI_ISL_17626865, EPI_ISL_17626875, EPI_ISL_17634656, EPI_ISL_17634658, EPI_ISL_17634665, EPI_ISL_17634667, EPI_ISL_17650981, EPI_ISL_17651140, EPI_ISL_17651266, EPI_ISL_17653472, EPI_ISL_17671371, EPI_ISL_17671374-17671375, EPI_ISL_17671377-17671381, EPI_ISL_17671383-17671385, EPI_ISL_17671387-17671388, EPI_ISL_17694534, EPI_ISL_17694536-17694540, EPI_ISL_17694542-17694543, EPI_ISL_17694545-17694548, EPI_ISL_17695416

FedeGueli commented 1 year ago

Ohio, Paraguay, Matogrosso, Alagoas last 4 seqs definetely expanding outside of the federal district. cc @InfrPopGen

FedeGueli commented 1 year ago

Designated XBB.1.4.2 : via https://github.com/cov-lineages/pango-designation/commit/bd0a1382430f11d728c1be1b40ece95e4675e489