HIV WGS - 400bp Amplicon Tiling - Oxford Nanopore Technology Protocol v1
Authors: Yeboah Eugene 
Published: October 2022

OSPHL in collaboration with APHL, will evaluate the performance of the Oxford Nanopore Technology sequencers for HIV genome sequencing using a modified protocol of the ARTIC amplicon v3: Nanopore Protocol PCR tiling of SARS-CoV-2 virus with rapid barcoding (SQK-RBK110.96) Library preparation Version: PCTR_9125_v110_revE_24Mar2021 The modifications include: Switching to the Nanopore RAPID barcoding, which requires less time (10 min) and fewer reagents. HIV Primer sequences designed by Primal Scheme. HIV-1: https://www.dropbox.com/sh/xnhpektoen7chdd/AAAT789gnEnwbbCjF_EMuRu8a?dl=0 HIV-2: https://www.dropbox.com/sh/2sco4ffr30ids7a/AAD0z-VXSXElamsuys7zsmpLa?dl=0 : Primer Sequences HIV-1: name pool seq size %gc tm (use 65) HIV-1_v1.0_1_LEFT 1 TGGTTAGACCAGATCTGAGCCT 22 50 60.48 HIV-1_v1.0_1_RIGHT 1 TTTCTTTCCCCCTGGCCTTAAC 22 50 60.68 HIV-1_v1.0_3_LEFT 1 GCTTTAGACAAGATAGAGGAAGAGCA 26 42.31 60.85 HIV-1_v1.0_3_RIGHT 1 TTCCTGCTATGTCACTTCCCCT 22 50 61.02 HIV-1_v1.0_5_LEFT 1 TTGGATGACAGAAACCTTGTTGG 23 43.48 59.62 HIV-1_v1.0_5_RIGHT 1 AAGAAAATTCCCTGGCCTTCCC 22 50 61.01 HIV-1_v1.0_7_LEFT 1 ATTAGAAGAAATGAGTTTGCCAGGAA 26 34.62 59.72 HIV-1_v1.0_7_RIGHT 1 TTCTTTATGGCAAATACTGGAGTATTGT 28 32.14 59.98 HIV-1_v1.0_9_LEFT 1 GAGACACCAGGGATTAGATATCAGT 25 44 59.61 HIV-1_v1.0_9_RIGHT 1 CCCTGGGTAAATCTGACTTGCC 22 54.55 61.13 HIV-1_v1.0_11_LEFT 1 AGAGCCATTTAAAAATCTGAAAACAGGA 28 32.14 60.77 HIV-1_v1.0_11_RIGHT 1 CAGTCTTCTGATTTGTTGTGTCAGT 25 40 60.08 HIV-1_v1.0_13_LEFT 1 GTCAGTGCTGGAATCAGGAAAGT 23 47.83 61.06 HIV-1_v1.0_13_RIGHT 1 CGTAGCACCGGTGAAATTGCT 21 52.38 61.64 HIV-1_v1.0_15_LEFT 1 AGACATAATAGCAACAGACATACAAACT 28 32.14 59.77 HIV-1_v1.0_15_RIGHT 1 CCAATCTAGCATCCCCTAGTGG 22 54.55 59.88 HIV-1_v1.0_17_LEFT 1 CAAGCAGGACATAACAAGGTAGGA 24 45.83 60.65 HIV-1_v1.0_17_RIGHT 1 TCCAGGGCTCTAGTCTAGGATC 22 54.55 59.81 HIV-1_v1.0_19_LEFT 1 TCTCTATCAAAGCAGTAAGTAGTACATGT 29 34.48 60.52 HIV-1_v1.0_19_RIGHT 1 GCATGTGTGGCCCAAACATTAT 22 45.45 60.28 HIV-1_v1.0_21_LEFT 1 AGCGGGAGAATGATAATGGAGAA 23 43.48 59.61 HIV-1_v1.0_21_RIGHT 1 GCATTGTCCGTGAAATTGACAGA 23 43.48 60.31 HIV-1_v1.0_23_LEFT 1 AGCTAGCAAATTAAGAGAACAATTTGGA 28 32.14 60.61 HIV-1_v1.0_23_RIGHT 1 TTCACTTCTCCAATTGTCCCTCA 23 43.48 59.86 HIV-1_v1.0_25_LEFT 1 CTATTGAGGCGCAACAGCATCT 22 50 61.5 HIV-1_v1.0_25_RIGHT 1 ACCTACCAAGCCTCCTACTATCA 23 47.83 60.05 HIV-1_v1.0_27_LEFT 1 ACCACCGCTTGAGAGACTTACT 22 50 61.27 HIV-1_v1.0_27_RIGHT 1 TGCTCCATGTTTTTCCAGGTCT 22 45.45 60.34 HIV-1_v1.0_29_LEFT 1 CACACACAAGGCTACTTCCCTG 22 54.55 61.31 HIV-1_v1.0_29_RIGHT 1 AACCAGAGAGACCCAGTACAGG 22 54.55 61.01 HIV-1_v1.0_2_LEFT 2 TAGAAGGAGAGAGATGGGTGCG 22 54.55 61.19 HIV-1_v1.0_2_RIGHT 2 TTTTGGCTGACCTGATTGCTGT 22 45.45 61.2 HIV-1_v1.0_4_LEFT 2 GCTGCAGAATGGGATAGAGTGC 22 54.55 61.56 HIV-1_v1.0_4_RIGHT 2 TTCTTCTAGTGTAGCCGCTGGT 22 50 61.33 HIV-1_v1.0_6_LEFT 2 GGAAGGACACCAAATGAAAGATTGT 25 40 60.37 HIV-1_v1.0_6_RIGHT 2 TGTCCACAGATTTCTATGAGTATCTGA 27 37.04 59.94 HIV-1_v1.0_8_LEFT 2 AGTAGAAATTTGTACAGAGATGGAAAAGG 29 34.48 60.47 HIV-1_v1.0_8_RIGHT 2 AAGGCTCTAAGATTTTTGTCATGCT 25 36 59.67 HIV-1_v1.0_10_LEFT 2 CAGCCTATAGTGCTGCCAGAAA 22 50 60.6 HIV-1_v1.0_10_RIGHT 2 TTTGCACTGCCTCTGTTAATTGT 23 39.13 59.62 HIV-1_v1.0_12_LEFT 2 GGGAGACTAAATTAGGAAAAGCAGGA 26 42.31 61.02 HIV-1_v1.0_12_RIGHT 2 AGCCATTGCTCTCCAATTACTGT 23 43.48 60.57 HIV-1_v1.0_14_LEFT 2 GGGCAGGAAACAGCATATTTTCT 23 43.48 59.81 HIV-1_v1.0_14_RIGHT 2 TGCTGTCCCTGTAATAAACCCG 22 50 60.54 HIV-1_v1.0_16_LEFT 2 GGGAAAGCTAGGGGATGGTTTT 22 50 60.48 HIV-1_v1.0_16_RIGHT 2 TCGTAACACTAGGCAAAGGTGG 22 50 60.47 HIV-1_v1.0_18_LEFT 2 GCAACAACTGCTGTTTATCCATTTT 25 36 59.91 HIV-1_v1.0_18_RIGHT 2 TTTCCTATATTCTATGATTACTATGGACCAC 31 32.26 59.61 HIV-1_v1.0_20_LEFT 2 TACCTGTGTGGAAGGAAGCAAC 22 50 60.67 HIV-1_v1.0_20_RIGHT 2 TGCATATTCTTTCTGCACCTTACCT 25 40 60.96 HIV-1_v1.0_22_LEFT 2 GCCAGTAGTATCAACTCAACTGCT 24 45.83 60.94 HIV-1_v1.0_22_RIGHT 2 ACAGTAGAAAAATTCCCCTCCACA 24 41.67 60.22 HIV-1_v1.0_24_LEFT 2 GGGCTGCTATTAACAAGAGATGGT 24 45.83 61.01 HIV-1_v1.0_24_RIGHT 2 AGGTATCTTTCCACAGCCAGGA 22 50 61.02 HIV-1_v1.0_26_LEFT 2 TGGGCAAGTTTGTGGAATTGGT 22 45.45 61.41 HIV-1_v1.0_26_RIGHT 2 ACCAATATTTGAGGGCTTCCCAC 23 47.83 61.14 HIV-1_v1.0_28_LEFT 2 TGGATGGCCTACTGTAAGGGAA 22 50 60.75 HIV-1_v1.0_28_RIGHT 2 AGCTTGTAGCACCATCCAAAGG 22 50 61.06 HIV-2: name pool seq size %gc tm (use 65) HIV-2_v1.0_1_LEFT 1 TGCAAGGGATGTTTTACAGTAGGA 24 41.67 60.28 HIV-2_v1.0_1_RIGHT 1 CCAAGTATGGTTGTTCCTGTTATTCA 26 38.46 60.01 HIV-2_v1.0_3_LEFT 1 GCATTGTATTCAGTCGCTCTGC 22 50 60.46 HIV-2_v1.0_3_RIGHT 1 ACTCCGTCGTGGTTTGTTCCT 21 52.38 62.01 HIV-2_v1.0_5_LEFT 1 AAAACATATTGTGTGGGCAGCG 22 45.45 60.53 HIV-2_v1.0_5_RIGHT 1 TCCTCCACTAATTTTACCCATGCAT 25 40 60.73 HIV-2_v1.0_7_LEFT 1 ATTCGCAGCACCCAATACCAG 21 52.38 61.12 HIV-2_v1.0_7_RIGHT 1 GCGGTTAGCATCTCTTCTAGGG 22 54.55 60.47 HIV-2_v1.0_9_LEFT 1 CAGGACACATCATGGCAAACTG 22 50 60.27 HIV-2_v1.0_9_RIGHT 1 TTGTCCCCTAATTCTATTCCTGCT 24 41.67 59.6 HIV-2_v1.0_11_LEFT 1 GGAAAGATGGACCAAGGCTGAA 22 50 60.74 HIV-2_v1.0_11_RIGHT 1 CTTCCATCCTTGTGGCAAGACT 22 50 60.74 HIV-2_v1.0_13_LEFT 1 GGGTTTTCTACTCCAGATGAGAAGT 25 44 60.43 HIV-2_v1.0_13_RIGHT 1 ACTTTTAGGATTTTCTCTTCCTGGTGT 27 37.04 61.14 HIV-2_v1.0_15_LEFT 1 GGTTAACATTTAACCTAGTAGGAGATCCT 29 37.93 60.78 HIV-2_v1.0_15_RIGHT 1 ACTTGTCTGATGCCTTGACTTACT 24 41.67 60.28 HIV-2_v1.0_17_LEFT 1 TCATTATAGTAGCAGTACATGTTGCAA 27 33.33 59.51 HIV-2_v1.0_17_RIGHT 1 CATGTTGATTAGTCTTTCTGCTGGG 25 44 60.54 HIV-2_v1.0_19_LEFT 1 ACTGGATAGTAGTCCCCACCTG 22 54.55 60.55 HIV-2_v1.0_19_RIGHT 1 ATGAGCTTGGGGATAGTTGCAG 22 50 60.61 HIV-2_v1.0_21_LEFT 1 GGGATGTCAGCAAGCTACACAA 22 50 61.06 HIV-2_v1.0_21_RIGHT 1 GGTTACATCCCGCTCTGAAGTG 22 54.55 61.17 HIV-2_v1.0_23_LEFT 1 TGGTAGGAATCAGCTGTTTGTTGT 24 41.67 61.01 HIV-2_v1.0_23_RIGHT 1 ATGTGGGTGGTCTCGAGGTT 20 55 60.85 HIV-2_v1.0_25_LEFT 1 AGCACTATTGGGATGCTATGAGG 23 47.83 60.25 HIV-2_v1.0_25_RIGHT 1 CTTCCCTCCATCTGCCTCCAAA 22 54.55 62.21 HIV-2_v1.0_27_LEFT 1 AGCAGATAATTAATACCTGGCATAAAGT 28 32.14 59.66 HIV-2_v1.0_27_RIGHT 1 CTGTTGCTGTTGCTGCACTATC 22 50 60.59 HIV-2_v1.0_29_LEFT 1 AATATGACATGGCAGGAGTGGG 22 50 60.34 HIV-2_v1.0_29_RIGHT 1 CAAGGCCACAAGTCGTAACCA 21 52.38 60.91 HIV-2_v1.0_31_LEFT 1 ATTCGCGAGGACTACGAGAGAG 22 54.55 61.55 HIV-2_v1.0_31_RIGHT 1 CCCTTCCTCTTTTTCTAGGTATATGTCT 28 39.29 60.51 HIV-2_v1.0_33_LEFT 1 ACTACAAGGCCTTCACTCTGTAC 23 47.83 60 HIV-2_v1.0_33_RIGHT 1 AGTACCGGCCAAGTACTGGT 20 55 60.56 HIV-2_v1.0_2_LEFT 2 GAGTTTGGGCACAAGTCAGGAT 22 50 61 HIV-2_v1.0_2_RIGHT 2 ACTGGCAGCTTTATTGAAGAGGT 23 43.48 60.5 HIV-2_v1.0_4_LEFT 2 CGAACAGGGACTTGAAGAGGAC 22 54.55 60.79 HIV-2_v1.0_4_RIGHT 2 TGGCAACCTTCTTTTGACTCCA 22 45.45 60.54 HIV-2_v1.0_6_LEFT 2 AAAAGAGGAAACTACCCCGTGC 22 50 60.99 HIV-2_v1.0_6_RIGHT 2 TCTGTAGATGTTCCCTACCGGT 22 50 60.21 HIV-2_v1.0_8_LEFT 2 TGGATGACCCAAACGCTGCTA 21 52.38 62.16 HIV-2_v1.0_8_RIGHT 2 GGGAAGTTGCGAGGCTTCTTTC 22 54.55 62.2 HIV-2_v1.0_10_LEFT 2 GTCACAGCGTACATCGAGGATC 22 54.55 61.03 HIV-2_v1.0_10_RIGHT 2 AGCTGGCCCTCTTTTTCCATTT 22 45.45 60.95 HIV-2_v1.0_12_LEFT 2 CTGCATTTACCCTACCAGCAGT 22 50 60.54 HIV-2_v1.0_12_RIGHT 2 GCTTTTGGATGTCATTGACTGTCC 24 45.83 60.93 HIV-2_v1.0_14_LEFT 2 ACCAAGAAGAAAAAGAATTAGAGGCA 26 34.62 59.67 HIV-2_v1.0_14_RIGHT 2 TCCTGCTTTTCCCTCTTTTGACT 23 43.48 60.38 HIV-2_v1.0_16_LEFT 2 AGCAGTCTATGTTGCATGGGTC 22 50 60.86 HIV-2_v1.0_16_RIGHT 2 GAAGAGTGCTGTCTGCCTTCCT 22 54.55 62.44 HIV-2_v1.0_18_LEFT 2 ACAATAGAAACAATAGTACTGATGGCAG 28 35.71 60.29 HIV-2_v1.0_18_RIGHT 2 CCTCCTCTAGGTCTTTTGTTCTGT 24 45.83 60.04 HIV-2_v1.0_20_LEFT 2 TCTTGCTTTACGGCAGGTGAAG 22 50 61.31 HIV-2_v1.0_20_RIGHT 2 GCAAGTGCACCCTCTCTTGAAA 22 50 61.51 HIV-2_v1.0_22_LEFT 2 GACATGGAGACACCCTTGAAGG 22 54.55 60.8 HIV-2_v1.0_22_RIGHT 2 CACGCGGGTATGCCATAGAAAA 22 50 61.5 HIV-2_v1.0_24_LEFT 2 TGGCAATGAATTGTAGCAGGGT 22 45.45 60.74 HIV-2_v1.0_24_RIGHT 2 AGCCTGAATAGTTGGTATCATTACATCT 28 35.71 60.77 HIV-2_v1.0_26_LEFT 2 TGTCAGGATTAGTGTTTCACTCTCA 25 40 60.08 HIV-2_v1.0_26_RIGHT 2 GCTGGTTACTGTTGATTCACAGG 23 47.83 60.06 HIV-2_v1.0_28_LEFT 2 CGTGCTAGGGTTCTTGGGTTTT 22 50 61.26 HIV-2_v1.0_28_RIGHT 2 TTCTTGTTGAATTTGGGCTTCTTCT 25 36 60.02 HIV-2_v1.0_30_LEFT 2 CCCGGTTATCTCCAACAGATCC 22 54.55 60.41 HIV-2_v1.0_30_RIGHT 2 CTTGGAACTGCGAGTATTCCCC 22 54.55 61.18 HIV-2_v1.0_32_LEFT 2 TCACATTTTATAAAAGAAAAAGGGGGACT 29 31.03 60.58 HIV-2_v1.0_32_RIGHT 2 CCCTCTTGCTTTCAGTTTTGCC 22 50 60.73 HIV-2_v1.0_34_LEFT 2 ACTTTCCAGAAGGGGCTGTAAC 22 50 60.41 HIV-2_v1.0_34_RIGHT 2 TGCTAGGGATTTTCCTGCCTTG 22 50 60.81