Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology
Abstract
:1. Introduction
2. Materials and Methods
2.1. Population Study and Samples
2.2. DNA Extraction and HPV Genotyping
2.3. DNA Amplification and Sequencing
2.4. Phylogenetic and Statistical Analyses
3. Results
3.1. Study Population
3.2. Phylogenetic Analyses
3.3. Relationship between Cytology and HPV16 Lineage Distribution
3.4. LCR and E6 Regions Nucleotide Sequences
3.5. SNPs Distribution According to the Sequence Lineages
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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HSIL n (%) | LSIL n (%) | ASCUS n (%) | NILM n (%) | |
---|---|---|---|---|
South Africa (N = 52) | 31 (60) | 7 (13) | 6 (12) | 8 (15) |
Mozambique (N = 6) | 1 (17) | 0 (0.0) | 1 (17) | 4 (66) |
HPV16 Lineages | Cytology | ||
---|---|---|---|
HSIL (n/%) | Non-HSIL (n/%) | Total (%) | |
A1–3 (European) | 14 (24) | 12 (21) | 26 (45) |
B1–4 (African 2) | 4 (7) | 5(9) | 9 (16) |
C1–4 (African 1) | 13 (22) | 7 (12) | 20 (34) |
D1–3 (North, Asian-American) | 1 (2) | 2 (3) | 3 (5) |
Total | 32 (55) | 26 (45) | 58 |
Nucleotide Position | Nucleotide Change | n | % | Clustering Sublineages |
---|---|---|---|---|
7179 | C > A | 1 | 1.72 | |
7198 | G > T | 2 | 3.45 | |
7209 | G > T | 8 | 13.79 | |
7226 | G > C | 3 | 5.17 | |
7226 | T > C | 1 | 1.72 | |
7232 | C > A | 2 | 3.45 | |
7252 | T > A | 2 | 3.45 | |
7284 | C > T | 1 | 1.72 | |
7288 | C > A | 2 | 3.45 | |
7303 | A > G | 2 | 3.45 | |
7303 | C > G | 17 | 29.31 | C1 |
7310–7311 | TT > CC | 2 | 3.45 | |
7351 | A > G | 19 | 32.76 | C1 |
7352 | C > G | 1 | 1.72 | |
7354 | A > C | 1 | 1.72 | |
7360–7362 | TGT > GTA | 1 | 1.72 | |
7366 | C > T | 1 | 1.72 | |
7374 | T > A | 1 | 1.72 | |
7388 | A > T | 1 | 1.72 | |
7401 | C > A | 23 | 39.66 | C1–4 and D1–4 |
7405 | G > A | 27 | 46.55 | A4 |
7437 | G > A | 15 | 25.86 | A1 |
7552 | C > A | 1 | 1.72 | |
7576 | G > A | 2 | 3.45 | |
7582 | C > A | 1 | 1.72 | |
7585 | T > C | 22 | 37.93 | C1–4 and D4 |
7605 | C > A | 27 | 46.55 | A1–4 and C1 |
7629 | G > T | 1 | 1.72 | |
7630 | A > T | 8 | 13.79 | |
7630 | G > T | 1 | 1.72 | |
7645 | C > A | 3 | 5.17 | |
7659 | G > T | 2 | 3.45 | |
7680 | C > T | 26 | 44.83 | A1–4 |
7702 | C > T | 26 | 44.83 | A1–4 |
7715 | C > G | 1 | 1.72 | |
7742 | A > G | 20 | 34.48 | C1–4 |
7749 | G > T | 4 | 6.90 | |
7750 | G > T | 28 | 48.28 | A1–4 and D2–3 |
7753 | C > A | 20 | 34.48 | C1–4 |
7755 | G > A | 20 | 34.48 | C1–4 |
7792 | A > C | 10 | 17.24 | B1–4 |
7802 | G > C | 2 | 3.45 | |
7813 | C > A | 1 | 1.72 | |
7834 | C > T | 3 | 5.17 | |
7853 | C > T | 30 | 51.72 | A1–4 and D1–4 |
7885 | G > A | 1 | 1.72 | |
7895 | T > C | 3 | 5.17 | |
7903 | G > T | 1 | 1.72 | |
7904 | C > T | 1 | 1.72 |
Nucleotide Position | Nucleotide Change | n | % | Clustering Sublineages |
---|---|---|---|---|
83 | C > A | 8 | 13.79 | |
110 | C > T | 20 | 34.48 | C1 |
132 | G > A | 3 | 5.17 | |
133 | T > G | 20 | 34.48 | C1 |
133 | C > G | 8 | 13.79 | |
144 | G > C | 28 | 48.28 | B1–4 and C1–4 |
146 | G > T | 26 | 44.83 | A1–4 |
287 | T > A | 26 | 44.83 | A1–4 |
290 | A > G | 26 | 44.83 | A1–4 |
336 | C > T | 26 | 44.83 | A1–4 |
351 | G > T | 6 | 10.34 | |
404 | G > A | 21 | 36.21 | C1 |
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Maueia, C.; Carulei, O.; Murahwa, A.T.; Taku, O.; Manjate, A.; Mussá, T.; Williamson, A.-L. Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology. Viruses 2024, 16, 1314. https://doi.org/10.3390/v16081314
Maueia C, Carulei O, Murahwa AT, Taku O, Manjate A, Mussá T, Williamson A-L. Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology. Viruses. 2024; 16(8):1314. https://doi.org/10.3390/v16081314
Chicago/Turabian StyleMaueia, Cremildo, Olivia Carulei, Alltalents T. Murahwa, Ongeziwe Taku, Alice Manjate, Tufária Mussá, and Anna-Lise Williamson. 2024. "Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology" Viruses 16, no. 8: 1314. https://doi.org/10.3390/v16081314