HIV-1 Subtypes and 5’LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Genomic DNA Isolation and Nested PCR Amplification of Partial 5′LTR of HIV-1
2.3. Cloning and Sequencing of Amplified Partial 5′LTR Sequences
2.4. Sequence and Phylogenetic Analyses
2.5. Sequence Variant Classification by Recursive Partitioning Analysis
3. Results
3.1. Uganda A1 and D Subtype 5′LTR-Leader Sequences Were Significantly Enriched in HIV Viral Population from Late Seroconverters
3.2. Unique Sequences and Combinations of PBS, SD, and Ps Sequences in Late Seroconverters
3.3. Combinations of Subtype A1.KE or D with Unique PBS and SD Sequence Variants in Late Seroconverters
3.4. Potential Functional Differences among PBS Variants in Late Seroconverters
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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HIV-1 Subtype | A1 | A1.KE | A1.UG | B | C | D | D.UG | Total | Ave Seq./ind. | p Value | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
A | All 142 individuals | No. | 30 | 2162 | 135 | 97 | 263 | 945 | 46 | 3678 | ||
% | 0.8 | 58.8 | 3.7 | 2.6 | 7.2 | 25.7 | 1.3 | 100 | ||||
B | Late seroconverter (n = 20) | No. | 0 | 452 | 91 | 0 | 0 | 211 | 46 | 800 | 40 (19–47) | <0.0001 |
% | 0 | 56.5 | 11.4 | 0 | 0 | 26.4 | 5.8 | 100 | ||||
Early seroconverter (n = 122) | No. | 30 | 1710 | 44 | 97 | 263 | 734 | 0 | 2878 | 30 (11–75) | ||
% | 1.0 | 59.4 | 1.5 | 3.4 | 9.1 | 25.5 | 0 | 100 |
Group | Sequences | Subtypes | Frequency in EC or LSC |
---|---|---|---|
PBS-1 | GAGAAAGTTAACAGGGAC, GCGAAAGATAACAGGGAC, GCGAAAGCTAACAGGGAC, GCGAAAGTTAATAGGGA-C, GCGAAAGTTAACAGGGAC, GCGAAAGTTAATAGGGAC, GCGAGAGTTAACAGGGAC, GTGAAAGTTAACAGGGAC, TGGCGCCCGAAGAGGGAC, TGGCGCCCAAACAGGGAC, TGGGCGCCCCAACGGGGAC, TGG-GCCCGAACAGGGAC | A1.KE (1.1%), A1.UG (93.67%), D (3.2%), D.UG (2.1%) | 0/122 EC, 5/12 LSC |
PBS-4 | TG-GCGCC-GAACAGGGA, TGGCGCCCGAACAGGGTAC, TGGCGCCGGAACAGGGAC, TGGCGCCCGACGTGGGGC, TGGCGCCCGAACCGGGAC, TGGCGCCCGACCAGGGAC, TGGC-CCCGAACAGGAAC, TGGCGCCCGA-CAGGGAC, TG-CGCC-CGAACAGGGAC, TGGCGCCCGTACAGGGAC, TGGCGCCCGAACAGGGTTC, TGGCGCC-GAACAGGGA, TGGCGACCGAACAGGGAC, TGGCGCCCGAAT-GGGAC, TGGCGCCCCAACAGGGAC, TGGCGCCC-AACAGGGAC, TGGCGCCCCGAACAGGGAC, -GCGCCC-GAACAGGGAC, TGGCGCCCGATCAGGGAC, CGGCGCCCGAACAGGGAC, TGGC-GCC-GAACAGGGAC, TGGCGCCCGAACAGG-AC, TG--GCGCCCGAACTGGGA | A1 (2.2%), A1.KE (38%), B (2.2%), C (12.0%), D (42%) | 36/122 EC, 0/20 LSC |
SD1-1 | AAGGCGAGTAC, GAGGTGAGTAC, CTAGGTGAGTAC, CTAGGTGGGTAC, CTGGTAGGTGC, ACGGTGTTTAC, ATGGTGAGTAC, ACGGTGTGTAC, ACGGTGAATAC | A1.KE (92.4), D (6.2%), D.UG (1.4%) | 0/122 EC, 6/20 LSC |
SD1-5 | ACGGTAAGTAC, CGGGGGAGTAC, TTGGTGAGTAC, CTGG-TGAGTGC, CCGGTGAGCAC, CTGGGTGAGTAC, CAGGTGAGTGC, CAGGTGAGTAC, CTGGGGAGTAC, GTGGGTGAGTAC, CTGGTGAATAC, CTGGTGAGTGT, CGGGTGAGTAC, ACGGTGAGTGC, CTGGTGAGTGC | A1 (1.4%), A1.KE (90%), B (1.4%), C (2.9%), D (4.3%) | 15/122 EC, 0/20 LSC |
PS-1 | AGTG, GGAC, CGAG, GGCG, AGGG | A1.KE (50%), A1.UG (16.7%), D (33.3%) | 0/122 EC, 6/20 LSC |
PS-3 | GGAA, GAAG, GGAT, AGAG, ? | A1.KE (66.8%), A1.UG (1.3%), C (24.1%), D (7.8%) | 30/122, EC, 4/20 LSC |
Subtypes or PBS | SD or PBS | Seroconverter |
---|---|---|
TGGCGCCCGAACAGGGGC TGGCGCCCGAACAGGGTC TGGCGCCCGAATAGGGAC TGGCGCCCGAACAGGAAC TGGCGCCCGCACAGGGAC? (PBS-2) | CTGGTGAGTAC AAGGTGAGTAC ACGGTGTTTAC ACAGTGAGTAC | LSC |
CAGGTGAGTAC CAGGTGAGTGC | EC | |
TGGCGCCCGAACAGGGAC TGGCGCCCGAACAGAGAC TGGCGCC-GAACAGGGAC TGGCGCCCGAACGGGGAC TGGC-CCCGAACAGGGAC TGGCCGCCCGAACAGGGAC TG-CGCCCGAACAGGGAC TGGCGCCCGAACTGGGAC (PBS-3) | AAGGCGAGTAC ACGGTGAATAC ATGGTGAGTAC CTAGGTAGGTGC CTAGGTGGGTAC CTGGTAGGTGC GAGGTGAGTAC | LSC |
ACGGTGAGTGC ACGGTAAGTAC CAGGTGAGTAC CAGGTGAGTGC CCGGTGAGCAC CGGGGGAGTAC CGGGTGAGTAC CTGGTGAGTGT CTGGGGAGTAC CTGGGTGAGTAC CTGG-TGAGTGC CTGGTGAATAC GTGGGTGAGTAC TTGGTGAGTAC | EC | |
Subtype D | AAGGCGAGTAC ACGGTGAATAC ACGGTGTGTAC ACGGTGTTTAC ATGGTGAGTAC ? | LSC |
ACGGTAAGTAC ACGGTGAGTGC CCGGTGAGTAC CTAGTGAGTAC CTGGTAAGTAC CTGGTGAATAC CTGGTGAGCAC CTGGCGAGTAC | EC | |
Subtype D | TGGCGCCCGAACAGGGTC TGGCGCCCCAACGGGGAC TGGCGCCCGAACAGGAAC TGG-GCCCGAACAGGGAC TGGCGCCCAAACAGGGAC TG-CGCCCGAACAGGGAC TGGCCGCCCGAACAGGGAC (D-PBS-1) | LSC |
TGGCGCCGGAACAGGGAC TGGCGCCCGAACAGGGTAC TGGCGCCCGACGTGGGGC TGGCGACCGAACAGGGAC TGGCGCCCGAACCGGGAC TGGCGCCCGTACAGGGAC TGGC-CCCGAACAGGGAC TGGCCGCCCGATCAGGGAC TG-CGCC-CGAACAGGGAC TGGCGCCCCGAACAGGGAC (D-PBS-3) | EC | |
A1.KE | CTAGGTGAGTAC CTAGGTGGGTAC CTAGTGAGTAC CTGGTAGGTGC (A1.KE-SD-1) | LSC |
ACGGTGAGTAC ACGGTGAGTGC CAGGTGAGTAC CAGGTGAGTGC CCGGTGAGTAC CGGGGGAGTAC CTGGGTGAGTAC CTGGTGAGTGT CTGG-TGAGTGC TTGGTGAGTAC ? (A1.KE-SD-4) | EC |
mlno | PBS1 | SD1 | PS1 | PBS-2/SD-1 | PBS2/A1.UG | PBS-3/SD-1 | PBS-3/SD-2 | SD2 | A1-UG/D.UG | A1.KE/SD1 | D-SD-1 | D-PBS-1 |
---|---|---|---|---|---|---|---|---|---|---|---|---|
37 | + | |||||||||||
58 | + | + | + | + | + | |||||||
290 | + | + | + | |||||||||
452 | + | + | + | |||||||||
546 | + | + | + | |||||||||
768 | + | + | + | + | ||||||||
814 | + | + | + | |||||||||
825 | ||||||||||||
888 | + | + | + | + | + | + | + | |||||
890 | + | + | + | + | + | |||||||
1072 | + | + | + | |||||||||
1102 | + | + | + | + | ||||||||
1232 | + | + | ||||||||||
1248 | ||||||||||||
1250 | + | + | + | + | ||||||||
1287 | + | + | + | + | + | |||||||
1430 | + | |||||||||||
1626 | + | + | + | |||||||||
1707 | ||||||||||||
1730 |
mlno | A1.KE | A1.UG | D | D.UG |
---|---|---|---|---|
37 | * | |||
58 | * | |||
290 | * | |||
452 | * | |||
546 | * | |||
768 | * | * | ||
814 | * | |||
825 | * | * | ||
888 | * | |||
890 | * | |||
1072 | * | * | ||
1102 | * | |||
1232 | * | |||
1248 | * | |||
1250 | * | |||
1287 | * | |||
1430 | * | * | ||
1626 | * | |||
1707 | * | |||
1730 | * |
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Sampathkumar, R.; Scott-Herridge, J.; Liang, B.; Kimani, J.; Plummer, F.A.; Luo, M. HIV-1 Subtypes and 5’LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort. Viruses 2018, 10, 4. https://doi.org/10.3390/v10010004
Sampathkumar R, Scott-Herridge J, Liang B, Kimani J, Plummer FA, Luo M. HIV-1 Subtypes and 5’LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort. Viruses. 2018; 10(1):4. https://doi.org/10.3390/v10010004
Chicago/Turabian StyleSampathkumar, Raghavan, Joel Scott-Herridge, Binhua Liang, Joshua Kimani, Francis A. Plummer, and Ma Luo. 2018. "HIV-1 Subtypes and 5’LTR-Leader Sequence Variants Correlate with Seroconversion Status in Pumwani Sex Worker Cohort" Viruses 10, no. 1: 4. https://doi.org/10.3390/v10010004