HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Subtyping of Pol Region
3.2. Near Full-Length HIV Genome Sequencing and Characterization
3.2.1. Sample 11
3.2.2. Sample 12
3.2.3. Sample 25
3.2.4. Sample 29
3.2.5. Sample 31
3.2.6. Sample 34
3.2.7. Sample 37
3.2.8. Sample 39
3.2.9. Sample 43
3.2.10. Sample 54
3.2.11. Sample 56
3.2.12. Sample 65
3.2.13. Sample 68
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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No. | Accession Number | Rega 2.0 | Rega 3.0 | Comet 1.0 | jpHMM | SCUEAL | Stanford | Geno2pheno 3.3 |
---|---|---|---|---|---|---|---|---|
1 | AJ971094 | NA | 02_AG | 02_AG | A1, G | 02_AG-like | 02_AG/02_AG | 02_AG |
2 | AJ971095 | NA | 02_AG | 02_AG | A1, G | 02_AG-like/complex | 02_AG/02_AG | 02_AG |
3 | AJ971100 | F (F1) | F (F1) | F1 | F1 | F1 | D/F | F1 |
4 | AJ971096 | NA | 02_AG | 02_AG | A1, G | 02_AG-like | 02_AG/02_AG | 02_AG |
5 | AJ971133 | NA | B-like | B | B | B, D recombinant/B | B/B | B |
6 | GQ399318 | B | Recombinant of B, D | B | B | B | B/B | B |
7 | AM113750 | NA | 02_AG | 02_AG | A1, G | complex | 02_AG/02_AG | 02_AG |
8 | JX046417 | A (A1) | A (A1) | A1 | A1 | A-ancestral, A1 rec/A, A1 recombinant/A1 | A/CRF01_AE | 01_AE |
9 | JX046416 | A (A1) | A (01_AE) | 01_AE | 01_AE | AE | 01_AE/01_AE | 01_AE |
10 | JX046415 | NA | 02_AG | 02_AG | A1, G | complex | 02_AG/02_AG | 02_AG |
11 | JX046413 | A (A1) | A (A1) | A1 | A1 | complex/A, A-ancestral recombinant | A/01_AE | 01_AE |
12 | JX028352 | B | NA (recombinant of B, D) | B | B | B | B/B | B |
13 | JX046414 | 19_cpx | 19_cpx | unassigned; D, 11_cpx, G, 20_BG | D | complex | D/D | D |
14 | JX028338 | NA | B | B | B | B | B/B | B |
15 | JX046406 | D | D | D | B, D | D | D/D | D |
16 | JX046405 | D | D | D | B, D | D | D/D | D |
17 | JX028323 | NA | B | B | B | B | B/B | B |
18 | JX046407 | NA | B, potential recombinant | B | B | B | B/B | B |
19 | JX046408 | NA | Recombinant of F1, 05_DF | unassigned; B, F1 | B, F1 | B, F1 recombinant | B/F | F1 |
20 | JX046409 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
21 | JX046410 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
22 | KP013668 | G | G | unassigned; 18_cpx, 02_AG, G | G | G | G/G | 02_AG |
23 | JX046412 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
24 | JX046404 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
25 | JX046411 | A (A1) | A (A1) | A1 | A1 | A1 | 01_AE/01_AE | 01_AE |
26 | KP013669 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
27 | JX028308 | B | NA, Recombinant of B, D | B | B | B | B/B | B |
28 | JX046403 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
29 | KF753740 | NA | Recombinant of B, D | B | B | B | B/B | B |
30 | KF753737 | NA | Recombinant of B, D | B | B | B | B/B | B |
31 | KF753747 | NA | C, potential recombinant | unassigned; F1, A1, 01_AE, B, C, 60_BC | A1, B, C | complex | C/D | C |
32 | KF753751 | A (A1) | A (A1) | A1 | A1 | A1 | 01_AE/01_AE | 01_AE |
33 | KF753741 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
34 | KF753731 | G | G | unassigned; D, J, G | G, J | AE, G recombinant | A/G | G |
35 | KF753711 | B | B | unassigned; B-D | B | B | B/B | B |
36 | KP013665 | B | B | B | B | B, D recombinant/B | B/B | B |
37 | KF753704 | NA | NA (G, B) | G (check for 02_AG) | A1, B, G | complex | 02_AG/B | 02_AG |
38 | KF753709 | NA | B | B | B | B | B/B | B |
39 | KF753699 | A (A1) | A (01_AE) | 01_AE | 01_AE | 15_01B/A1, AE recombinant/AE, F-ancestral recombinant | 01_AE/01_AE | 01_AE |
40 | KP013656 | B | B | B (check for 29_BF) | B | B | B/B | B |
41 | KP013648 | A (A1) | A (A1) | A1 | A1 | A1 | 01_AE/A | A1 |
42 | KP013643 | NA | B-like | B | B | B | B/B | B |
43 | KP013657 | NA | Recombinant of B, D | B | B | B | B/B | B |
44 | KP013641 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
45 | KP013660 | A (A1) | A (A1) | unassigned; D, 10_CD, 01_AE, B | 01_AE | A1, AE recombinant | 01_AE/01_AE | 01_AE |
46 | KP013644 | NA | B | B | B | B | B/B | B |
47 | KY656620 | B | B-like | B | B | B | B | B |
48 | KY656621 | NA | B-like | B | B | B | B | B |
49 | MN736711 | B | B | B | B | B, C recombinant | B | B |
50 | KY656626 | A (A1) | A (A1) | A1 | A1 | A1 | A (A_FSU) | 01_AE |
51 | KY656630 | NA | 02_AG | 02_AG | A1, G | A4, G recombinant | 02_AG | 02_AG |
52 | KY656636 | A (A1) | A (A1) | A1 | A1 | A1 | A (A_FSU) | 01_AE |
53 | KY656616 | NA | B-like | B | B | B | B | B |
54 | KY656639 | NA | G (02_AG) | 02_AG | F1, G | G | 02_AG | 02_AG |
55 | KY656643 | A (A1) | A (A1) | A1 | A1 | A1 | A | 01_AE |
56 | KY656648 | NA | Recombinant of B, D | B | B | B | B | B |
57 | KY656649 | B | B | B | B | B, F1 recombinant | B | B |
58 | KY656650 | B | Recombinant of B, D | B | B | B | B | B |
59 | KY656640 | A (01_AE) | A (01_AE) | 01_AE (check for 15_01B) | 01_AE | AE | 01_AE | 01_AE |
60 | KY656656 | NA | B-like | B | B | B | B | B |
61 | KY656657 | A (A1) | A (A1) | A1 | A1 | A1 | A, 01_AE | 01_AE |
62 | KY656658 | A (A1) | A (A1) | A1 | A1 | A1 | A, 01_AE | 01_AE |
63 | KY656659 | A (A1) | A (A1) | A1 | A1 | A1 | A, 01_AE | 01_AE |
64 | MF987697 | NA | Recombinant of B, D | B | B | B | B | B |
65 | KY656670 | NA | Recombinant of B, D | B | B | B | B | B |
66 | KY656671 | A (A1) | A (A1) | A1 | A1 | A1 | A/01_AE | 01_AE |
67 | MF987719 | NA | NA | unassigned, B–G | D | complex | D | D |
68 | MF987720 | NA | NA | unassigned, B–G | D | complex | D | D |
No. | Accession Number | Genome Sequence Range 1 | Rega 3.0 | Comet | jpHMM | SimPlot | Final Result |
---|---|---|---|---|---|---|---|
11 | MN736709 | 497–7842 | A (A1) | A1 | A1, K, A1 | A1/K or 45_cpx | A|A/U|A|K|A |
12 | MN736698 | 497–9496 | B | B | B | B | B |
25 | MN736699 | 497–9487 | A (A1) | A1 | A1 | A6 | A6 |
29 | MN736700 | 497–9496 | B | B | B | B | B |
31 | MN736710 | 497–7843 | C | unassigned; 60_BC, B, 82_cpx, 01_AE, 58_01B, 01_AE, 58_01B, 01_AE, 58_01B, 59_01B, 58_01B, 59_01B, 58_01B, 59_01B, 01_AE, 59_01B, 58_01B, 02_AG, 58_01B, 02_AG, A1, 69_01B, 59_01B, 69_01B, 53_01B, 69_01B, 53_01B, 69_01B, 55_01[..] | C, B, C, 01_AE, C | 60_BC | 60_BC|01_AE|60_BC |
34 | MN736701 | 497–9496 | recombinant of 13_cpx, G, A1, J, H | unassigned; G, A1, 01_AE, D, J, C, A2, C, B, D, B, D, B, D, J, C, A1, 01_AE | A1, G, D, J, B, J, G, A1, 01_AE | complex | U|A|G|U|G|J| G|U|J|U|G| A|01_AE |
37 | MN736702 | 497–9433 | recombinant of 02_AG, B, G, A1 | unassigned; 02_AG, 20_BG, 56_cpx, 20_BG, 56_cpx, 90_BF1, B, 56_cpx, B, 56_cpx, B, 71_BF1, 51_01B, 71_BF1, 39_BF, B, 69_01B, B, 69_01B, B, 69_01B, B, 56_cpx, 19_cpx, 24_BG, 19_cpx, 56_cpx, 24_BG, 56_cpx, G, 14_BG, 43_02G, G, 43_02G[..] | A1, B, A1, G, B, A1, G, B, A1, B, G | 56_cpx, B | 56_cpx|B|56_cpx |
39 | MN736703 | 497–9496 | 01_AE | unassigned; 01_AE, B, D | 01_AE | 01_AE | 01_AE |
43 | MN736704 | 497–9412 | B | unassigned; B, C, G | B | B, B/D, B, B/D | B |
54 | MN736705 | 497–9445 | 02_AG | 02_AG | A1, G, A1, G, A1, G, A1, G, A1 | 02_AG | 02_AG|A|02_AG |
56 | MN736706 | 497–9496 | B | B | B | B | B |
65 | MN736707 | 497–9496 | B | B | B | B | B |
68 | MN736708 | 497–9496 | recombinant of G, A1, D, B, F1 | unassigned; G, D, B, D, B, D, A1 | A1, G, D, B, A1, G, A2, G, A1, G, A1, G | complex | U|19_cpx|G|19_cpx| B|19_cpx|A|19_cpx|U|19_cpx|G|19_cpx|G|19_cpx|G |
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Lunar, M.M.; Mlakar, J.; Zorec, T.M.; Poljak, M. HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses 2020, 12, 63. https://doi.org/10.3390/v12010063
Lunar MM, Mlakar J, Zorec TM, Poljak M. HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses. 2020; 12(1):63. https://doi.org/10.3390/v12010063
Chicago/Turabian StyleLunar, Maja M., Jana Mlakar, Tomaž Mark Zorec, and Mario Poljak. 2020. "HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing" Viruses 12, no. 1: 63. https://doi.org/10.3390/v12010063
APA StyleLunar, M. M., Mlakar, J., Zorec, T. M., & Poljak, M. (2020). HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing. Viruses, 12(1), 63. https://doi.org/10.3390/v12010063