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. Author manuscript; available in PMC: 2018 Nov 1.
Published in final edited form as: Virology. 2018 Feb 20;518:87–94. doi: 10.1016/j.virol.2018.01.030

Table 1.

Primers used in this study.

Primers Sequences (5′-3′) Usage
Fitness-U AGGACCGGTGAAGAAACCTGTCG For 3tness assay
Fitness-L AAATAGGAAGCGGGAAAAGCC
Frequency-U CTGACCCCGCCTACGGGAAAGTG For mutation frequency assay
Frequency-L AGTAGTAAGTGGCAGTACGGAGG
3D-D5N-U CGAGGGATTGATAGTTAACACCAGAGATGTTGAG Production of the D5N mutant
3D-D5N-L CTCAACATCTCTGGTGTTAACTATCAATCCCTCG
3D-A38V-U GAATTTGGGCCTGCCGTCTTGTCCAACCAG Production of the A38V mutant
3D-A38V-L GTCCTGGTTGGACAAGACGGCAGGCCCAAATTC
3D-M194I-U CATTCTTTACACCAGGATTATGATTGGTAGATTTT Production of the M194I mutant
3D-M194I-L GCAAAATCTACCAATCATAATCCTGGTGTAAAGAA
3D-M296V-U CACTGTTGAAGGCGGGGTGCCGTCTGGTTGTT Production of the M296V mutant
3D-M296V-L GAACAACCAGACGGCACCCCGCCTTCAACA GTG
3D-A122T-U CTGGCCTCCCCTGGACCCTCCAGGGGAAACGCC Production of the A122T mutant
3D-A122T-L GTTTCCCCTGGAGGGTCCAGGGGAGGCCAGGCG
3D-M296I-U CTGTTGAAGGCGGGATACCGTCTGGTTGTTCCGCG Production of the M296I mutant
3D-M296I-L GAACAACCAGACGGTATCCCGCCTTCAACAGTG
3D-R440W-U GACCTGATGAGTACTGGCGTCTCTTTGAGCCTTTC Production of the R440W mutant
3D-R440W-L AAAGGCTCAAAGAGACGCCAGTACTCATCAGGTCC
3D-T64I-U TAAACACAAGGAAAACATCAAGATGTCTGAGGAGG Production of the T64I mutant
3D-T64I-L CTCCTCAGACATCTTGATGTTTTCCTTGTGTTTAG
3D-D133N-U CCGTGGTGCGCTCATTAACTTCGAGAACGGCACTG Production of the D133N mutant
3D-D133N-L GACAGTGCCGTTCTCGAAGTTAATGAGCGCACCAC