GISAID lineage information

From: 

https://www.gisaid.org/references/statements-clarifications/clade-and-lineage-nomenclature-aids-in-genomic-epidemiology-of-active-hcov-19-viruses/

Clade and lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses

Due to the naturally expanding genetic diversity of hCoV-19 viruses, GISAID introduced a nomenclature system for major clades, developed by Sebastian Maurer-Stroh et al, based on marker mutations within 8 high-level phylogenetic groupings from the early split of S and L, to the further evolution of L into V and G, and later of G into GH, GR and GV, and more recently GR into GRY.

GISAID clades are augmented with more detailed lineages assigned by the Phylogenetic Assignment of Named Global Outbreak LINeages (Pango lineage) tool, aiding in the understanding of patterns and determinants of the global spread of the pandemic strain causing COVID-19. A third effort uses a Year-Letter nomenclature to facilitate discussion of large-scale diversity patterns of hCoV-19 and label clades that persist for at least several months and have significant geographic spread. 

The list of the marker variants is as follows:

   S: C8782T,T28144C includes NS8-L84S
   L: C241,C3037,A23403,C8782,G11083,G26144,T28144 (early clade markers in WIV04-reference sequence)
   V: G11083T,G26144T NSP6-L37F + NS3-G251V
   G: C241T,C3037T,A23403G includes S-D614G
   GK: C241T,C3037T,A23403G,C22995A S-D614G + S-T478K
   GH: C241T,C3037T,A23403G,G25563T includes S-D614G + NS3-Q57H
   GR: C241T,C3037T,A23403G,G28882A includes S-D614G + N-G204R
   GV: C241T,C3037T,A23403G,C22227T includes S-D614G + S-A222V
   GRY: C241T,C3037T,21765-21770del,21991-21993del,A23063T,A23403G,G28882A includes S-H69del, S-V70del, S-Y144del, S-N501Y + S-D614G + N-G204R