Generally, viral capsids are considered to be sufficiently protective against nucleases. Thus RNases are not able to act upon the viral RNA present inside the intact capsid particles. So if you wish to remove exogenous RNA and to purify capsid associated RNA for nucleic acid amplification/ sequencing/ NGS, you will have to use strong RNA stabilizer immediately after RNase treatment, such as TRI Reagent. This will instantly inactivate the RNases, denature the capsid, release the capsid associated RNA and will stabilize it for subsequent purification. However, if you are interested in isolating the intact capsids after RNase treatment, you have to purify the viral particles by classical method using ultracentrifugation of the sample through a suitable gradient.

Best of Luck,

SD

thank you for your generous answer!

Also, if I want get rid of viral DNA, should I just add (hopefully RNase-free) DNase after the extraction?

Yes use Rnase free Dnase (amplification grade) from a good company. 

RNases are enzymes that degrade RNA molecules, and their ability to degrade RNA inside viral particles depends on the nature of the viral particle and the type of RNase. In general, viral particles are designed to protect their genetic material (RNA or DNA) from environmental hazards, including nucleases like RNases.

RNA Viruses and RNase Resistance

• Capsid Protection: Most RNA viruses encapsulate their RNA genome within a protein shell known as a capsid. This capsid provides physical and chemical protection against RNases. The capsid must be disrupted or removed for RNases to access and degrade the viral RNA.
• Envelope Protection: Some RNA viruses are also enveloped, having an additional lipid membrane surrounding the capsid. This envelope, derived from host cell membranes, can provide further protection against environmental factors, including RNases. However, the primary role of the envelope is in virus entry and egress, not necessarily RNase protection.

Factors Affecting RNase Activity Against Viral RNA

Experimental Considerations

In experimental settings, treatments like detergents, chaotropic agents, or ultrasonication are often used to disrupt viral particles before applying RNases to degrade viral RNA. This step is crucial in processes like viral RNA extraction and purification, where the goal is to release and then protect or analyze the viral RNA.

Conclusion

While RNases are capable of degrading RNA, the RNA within intact viral particles is generally protected from degradation due to the physical barriers provided by the capsid and, in some cases, the viral envelope. Disruption of the viral particle is necessary for RNases to access and degrade the viral RNA effectively.

l Reviewing the protocols listed here may offer further guidance in addressing this issue