Why does sequencing virus proteins take time?
Sequencing a viral genome requires isolation of the virus, propagation in cell culture, extraction of nucleic acids, and preparation of a sequencing library.  Once sequences are obtained, a genome can be assembled de novo using (untargeted) shotgun reads, and gaps in the genome can be spanned with (targeted) Sanger sequencing.  This process can take weeks to months depending on the availability of resources and the growth characteristics of the virus.
For details on how the 2019-nCoV genome was sequenced, see Zhu et al., published January 2020:
A Novel Coronavirus from Patients with Pneumonia in China, 2019