Mary Wilson
Well-known member
JosieLikes...opened this issue Jul 14, 2022
Hi everyone, I'm just opening this issue to highlight that there are several sequences with an unusual mutation pattern in our most recent upload from South Africa, which will potentially represent two new lineages if more sequences are detected. The teams in our genomic surveillance network (NGS-SA) as well as our public health institute (NICD) are closely monitoring the sequences and cases in the country. These new constellations have been detected only in a small proportion of recent data, and our cases remain low.
I know these do not yet meet requirements for designation, as there are only N=4 and N=3 (2 available on GISAID, last 1 will be released tomorrow) sequences for each constellation, but we thought they would probably be of interest and picked up here/on Twitter eventually. For now, please see below for some details and the major mutation profiles for the two groups of sequences.
silcn commented Aug 23, 2022
... silcn commented Aug 25, 2022
https://github.com/cov-lineages/pango-designation/issues/844?s=16
Hi everyone, I'm just opening this issue to highlight that there are several sequences with an unusual mutation pattern in our most recent upload from South Africa, which will potentially represent two new lineages if more sequences are detected. The teams in our genomic surveillance network (NGS-SA) as well as our public health institute (NICD) are closely monitoring the sequences and cases in the country. These new constellations have been detected only in a small proportion of recent data, and our cases remain low.
I know these do not yet meet requirements for designation, as there are only N=4 and N=3 (2 available on GISAID, last 1 will be released tomorrow) sequences for each constellation, but we thought they would probably be of interest and picked up here/on Twitter eventually. For now, please see below for some details and the major mutation profiles for the two groups of sequences.
silcn commented Aug 23, 2022
| 2 more sequences from Constellation 1: EPI_ISL_14585888, EPI_ISL_14585891 Both from Western Cape, South Africa, sampled 2022-08-08. |
... silcn commented Aug 25, 2022
| Looks like XAY encompasses both clusters. Possibly not strictly following the Pango rules, but there clearly is shared ancestry between the two clusters even if it's impossible to say what the "common ancestor" is. In my opinion the larger cluster should immediately be designated XAY.1, and if the smaller cluster reaches 5 sequences then it should be XAY.2. |
| aq-sun commented Aug 26, 2022 This seems like the appropriate thing to do - I'll reopen the issue and monitor for further development in constellation 2, and designate the larger constellation as XAY.1. |
https://github.com/cov-lineages/pango-designation/issues/844?s=16