JN.1.42.2 plus S:S31del and Orf1a:E940G (62 , Central America - <10% of samples related to El Salvador and collected after July 1)

[FedeGueli]

I spotted back weeks ago in #1502 a sublineage of JN.1.42.2 (346T) with S:S31del, it turned out to have grown a lot and more interestingly it has been sampled multiple times by GBW in American airports. This could point to some sort of prevalence in some undersampled area or more unlikely towarrd a rapid growth.

Defining mutations: JN.1.42.2 > Orf1a:E940G (A3084G),S:S31del (del21653-55 ) Query:A3084G,del21653 Samples:35 Countries: GBW (8 El Salvador, 2 Mexico, 1 Nicaragua, Uk, HK-CHN ),California, Spain

Genomes

EPI_ISL_19168259, EPI_ISL_19175848, EPI_ISL_19188499, EPI_ISL_19191567, EPI_ISL_19195014, EPI_ISL_19195593, EPI_ISL_19195602, EPI_ISL_19195715, EPI_ISL_19195722, EPI_ISL_19195777, EPI_ISL_19195906, EPI_ISL_19195930, EPI_ISL_19197516, EPI_ISL_19199370, EPI_ISL_19199486, EPI_ISL_19199496, EPI_ISL_19203034, EPI_ISL_19203037, EPI_ISL_19205991, EPI_ISL_19210165, EPI_ISL_19210174, EPI_ISL_19210253, EPI_ISL_19210334, EPI_ISL_19215294, EPI_ISL_19215331, EPI_ISL_19215344, EPI_ISL_19221242, EPI_ISL_19222839, EPI_ISL_19223237, EPI_ISL_19229608, EPI_ISL_19229634, EPI_ISL_19229675, EPI_ISL_19229787, EPI_ISL_19229800, EPI_ISL_19229818

Tree:

[FedeGueli]

57 now but its prevalence in the area where emerged is decreasing.

[aviczhl2]

Designated MS.1 via https://github.com/cov-lineages/pango-designation/commit/beb1f1f8a92e2d8d5084cfc06cd2c31984f5c52d