1
|
Rusine J, Jurriaans S, van de Wijgert J, Cornelissen M, Kateera B, Boer K, Karita E, Mukabayire O, de Jong M, Ondoa P. Molecular and phylogeographic analysis of human immuno-deficiency virus type 1 strains infecting treatment-naive patients from Kigali, Rwanda. PLoS One 2012; 7:e42557. [PMID: 22905148 PMCID: PMC3419187 DOI: 10.1371/journal.pone.0042557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/09/2012] [Indexed: 01/18/2023] Open
Abstract
This study aimed at describing the genetic subtype distribution of HIV-1 strains circulating in Kigali and their epidemiological link with the HIV-1 strains from the five countries surrounding Rwanda. One hundred and thirty eight pol (RT and PR) sequences from 116 chronically- and 22 recently-infected antiretroviral therapy (ART)-naïve patients from Kigali were generated and subjected to HIV drug resistance (HIV-DR), phylogenetic and recombinant analyses in connection with 366 reference pol sequences from Rwanda, Burundi, Kenya, Democratic Republic of Congo, Tanzania and Uganda (Los Alamos database). Among the Rwandan samples, subtype A1 predominated (71.7%), followed by A1/C recombinants (18.1%), subtype C (5.8%), subtype D (2.9%), one A1/D recombinant (0.7%) and one unknown subtype (0.7%). Thirteen unique and three multiple A1/C recombinant forms were identified. No evidence for direct transmission events was found within the Rwandan strains. Molecular characteristics of HIV-1 were similar between chronically and recently-infected individuals and were not significantly associated with demographic or social factors. Our report suggests that the HIV-1 epidemic in Kigali is characterized by the emergence of A1/C recombinants and is not phylogenetically connected with the HIV-1 epidemic in the five neighboring countries. The relatively low level of transmitted HIV-DR mutations (2.9%) reported here indicates the good performance of the ART programme in Rwanda. However, the importance of promoting couples' counseling, testing and disclosure during HIV prevention strategies is highlighted.
Collapse
Affiliation(s)
- John Rusine
- National Reference Laboratory, Kigali, Rwanda
| | - Suzanne Jurriaans
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Janneke van de Wijgert
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Marion Cornelissen
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Brenda Kateera
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Kimberly Boer
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | | | | | - Menno de Jong
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
2
|
Quesnel-Vallières M, Kouzayha I, Tran E, Barry I, Lasgi C, Merindol N, Monteil V, Ransy DG, Boucher M, Lapointe N, Soudeyns H. Novel HIV-1 recombinant forms in antenatal cohort, Montreal, Quebec, Canada. Emerg Infect Dis 2011; 17:271-4. [PMID: 21291604 PMCID: PMC3204757 DOI: 10.3201/eid1702.100629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Near full-length genomes of 4 unclassified HIV-1 variants infecting patients enrolled in an antenatal cohort in Canada were obtained by sequencing. All 4 variants showed original recombination profiles, including A1/A2/J, A1/D, and A1/G/J/CRF11_cpx structures. Identification of these variants highlights the growing prevalence of unique recombinant forms of HIV-1 in North America.
Collapse
|
3
|
Ntemgwa M, Gill MJ, Brenner BG, Moisi D, Wainberg MA. Discrepancies in assignment of subtype/recombinant forms by genotyping programs for HIV type 1 drug resistance testing may falsely predict superinfection. AIDS Res Hum Retroviruses 2008; 24:995-1002. [PMID: 18593348 DOI: 10.1089/aid.2008.0064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
With the growing diversity of the HIV pandemic, routine genotyping is an important tool for monitoring viral subtype as well as drug resistance. In this regard, numerous subtyping tools and drug resistance algorithms are available online. However, there are discrepancies in the use of these online tools in the designation of HIV-1 subtypes or recombinant forms that may have an impact on drug susceptibility profiles. Indeed, inconsistencies in some of these tools may lead to a false designation of dual infection and/or superinfection. In this case study, we evaluated the sequence diversity of an infection that was referred to us as a potential case of superinfection as a result of variations in designation of subtype. We evaluated sequences using five different online tools and finally determined by phylogenetic analysis that the sequence was a unique A1/C intersubtype recombinant at baseline and not a case of superinfection.
Collapse
Affiliation(s)
- Michel Ntemgwa
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - M. John Gill
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Bluma G. Brenner
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Daniela Moisi
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A. Wainberg
- McGill University AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| |
Collapse
|