distributing a sample or set of samples into one or more individual discrete volumes, the individual discrete volumes comprising a nucleic acid detection system comprising: a Type VI Cas effector protein having collateral cleavage activity and one or more guide RNAs capable of forming a complex with the Type VI Cas effector protein and directing sequence-specific binding of the complex to one or more corresponding virus polynucleotides in the sample or set of samples; and an RNA-based masking construct comprising a non-target RNA sequence;

incubating the sample or set of samples under conditions sufficient to allow binding of the one or more guide RNAs to one or more virus target polynucleotides;

activating the Type VI Cas effector protein via binding of the one or more guide RNAs to the one or more virus target polynucleotides, wherein activating the Type VI Cas effector protein results in collateral cleavage of the non-target RNA sequence of the RNA-based masking construct, such that a detectable signal is generated; and

detecting the detectable signal, wherein detection of the detectable signal indicates a presence of one or more viruses in the sample,

wherein, prior to incubating the sample or set of samples, the method further comprises: conducting a nuclease inactivation step and a viral inactivation step on the sample or the set of samples, wherein the sample(s) is/are a crude sample(s) and/or wherein the virus target polynucleotides are not extracted or isolated from the sample(s) after the inactivation steps, and

wherein, prior to conducting a nuclease inactivation step and a viral inactivation step on the sample or the set of samples, or prior to distributing a sample or set of samples into one or more individual discrete volumes, the method further comprises amplifying the virus target polynucleotides in the sample.