Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JCM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Journal of Clinical Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JCM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Epidemiology

Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of Non-B and Non-G Subtypes

Alexandre Carvalho, Patrício Costa, Vera Triunfante, Fernando Branca, Fernando Rodrigues, Catarina L. Santos, Margarida Correia-Neves, Margarida Saraiva, Henrique Lecour, António G. Castro, Jorge Pedrosa, Nuno S. Osório
E. Munson, Editor
Alexandre Carvalho
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
cHospital de Braga, Braga, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrício Costa
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vera Triunfante
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fernando Branca
cHospital de Braga, Braga, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fernando Rodrigues
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catarina L. Santos
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Margarida Correia-Neves
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Margarida Saraiva
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Henrique Lecour
dInstitute of Health Sciences, Universidade Católica Portuguesa (Portuguese Catholic University, UCP), Porto, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
António G. Castro
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jorge Pedrosa
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nuno S. Osório
aLife and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
bICVS/3B PT Government Associate Laboratory, Braga/Guimarães, Portugal
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
E. Munson
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/JCM.03611-14
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    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
    • Open in new tab
    • Download powerpoint
    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
    • Open in new tab
    • Download powerpoint
    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

  • Figures
  • Additional Files
  • TABLE 1

    Demographics of the study population

    VariableaNo.%
    Gender
        Male22276.8
        Female6723.2
    Age at diagnosis (yr)
        ≤20175.9
        21–4019065.7
        41–504114.2
        >504114.2
    Patient nationality
        Portuguese26090.0
        Other2910.0
    Ethnicity
        White27494.8
        Black155.2
    Presumed country of infection
        Portugal28096.9
        Other93.1
    Route of transmission
        Heterosexual contact16155.7
        MSM269.0
        IDU9934.2
        Other31.1
    Total289100
    • ↵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 comparisonVariableBeSEWaldaORb95% CIc
    LBUB
    Recombinants vs A1/F1Days (or yr) since date of diagnosis−0.00040.0006.278*1.000 (0.852)0.9991.000
    Age−0.0060.0190.0910.9940.9591.031
    Male0.2980.6380.2181.3470.3864.699
    Heterosexual−0.8080.7351.2070.4460.1061.884
    IDUd−0.3460.8200.1780.7080.1423.533
    G vs A1/F1Days (or yr) since date of diagnosis−0.0010.00010.774**0.999 (0.824)0.9991.000
    Age0.0160.0161.1001.0160.9861.048
    Male−0.8470.4763.1670.4290.1691.090
    Heterosexual1.4501.1611.5594.2640.43841.537
    IDU2.0121.2142.7477.4750.69380.672
    B vs A1/F1Days (or yr) since date of diagnosis−0.0010.00017.319***0.999 (0.781)0.9991.000
    Age−0.0160.0170.9320.9840.9521.017
    Male−0.4730.5120.8560.6230.2291.698
    Heterosexual−1.2340.6633.4590.2910.0791.069
    IDU−1.5930.7714.269*0.2030.0450.921
    C vs A1/F1Days (or yr) since date of diagnosis−0.0000.0005.154*1.000 (0.862)0.9991.000
    Age0.0170.0190.8151.0170.9801.056
    Male−0.6460.5791.2420.5240.1681.632
    Heterosexual−0.2670.9490.0790.7660.1194.919
    IDU1.2160.9961.4913.3740.47923.754
    • ↵a *, P < 0.05; **, P < 0.01; ***, P < 0.001.

    • ↵b OR, odds ratio.

    • ↵c 95% CI, 95% confidence interval; LB, lower bound; UB, upper bound.

    • ↵d IDU, intravenous drug users.

    • ↵e B, regression coefficient.

  • TABLE 3

    Characterization of the 17 HIV-1 transmission clusters identified in the study population of the Portuguese region of Minho

    Cluster nameNo. of individualsHIV-1 subtypeYr of diagnosis (mean, range)Route of transmission (n)aTime of MRCA
    Yr95% HPD
    01DB3DB URF2009, 2006–2012IDU (4), heterosexual (1)20021998.2–2006.1
    02B3B2006, 2003–2008IDU (2), heterosexual (1)19991994.2–2003.3
    03B5B2003, 2000–2009Heterosexual (2), MSM (1)20042001.9–2006.5
    04B3B2007, 2006–2009Heterosexual (4)20042000.7–2006.9
    05B3B2006, 2003–2008MSM (3), heterosexual (2)20032000.0–2005.6
    06B3B2008, 2005–2010Heterosexual (3)20021998.4–2004.8
    07B3B2009, 2008–2010Heterosexual (3)20042000.0–2006.9
    08B5B2007, 2000–2010Heterosexual (2), MSM (1)20021998.1–2004.4
    09G7G2006, 1999–2009Heterosexual (5), IDU (2)20001997.1–2003.2
    10G3G2010, 2008–2011Heterosexual (2), IDU (1)20082004.8–2010.4
    11C31C2004, 1999–2011IDU (27), heterosexual (4)19941990.4–1998.1
    12C3C2006, 2001–2009Heterosexual (3)20052001.6–2007.6
    13F110F12006, 2000–2011Heterosexual (7), IDU (3)20001993.2–2003.5
    14F17F12009, 2007–2011Heterosexual (6), IDU (1)20052002.7–2007.2
    15F14F12010, 2009–2010Heterosexual (4)19941987.5–2001.6
    16A18A12009, 2006–2011Heterosexual (5), MSM (3)19991994.0–2003.3
    17BG12CRF14_BG2002, 2000–2006IDU (10), heterosexual (2)19991994.5–2002.8
    • ↵a IDU, intravenous drug users; MSM, men who have sex with men.

    • b MRCA, most recent common ancestor; HPD, high posterior density.

Additional Files

  • Figures
  • Tables
  • 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

PreviousNext
Back to top
Download PDF
Citation Tools
Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of Non-B and Non-G Subtypes
Alexandre Carvalho, Patrício Costa, Vera Triunfante, Fernando Branca, Fernando Rodrigues, Catarina L. Santos, Margarida Correia-Neves, Margarida Saraiva, Henrique Lecour, António G. Castro, Jorge Pedrosa, Nuno S. Osório
Journal of Clinical Microbiology Apr 2015, 53 (5) 1506-1514; DOI: 10.1128/JCM.03611-14

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Journal of Clinical Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of Non-B and Non-G Subtypes
(Your Name) has forwarded a page to you from Journal of Clinical Microbiology
(Your Name) thought you would be interested in this article in Journal of Clinical Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of Non-B and Non-G Subtypes
Alexandre Carvalho, Patrício Costa, Vera Triunfante, Fernando Branca, Fernando Rodrigues, Catarina L. Santos, Margarida Correia-Neves, Margarida Saraiva, Henrique Lecour, António G. Castro, Jorge Pedrosa, Nuno S. Osório
Journal of Clinical Microbiology Apr 2015, 53 (5) 1506-1514; DOI: 10.1128/JCM.03611-14
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • MATERIALS AND METHODS
    • RESULTS
    • DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About JCM
  • Editor in Chief
  • Board of Editors
  • Editor Conflicts of Interest
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Resources for Clinical Microbiologists
  • Ethics
  • Contact Us

Follow #JClinMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

 

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0095-1137; Online ISSN: 1098-660X