Dual RNA-Seq with Flu as guest

Question

[yoshifumimiya]

I would like to do Dual RNA-Seq with Flu as guest. (of course, the host is human).

I tried to do a sample of Flu infection using the fastq file in the public database, but I could not detect the read of guest.

Question 1) Why can't I detect guest reads?

Question 2) Is it OK to use the usual FASTA as a reference? Flu is a negative strand RNA virus, so we tried (1) normal FASTA, (2) complementary strand, and (3) reverse complementary strand as references, but none of them could be detected.

Question 3) When performing Dual RNA-Seq, is there any special sample preparation required, unlike when performing bulk RNA-Seq?

We would appreciate your opinion. Thank you in advance.