Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. Phylodynamic Analysis
2.3. Estimation of Transmission Rates
2.4. Statistical Analysis
3. Results
3.1. Validation of Molecular Clock Calculations
3.2. Dating the HIV-1 Epidemic in Greece
3.3. HIV Transmission Rates
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Characteristic | |
---|---|
Median age [in years, (IQR)] | 35.2 (29.2–43.3) |
HIV subtype, n (%) | |
A1 | 1533 (49.6) |
B | 1560 (50.4) |
Gender, n (%) | |
Male | 2708 (87.5) |
Female | 272 (8.8) |
Unknown | 113 (3.7) |
Transmission risk group, n (%) | |
MSM 1 | 2110 (68.2) |
PWID 2 | 236 (7.6) |
Heterosexuals | 505 (16.3) |
Other | 23 (0.8) |
Unknown | 219 (7.1) |
Antiretroviral therapy, n (%) | |
Naive | 2429 (78.5) |
Treated | 501 (16.2) |
Unknown | 163 (5.3) |
Ethnicity, n (%) | |
Greek | 2527 (81.7) |
Non-Greek | 211 (6.8) |
Unknown | 355 (11.5) |
Region of sampling, n (%) | |
Northern Greece | 694 (22.4) |
Central/Southern Greece | 2351 (76.0) |
Crete | 48 (1.6) |
Total, n (%) | 3093 (100.0) |
Subtype A1 cluster number | tMRCA, years, median (95% HPD 1) |
1 | 2008.94 (2007.70–2009.68) |
2 | 1982.58 (1972.80–1990.21) |
3 | 1992.65 (1988.29–1996.01) |
4 | 1983.84 (1974.87–1990.76) |
5 | 1992.35 (1988.02–1995.56) |
6 | 1992.56 (1987.46–1996.37) |
7 | 1990.17 (1985.50–1994.03) |
8 | 1993.07 (1989.22–1996.28) |
9 | 2006.84 (2003.93–2008.95) |
10 | 1987.85 (1983.71–1991.18) |
11 | 1984.71 (1977.77–1990.40) |
12 | 1990.47 (1987.23–1993.29) |
13 | 1994.18 (1990.28–1997.25) |
14 | 1997.70 (1994.30–2000.50) |
Subtype B cluster number | tMRCA, years, median (95% HPD) |
1 | 1997.28 (1994.73–1999.41) |
2 | 1993.13 (1987.73–1997.03) |
3 | 1993.86 (1991.37–1995.89) |
4 | 2006.96 (2004.92–2008.55) |
5 | 1989.18 (1985.08–1992.52) |
6 | 1991.81 (1987.76–1995.30) |
7 | 1992.83 (1989.42–1995.53) |
8 | 2002.06 (1995.41–2005.87) |
9 | 1999.64 (1996.72–2001.89) |
10 | 1985.47 (1978.57–1991.58) |
11 | 1991.43 (1987.12–1995.18) |
12 | 1994.31 (1990.45–1997.40) |
13 | 1998.52 (1992.76–2002.46) |
14 | 2010.90 (2009.94–2011.43) |
15 | 1988.09 (1982.96–1992.19) |
16 | 1998.71 (1995.06–2000.70) |
17 | 1992.40 (1988.70–1995.47) |
18 | 1993.56 (1989.62–1996.87) |
19 | 1994.30 (1990.20–1997.13) |
20 | 1988.47 (1983.94–1992.19) |
21 | 1995.63 (1991.51–1998.85) |
22 | 1991.33 (1986.36–1995.70) |
23 | 1995.86 (1991.72–1999.11) |
24 | 1996.77 (1992.69–1999.85) |
25 | 1997.34 (1989.30–2002.14) |
26 | 1995.87 (1992.66–1998.53) |
27 | 2002.95 (1999.74–2004.81) |
28 | 1993.55 (1987.53–1997.52) |
29 | 2004.48 (2001.66–2006.58) |
30 | 1988.32 (1984.63–1991.53) |
31 | 1994.86 (1991.27–1997.55) |
Cluster Number | Number of Sequences | HIV-1 Subtype | Transmission Rate (Number of Transmissions/100 Person Years) | Region of Sampling (Athens, %) | Age (Median) | Gender (Male, %) | Risk Group (%) | Ethnicity (Greek, %) | |
---|---|---|---|---|---|---|---|---|---|
1 | 15 | A1 | 39.608 | 0.0 | 35.5 | 53.3 | MSM | 6.7 | 46.7 |
PWID | 33.3 | ||||||||
HETERO | 6.7 | ||||||||
2 | 68 | A1 | 9.390 | 61.2 | 34.0 | 76.5 | MSM | 58.8 | 75.0 |
PWID | 2.9 | ||||||||
HETERO | 23.5 | ||||||||
3 | 124 | A1 | 13.702 | 90.3 | 36.0 | 95.2 | MSM | 76.6 | 90.3 |
PWID | 1.6 | ||||||||
HETERO | 17.4 | ||||||||
4 | 83 | A1 | 8.736 | 84.3 | 37.0 | 96.4 | MSM | 89.2 | 94.0 |
PWID | 1.2 | ||||||||
HETERO | 6.0 | ||||||||
5 | 83 | A1 | 12.870 | 83.1 | 36.5 | 77.1 | MSM | 62.7 | 85.5 |
PWID | 3.6 | ||||||||
HETERO | 30.1 | ||||||||
6 | 28 | A1 | 7.540 | 75.0 | 40.5 | 67.9 | MSM | 53.6 | 71.4 |
PWID | 0.0 | ||||||||
HETERO | 35.7 | ||||||||
7 | 164 | A1 | 11.498 | 34.4 | 38.0 | 84.2 | MSM | 67.1 | 76.2 |
PWID | 0.6 | ||||||||
HETERO | 17.7 | ||||||||
8 | 93 | A1 | 12.043 | 83.9 | 49.0 | 81.7 | MSM | 52.7 | 78.5 |
PWID | 4.3 | ||||||||
HETERO | 33.3 | ||||||||
9 | 66 | A1 | 23.146 | 95.5 | 35.0 | 87.9 | MSM | 0.0 | 83.3 |
PWID | 95.5 | ||||||||
HETERO | 1.5 | ||||||||
10 | 348 | A1 | 13.068 | 57.2 | 37.0 | 84.5 | MSM | 65.2 | 80.5 |
PWID | 3.7 | ||||||||
HETERO | 21.6 | ||||||||
11 | 120 | A1 | 8.586 | 50.9 | 38.0 | 79.2 | MSM | 58.3 | 72.5 |
PWID | 5.0 | ||||||||
HETERO | 25.0 | ||||||||
12 | 74 | A1 | 10.406 | 93.2 | 44.0 | 78.4 | MSM | 50.0 | 60.8 |
PWID | 1.4 | ||||||||
HETERO | 36.5 | ||||||||
13 | 208 | A1 | 15.880 | 84.6 | 31.0 | 93.8 | MSM | 85.1 | 82.2 |
PWID | 0.5 | ||||||||
HETERO | 7.7 | ||||||||
14 | 59 | A1 | 15.911 | 88.1 | 30.0 | 98.3 | MSM | 89.8 | 91.5 |
PWID | 3.4 | ||||||||
HETERO | 5.1 | ||||||||
1 | 180 | B | 16.519 | 87.2 | 31.0 | 98.3 | MSM | 88.9 | 84.4 |
PWID | 0.0 | ||||||||
HETERO | 4.4 | ||||||||
2 | 34 | B | 9.447 | 85.3 | 33.0 | 94.1 | MSM | 82.4 | 91.2 |
PWID | 0.0 | ||||||||
HETERO | 14.7 | ||||||||
3 | 54 | B | 15.038 | 98.2 | 35.0 | 72.2 | MSM | 57.4 | 87.0 |
PWID | 3.7 | ||||||||
HETERO | 35.2 | ||||||||
4 | 112 | B | 26.152 | 99.1 | 34.0 | 83.9 | MSM | 0.9 | 80.4 |
PWID | 98.2 | ||||||||
HETERO | 0.9 | ||||||||
5 | 43 | B | 6.439 | 79.1 | 37.0 | 53.5 | MSM | 32.6 | 88.4 |
PWID | 4.7 | ||||||||
HETERO | 55.8 | ||||||||
6 | 13 | B | 6.295 | 100.0 | 37.0 | 92.3 | MSM | 76.9 | 84.6 |
PWID | 0.0 | ||||||||
HETERO | 23.1 | ||||||||
7 | 17 | B | 6.207 | 76.5 | 42.5 | 76.5 | MSM | 64.7 | 64.7 |
PWID | 5.9 | ||||||||
HETERO | 17.7 | ||||||||
8 | 11 | B | 9.335 | 100.0 | 34.0 | 100.0 | MSM | 100.0 | 72.7 |
PWID | 0.0 | ||||||||
HETERO | 0.0 | ||||||||
9 | 11 | B | 7.376 | 27.3 | 55.0 | 54.6 | MSM | 36.4 | 81.8 |
PWID | 0.0 | ||||||||
HETERO | 54.6 | ||||||||
10 | 76 | B | 10.452 | 37.3 | 40.0 | 84.2 | MSM | 54.0 | 75.0 |
PWID | 0.0 | ||||||||
HETERO | 25.0 | ||||||||
11 | 30 | B | 11.373 | 83.3 | 37.0 | 96.7 | MSM | 96.7 | 83.3 |
PWID | 0.0 | ||||||||
HETERO | 3.3 | ||||||||
12 | 11 | B | 4.469 | 63.6 | 39.5 | 90.9 | MSM | 72.7 | 90.9 |
PWID | 0.0 | ||||||||
HETERO | 27.3 | ||||||||
13 | 31 | B | 14.551 | 96.8 | 30.5 | 100.0 | MSM | 90.3 | 87.1 |
PWID | 0.0 | ||||||||
HETERO | 6.5 | ||||||||
14 | 25 | B | 36.436 | 92.0 | 32.0 | 96.0 | MSM | 88.0 | 76.0 |
PWID | 0.0 | ||||||||
HETERO | 0.0 | ||||||||
15 | 53 | B | 8.334 | 13.2 | 35.0 | 83.0 | MSM | 64.2 | 66.0 |
PWID | 5.7 | ||||||||
HETERO | 15.1 | ||||||||
16 | 39 | B | 16.677 | 94.9 | 33.0 | 100.0 | MSM | 94.9 | 97.4 |
PWID | 0.0 | ||||||||
HETERO | 5.1 | ||||||||
17 | 56 | B | 10.424 | 75.0 | 38.5 | 89.3 | MSM | 66.1 | 80.4 |
PWID | 5.4 | ||||||||
HETERO | 17.9 | ||||||||
18 | 12 | B | 4.415 | 91.7 | 39.5 | 91.7 | MSM | 66.7 | 100.0 |
PWID | 8.3 | ||||||||
HETERO | 25.0 | ||||||||
19 | 28 | B | 9.219 | 100.0 | 32.5 | 78.6 | MSM | 60.7 | 75.0 |
PWID | 7.1 | ||||||||
HETERO | 28.6 | ||||||||
20 | 137 | B | 11.978 | 92.7 | 34.0 | 92.0 | MSM | 79.6 | 86.9 |
PWID | 0.7 | ||||||||
HETERO | 16.1 | ||||||||
21 | 122 | B | 13.722 | 76.2 | 32.0 | 89.3 | MSM | 77.1 | 86.1 |
PWID | 0.0 | ||||||||
HETERO | 10.7 | ||||||||
22 | 66 | B | 16.164 | 89.2 | 30.0 | 95.5 | MSM | 86.4 | 84.9 |
PWID | 1.5 | ||||||||
HETERO | 4.6 | ||||||||
23 | 20 | B | 8.546 | 85.0 | 46.0 | 80.0 | MSM | 70.0 | 80.0 |
PWID | 0.0 | ||||||||
HETERO | 25.0 | ||||||||
24 | 12 | B | 5.847 | 83.3 | 35.0 | 100.0 | MSM | 91.7 | 66.7 |
PWID | 0.0 | ||||||||
HETERO | 8.3 | ||||||||
25 | 19 | B | 9.814 | 89.5 | 40.0 | 100.0 | MSM | 84.2 | 94.7 |
PWID | 0.0 | ||||||||
HETERO | 10.5 | ||||||||
26 | 18 | B | 6.480 | 94.4 | 35.0 | 83.3 | MSM | 66.7 | 83.3 |
PWID | 5.6 | ||||||||
HETERO | 16.7 | ||||||||
27 | 9 | B | 15.993 | 88.9 | 45.5 | 88.9 | MSM | 77.8 | 66.7 |
PWID | 0.0 | ||||||||
HETERO | 22.2 | ||||||||
28 | 25 | B | 11.309 | 84.0 | 33.5 | 92.0 | MSM | 68.0 | 60.0 |
PWID | 4.0 | ||||||||
HETERO | 8.0 | ||||||||
29 | 31 | B | 22.943 | 54.8 | 36.0 | 93.6 | MSM | 77.4 | 71.0 |
PWID | 0.0 | ||||||||
HETERO | 0.0 | ||||||||
30 | 218 | B | 10.864 | 90.4 | 34.0 | 94.0 | MSM | 83.0 | 87.2 |
PWID | 1.4 | ||||||||
HETERO | 12.8 | ||||||||
31 | 47 | B | 11.874 | 87.2 | 38.0 | 83.0 | MSM | 78.7 | 93.6 |
PWID | 2.1 | ||||||||
HETERO | 17.0 |
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Limnaios, S.; Kostaki, E.G.; Adamis, G.; Astriti, M.; Chini, M.; Mangafas, N.; Lazanas, M.; Patrinos, S.; Metallidis, S.; Tsachouridou, O.; et al. Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe. Viruses 2022, 14, 101. https://doi.org/10.3390/v14010101
Limnaios S, Kostaki EG, Adamis G, Astriti M, Chini M, Mangafas N, Lazanas M, Patrinos S, Metallidis S, Tsachouridou O, et al. Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe. Viruses. 2022; 14(1):101. https://doi.org/10.3390/v14010101
Chicago/Turabian StyleLimnaios, Stefanos, Evangelia Georgia Kostaki, Georgios Adamis, Myrto Astriti, Maria Chini, Nikos Mangafas, Marios Lazanas, Stavros Patrinos, Simeon Metallidis, Olga Tsachouridou, and et al. 2022. "Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe" Viruses 14, no. 1: 101. https://doi.org/10.3390/v14010101
APA StyleLimnaios, S., Kostaki, E. G., Adamis, G., Astriti, M., Chini, M., Mangafas, N., Lazanas, M., Patrinos, S., Metallidis, S., Tsachouridou, O., Papastamopoulos, V., Kakalou, E., Chatzidimitriou, D., Antoniadou, A., Papadopoulos, A., Psichogiou, M., Basoulis, D., Gova, M., Pilalas, D., ... Paraskevis, D. (2022). Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe. Viruses, 14(1), 101. https://doi.org/10.3390/v14010101