A method for enriching a target polynucleotide from a sample, the method comprising: a) providing a reaction mixture comprising the sample and a first target-specific primer, wherein the sample comprises single-stranded target polynucleotide having a 3' and a 5' end and a plurality of structurally different single-stranded non-target polynucleotides; b) hybridizing a first target-specific primer to the single-stranded target polynucleotide in the reaction mixture, wherein the first target-specific primer hybridizes at least 6 nucleotides from the 3' end of the single-stranded target polynucleotide; c) extending the hybridized first target-specific primer with a DNA polymerase to form a first double-stranded product comprising the target polynucleotide hybridized to the extended first target-specific primer, wherein the hybridized target polynucleotide comprises a single-stranded overhang region of at least 6 consecutive nucleotides at the 3' end; d) removing single-stranded target and non-target polynucleotides that are not hybridized to extended target-specific primer, if present from the reaction mixture; e) hybridizing a second target-specific primer to the single-stranded overhang region at the 3' end of the hybridized target polynucleotide, wherein the second target-specific primer comprises a 3' hybridizing region and a barcode region; and f) extending the hybridized second target-specific primer with a DNA polymerase, wherein the DNA polymerase comprises strand displacement activity, 5'-3' double stranded DNA exonuclease activity, or a combination thereof, thereby displacing or degrading the extended first target-specific primer and forming a second double-stranded product comprising a barcode, wherein the second double-stranded product comprises the target polynucleotide hybridized to an extended second target-specific primer, wherein the extended second target-specific primer comprises: i) a complement of at least a portion of the target polynucleotide; and, ii) a single-stranded 5' overhang region comprising the barcode. a) providing a reaction mixture comprising the sample and a first target-specific primer, wherein the sample comprises single-stranded target polynucleotide having a 3' and a 5' end and a plurality of structurally different single-stranded non-target polynucleotides; b) hybridizing a first target-specific primer to the single-stranded target polynucleotide in the reaction mixture, wherein the first target-specific primer hybridizes at least 6 nucleotides from the 3' end of the single-stranded target polynucleotide; c) extending the hybridized first target-specific primer with a DNA polymerase to form a first double-stranded product comprising the target polynucleotide hybridized to the extended first target-specific primer, wherein the hybridized target polynucleotide comprises a single-stranded overhang region of at least 6 consecutive nucleotides at the 3' end; d) removing single-stranded target and non-target polynucleotides that are not hybridized to extended target-specific primer, if present from the reaction mixture; e) hybridizing a second target-specific primer to the single-stranded overhang region at the 3' end of the hybridized target polynucleotide, wherein the second target-specific primer comprises a 3' hybridizing region and a barcode region; and f) extending the hybridized second target-specific primer with a DNA polymerase, wherein the DNA polymerase comprises strand displacement activity, 5'-3' double stranded DNA exonuclease activity, or a combination thereof, thereby displacing or degrading the extended first target-specific primer and forming a second double-stranded product comprising a barcode, wherein the second double-stranded product comprises the target polynucleotide hybridized to an extended second target-specific primer, wherein the extended second target-specific primer comprises: i) a complement of at least a portion of the target polynucleotide; and, ii) a single-stranded 5' overhang region comprising the barcode.