Article Figures & Data
Figures
- FIG 1
HIV-1 subtype diversity and temporal distribution of the date of diagnosis in the cohort of 289 HIV-1-infected individuals from the province of Minho, Portugal.
- FIG 2
Phylogenetic relationships among the HIV-1 sequences isolated from 289 infected individuals from Minho province, Portugal. Maximum likelihood (ML) phylogenetic analysis was performed using 289 partial HIV-1 sequences obtained in this study and 89 subtype reference sequences (colored in blue) and rooted using the M-group consensus sequence. The branch lengths are expressed as the number of nucleotide substitutions per site. The transmission clusters (colored in pink) were supported by an ML bootstrap support of ≥95% based on 1,000 replicates, an average genetic distance of ≤0.03 substitutions per site, and a Bayesian posterior probability equal to 1.
- FIG 3
Phylogenetic relationships between the 13F1 and 14F1 transmission cluster sequences and public sequences available in the databases. Maximum likelihood (ML) phylogenetic analysis was performed using 13F1 and 14F1 sequences (pink), 4 subtype references (blue), and the 50 most similar sequences obtained in the BLAST query of all publically available sequences. Highlighted in purple are the public sequences that are included in cluster 14F1. The tree was rooted using the M-group consensus.
Tables
- TABLE 1
Demographics of the study population
Variablea No. % Gender Male 222 76.8 Female 67 23.2 Age at diagnosis (yr) ≤20 17 5.9 21–40 190 65.7 41–50 41 14.2 >50 41 14.2 Patient nationality Portuguese 260 90.0 Other 29 10.0 Ethnicity White 274 94.8 Black 15 5.2 Presumed country of infection Portugal 280 96.9 Other 9 3.1 Route of transmission Heterosexual contact 161 55.7 MSM 26 9.0 IDU 99 34.2 Other 3 1.1 Total 289 100 ↵a IDU, intravenous drug users; MSM, men who have sex with men.
- TABLE 2
Multinomial logistic regression model relating HIV-1 subtypes with date of diagnosis, age, gender, and presumed transmission mode
Subtype comparison Variable Be SE Walda ORb 95% CIc LB UB Recombinants vs A1/F1 Days (or yr) since date of diagnosis −0.0004 0.000 6.278* 1.000 (0.852) 0.999 1.000 Age −0.006 0.019 0.091 0.994 0.959 1.031 Male 0.298 0.638 0.218 1.347 0.386 4.699 Heterosexual −0.808 0.735 1.207 0.446 0.106 1.884 IDUd −0.346 0.820 0.178 0.708 0.142 3.533 G vs A1/F1 Days (or yr) since date of diagnosis −0.001 0.000 10.774** 0.999 (0.824) 0.999 1.000 Age 0.016 0.016 1.100 1.016 0.986 1.048 Male −0.847 0.476 3.167 0.429 0.169 1.090 Heterosexual 1.450 1.161 1.559 4.264 0.438 41.537 IDU 2.012 1.214 2.747 7.475 0.693 80.672 B vs A1/F1 Days (or yr) since date of diagnosis −0.001 0.000 17.319*** 0.999 (0.781) 0.999 1.000 Age −0.016 0.017 0.932 0.984 0.952 1.017 Male −0.473 0.512 0.856 0.623 0.229 1.698 Heterosexual −1.234 0.663 3.459 0.291 0.079 1.069 IDU −1.593 0.771 4.269* 0.203 0.045 0.921 C vs A1/F1 Days (or yr) since date of diagnosis −0.000 0.000 5.154* 1.000 (0.862) 0.999 1.000 Age 0.017 0.019 0.815 1.017 0.980 1.056 Male −0.646 0.579 1.242 0.524 0.168 1.632 Heterosexual −0.267 0.949 0.079 0.766 0.119 4.919 IDU 1.216 0.996 1.491 3.374 0.479 23.754 - TABLE 3
Characterization of the 17 HIV-1 transmission clusters identified in the study population of the Portuguese region of Minho
Cluster name No. of individuals HIV-1 subtype Yr of diagnosis (mean, range) Route of transmission (n)a Time of MRCA Yr 95% HPD 01DB 3 DB URF 2009, 2006–2012 IDU (4), heterosexual (1) 2002 1998.2–2006.1 02B 3 B 2006, 2003–2008 IDU (2), heterosexual (1) 1999 1994.2–2003.3 03B 5 B 2003, 2000–2009 Heterosexual (2), MSM (1) 2004 2001.9–2006.5 04B 3 B 2007, 2006–2009 Heterosexual (4) 2004 2000.7–2006.9 05B 3 B 2006, 2003–2008 MSM (3), heterosexual (2) 2003 2000.0–2005.6 06B 3 B 2008, 2005–2010 Heterosexual (3) 2002 1998.4–2004.8 07B 3 B 2009, 2008–2010 Heterosexual (3) 2004 2000.0–2006.9 08B 5 B 2007, 2000–2010 Heterosexual (2), MSM (1) 2002 1998.1–2004.4 09G 7 G 2006, 1999–2009 Heterosexual (5), IDU (2) 2000 1997.1–2003.2 10G 3 G 2010, 2008–2011 Heterosexual (2), IDU (1) 2008 2004.8–2010.4 11C 31 C 2004, 1999–2011 IDU (27), heterosexual (4) 1994 1990.4–1998.1 12C 3 C 2006, 2001–2009 Heterosexual (3) 2005 2001.6–2007.6 13F1 10 F1 2006, 2000–2011 Heterosexual (7), IDU (3) 2000 1993.2–2003.5 14F1 7 F1 2009, 2007–2011 Heterosexual (6), IDU (1) 2005 2002.7–2007.2 15F1 4 F1 2010, 2009–2010 Heterosexual (4) 1994 1987.5–2001.6 16A1 8 A1 2009, 2006–2011 Heterosexual (5), MSM (3) 1999 1994.0–2003.3 17BG 12 CRF14_BG 2002, 2000–2006 IDU (10), heterosexual (2) 1999 1994.5–2002.8 ↵a IDU, intravenous drug users; MSM, men who have sex with men.
b MRCA, most recent common ancestor; HPD, high posterior density.
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Tables S1 (Comparison of transmission route, gender, and age at diagnosis between HIV-1-infected individuals followed at Hospital de Braga and all data available on HIV-1 infections in Portugal by the end of 2012) and S2 (Transmission cluster analysis)
PDF, 77K
- Supplemental file 1 -
