Why does the FASTA sequence for coronavirus look like DNA, not RNA? I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this:

&gt;MN988713.1 Wuhan seafood market pneumonia virus isolate 2019-nCoV/USA-IL1/2020, complete genome
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA
CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC
TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG
...  
...
TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC
GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT
TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAA


Coronavirus is an RNA virus, so I was expecting the sequence to consist of AUGC characters. But the letters here are ATGC, which looks like DNA!

I found a possible answer, that this is the sequence of a "complementary DNA". I read that


  The term cDNA is also used, typically in a bioinformatics context, to refer to an mRNA transcript's sequence, expressed as DNA bases (GCAT) rather than RNA bases (GCAU).


However, I don't believe this theory that I'm looking at a cDNA. If this were true, the end of the true mRNA sequence would be ...UCUUACUGUUUUUUUUUUUU, or a "poly(U)" tail. But I believe the coronavirus has a poly(A) tail.

I also found that the start of all highlighted genes begin with the sequence ATG. This is the DNA equivalent of the RNA start codon AUG.

So, I believe what I'm looking at is the true mRNA, in 5'→3' direction, but with all U converted to T.

So, is this really what I'm looking at? Is this some formatting/representation issue? Or does 2019-nCoV really contain DNA, rather than RNA?
That is the correct sequence for 2019-nCov. Coronavirus is of course an RNA virus and in fact, to my knowledge, every RNA virus in Genbank is present as cDNA (AGCT, i.e. thydmine) and not RNA (AGCU, i.e. uracil).

The reason is simple, we never sequence directly from RNA because RNA is too unstable and easily degraded by RNase. Instead the genome is reverse transcribed, either by targeted reverse transcription or random amplification and thus converted to cDNA. cDNA is stable and is essentially reverse transcribed RNA.

The cDNA is either sequenced directly or further amplified by PCR and then sequenced. Hence the sequence we observe is the cDNA rather than RNA, thus we observe thymine rather than uracil and that is how it is reported.