mRNA cap identification by sequencing?
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].