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Update nextclade dataset README to reflect clade changes [#12]
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genehack committed Aug 22, 2024
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## Scope of this dataset

This dataset assigns genotypes to yellow fever virus samples based on
This dataset assigns clades to yellow fever virus samples based on
strain and genotype information from [Mutebi et al.][] (J Virol. 2001
Aug;75(15):6999-7008) and [Bryant et al.][] (PLoS Pathog. 2007 May 18;3(5):e75)

Expand All @@ -21,6 +21,19 @@ comprises the 3' end of the pre-membrane protein (prM) gene, the
entire membrane protein (M) gene, and the 5' end of the envelope
protein (E) gene.

The clades we annotate (Clade I-VII) are roughly equivalent with the
following genotypes as described in the aforementioned two papers:

| Clade | Genotype |
|-----------|---------------------|
| Clade I | Angola |
| Clade II | East Africa |
| Clade III | East Central/Africa |
| Clade IV | West Africa I |
| Clade V | West Africa II |
| Clade VI | South America I |
| Clade VII | South America II |

(N.b., the reference sequence used in this data set is actually 672nt
long, from bases 641-1312 of the genome reference. The 2 extra bases
make the reference an complete open reading frame.)
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