I attempted a "Dual RNA-Seq" on a nasal sample from a person with RNA virus infection. The RNA virus infection was confirmed by PCR.
However, RNA-Seq sometimes detects guest reads and sometimes does not.
According to the reference , the sensitivity of Dual RNA-Seq seems to be 86%.
The reason why it cannot be detected is that
(1) Appearance of unanalyzable specimens due to the effect of new mutations
→ Is it possible to change the option to allow for mutations when mapping?
(2) Decreased detection sensitivity in samples with low viral nucleic acid content.
→ Is PCR more sensitive for detection?
Are there any other reasons why guest reads cannot be detected?
Your comments would be appreciated. Thank you in advance.
Reference : Burgess DJ. Gene expression: host-pathogen duels revealed by dual RNA-seq in vivo. Nat Rev Genet. 2017 Feb 15;18(3):143. doi 10.1038/nrg.2017.10. PMID: 28196982.