Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

Question

I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question...

one Bat Sars coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(28572..28784) proteins
Sars2 identify in GenBank as MN908947_3, has range 28284..28577
not labeled as ORF13 and the same 28734..28955 is not labeled as ORF14?

The ORF13(28122..28415) of Bat coronavirus and  PSEUDO_ORF13(28284..28577) of sars2 share 72% homology
and ORF14(28572..28784) of Bat coronavirus and  PSEUDO_ORF14(28734..28955) of sars2 share 75% homology

This seems one publication for ORF14 and ORF13 in Bat Viruses and relations in Sars2 here
The author say that ORF14 in Sars2 is all contained in N protein...
And ORF13 is know in that above link as ORF9B
and in that written is said ORF9B is implied in immunitary innate suppression...

M__ · Answer

The virus Rp3 stands for Rhi pea isolated in China in 2004.
The trees is here and groups with the Bulgarian sarbecoviruses and is closely related to the African sarbecoviruses. Thus although it is a Chinese sarbecovirus is not with the "Chinease originating" clade as is SARS and Covid-19.
Thats why the more mysterious ORFs ORF13 and 14 are missing, because over notable genetic distances these genes along with ORF10 are present/absent. This is a common feature of the betacoronaviruses.
In summmary this virus is notably distance from the major human pathogenic SARS/covid-19 viruses. Thus the absence of these auxilary genes isn't really surprising.
Its the very last taxa on the SARS-related viruses clade (monophyly) and is in a different group to SARS, which is the Beta-1 clade on this most excellent paper.

To answer the comment. They are outgroups, basically ancestral to COVID-19 and SARS-1 clade. So they lost these genes whilst the ingroup including COVID-109 and SARS-1 retained ORF13, 14 ... but I think lost ORF10 from memory

Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

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