mRNA cap identification by sequencing? If you sequence a positive-sense  RNA virus genome using NGS via Nanopore, Illumina or even the old Sanger method, is it possible to tell if the virus has 5' (five prime) cap at the 5' end of the RNA genome?
In short the answer is no, however the 'car-jumping method' described here it is possible, but it is about the enzymic MMLV reverse transcription in response to the capping structure. I assume that an alternative reverse transcriptase doesn't do 'car jumping' therefore any sequencing method will pick this up, but the difference between MMLV verse the heat-tolerant style reverse transcriptases. I would assume the secondary structure associated with viral capping prevents a low temperature reverse transcriptase, i.e. MMLV from correctly reproducing the vRNA into cDNA.
It is important to note that a cap, isn't just a virus thing, its mRNA eukaryotes per se. The cap is a 7-methylguanosine (m7G) linked to the 5′ end of the transcript by a 5′-5′ triphosphate bridge [m7G(5′)ppp(5′)N- or m7G(5′)ppp(5′)Nm in which Nm is a 2′-O methylated nucleoside].