C.1.X sublineage associated with Southern Africa

[grovesn]

C.1.X sublineage associated with Southern Africa

by Natalie Groves

Description

Sub-lineage of: C.1
Earliest sequence: 2021-05-11
Most recent sequence: 2021-06-27
Countries circulating: South Africa (7), UK (2)

Small clade of sequences within lineage C.1 that have a distinct spike profile. Most sequences are from South Africa but sequences have also been observed in travellers in the UK.

Mutations observed:

Gene	Mutations
orf1ab	E102K,T1246I,T1637I,L3201P,G3278S,3675-3677del,P4715L
S	P9L,P25L,C136F,144del,R190S,D215G,243-244del,Y449H,E484K,N501Y,D614G,H655Y,N679K,T716I,T859N
orf3a	255del
M	I82T
N	P13L,R203K,G204R,Q384H

Genomes

clade_sequences.csv

Evidence

Tree shows all GISAID C.1 sequences and clade described highlighted in yellow.

[rambaut]

There are now more genomes of this from various countries - probably needs designating.

[insapathogenomics]

We have also recently detected one sequence with this profile in Portugal with the additional Spike mutation N440K (EPI_ISL_2989113).

[AngieHinrichs]

These sequences seem to cluster with @grovesn and @insapathogenomics sequences:

Shenzhen/IVDC-0610-33/2021      EPI_ISL_2931281 2021-06-15
SouthAfrica/NICD-N10213/2021    EPI_ISL_2984801 2021-07-02
SouthAfrica/NICD-N10228/2021    EPI_ISL_2988404 2021-06-29
SouthAfrica/NICD-N10245/2021    EPI_ISL_2988878 2021-06-29
SouthAfrica/NICD-N10255/2021    EPI_ISL_2988405 2021-06-26
SouthAfrica/NICD-N10596/2021    EPI_ISL_2988409 2021-06-30
SouthAfrica/NICD-N9826/2021     EPI_ISL_2942287 2021-06-15
SouthAfrica/VIDA-KRISP-K018954/2021   EPI_ISL_2841668   2021-06-24
SouthAfrica/VIDA-KRISP-K018963/2021   EPI_ISL_2841677   2021-06-21
Switzerland/VD-CHUV-GEN5512/2021      EPI_ISL_2868597   2021-06

They are kind of messy though, lots of mutations that appear together (or not) inconsistently, so I also wonder how much contamination is muddling the waters here.

Here's a Nextstrain view of all 20 sequences with the most closely related outgroup sequence, from a modified version of the 2021-07-20 UCSC tree (a weird probably-contaminated branch in the UCSC tree attracted the sequences, so I removed that branch and added back these 20 to get this view):
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-139_2021_07_20_lopped.json?branchLabel=Spike%20mutations&c=pango_lineage&label=nuc%20mutations:C2485T,G2659A,C5175T,A7699G,T9867C,A14431C,T28516C

[AngieHinrichs]

Here's another parsimony-ish view when the 20 sequences are added back in a different order (outgroup sequence in red):
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-139_2021_07_20_lopped_addedBack.json?branchLabel=Spike%20mutations&c=pango_lineage&label=nuc%20mutations:G23012A,C23525T,C23709T,T26767C

[chrisruis]

Thanks @grovesn. We've added this as C.1.2 in v1.2.40 with 15 sequence designations (we didn't designate South_Africa/NICD-N10245/2021, South_Africa/NICD-N8122/2021, South_Africa/NICD-N8127/2021, South_Africa/NICD-N8104/2021 and South_Africa/VIDA-KRISP-K018963/2021 as they have >5% ambiguity)