(a) contacting a sample comprising one or more target nucleic acid species or amplicons thereof with one or more primer oligonucleotides, wherein each primer oligonucleotide comprises a region that corresponds to a portion of a target nucleic acid species or amplicon thereof and wherein each of the one or more target nucleic acid species or amplicon thereof (1) comprises at least two variants and (2) each of the one or more primer oligonucleotides is specific for a target nucleic acid species or amplicon thereof and is capable of hybridizing to the variants of the target nucleic acid species or amplicon thereof at a position 5′ to a single base position that differs between each of the variants of the target nucleic acid species or amplicon thereof, thereby generating hybridized oligonucleotides;

(b) contacting the hybridized oligonucleotides with an extension composition comprising one or more chain terminating reagents each specific for a variant of a target nucleic acid species or amplicon thereof under extension conditions, wherein the hybridized primer oligonucleotides are each extended up to, or through, the nucleotide position that is different between the variants of a corresponding target nucleic acid species or amplicon thereof, thereby generating extended primer oligonucleotides that each comprise a chain terminating reagent specific for one or more variants of the corresponding target nucleic acid species or amplicon thereof;

(c) contacting the products of (b) with an enzyme having 3′ to 5′ exonuclease activity, whereby unextended primer oligonucleotides are digested and extended primer oligonucleotides comprising a chain terminating reagent are not digested; and

(d) without subjecting the products of (b) or the products of (c) to selective capture of the extended primer oligonucleotides from the mixture of extended primer oligonucleotides and unextended primer oligonucleotides in (b) or (c), analyzing detecting the presence, absence or amount of the extended primer oligonucleotides, thereby detecting the presence, absence or amount of variants of the one or more target nucleic acid species or amplicons thereof in the sample.