Document the reasons that the reference is Josiah `NC_004296` and `NC_004297`

[j23414]

Context

Document rationale for using "Josiah" as reference

• Josiah has a longer reference sequence compared to Pinneo
• Commonly used as a comparison standard in laboratory settings
• Designated as the REFSEQ for Lassa virus

I got confused since the tree was rooted to "Pinneo", which highlights to me the need to clarify the distinctions between:

1. Reference sequence: Used for alignment and translation, affecting codon numbering and indel comparisons
2. Root sequence: Provides consistency in phylogenetic tree rooting
3. Reconstructed root: May be necessary for consistent tree rooting when dealing with numerous recent diverse samples but limited historic samples for resolving the tree's trunk

For more information: https://docs.nextstrain.org/en/latest/guides/bioinformatics/root-and-ref-seqs.html

Related to historic issue which set reference to Josiah:

• Consistently pick a reference strain for all builds #22

Description

Examples

Possible solution

[j23414]

• Update the shared references used for identifying L and S segments from Pinneo (shorter) to Josiah (longer reference)
  • shared/lassa_l.fasta
  • shared/lassa_s.fasta

The reason this matters is that if the Pinneo is used with nextclade, the samples are truncated to the Pinneo length.

[j23414]

Logging the idea after chatting with @genehack, to document root and reference in the description.md file similar to mpox here. This is also where one could document a fixed treetime rate if applicable.