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New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

Frange P, Galimand J, Vidal N, Goujard C, Deveau C, Souala F, Peeters M, Meyer L, Rouzioux C, Chaix ML - Retrovirology (2008)

Bottom Line: Others PHI were further observed in 2006-2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France.Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: EA 3620, Université Paris - Descartes, Laboratoire de Virologie, Hôpital Necker - Enfants Malades, AP-HP, Paris, France. pierre.frange@nck.aphp.fr

ABSTRACT

Background: Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs).

Methods: Among 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures.

Results: Among V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006-2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.

Conclusion: This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.

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Analysis of the recombinant structure of 06FR-CRN strain. Bootscan plots (a) showing the complex mosaic structure of the 06FR-CRN strain (9684bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8116 unambigously aligned base pairs). (b) Bootscan plots with B and C references performed to better characterize the geographic origin of the 06FR-CRN strain.
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Figure 4: Analysis of the recombinant structure of 06FR-CRN strain. Bootscan plots (a) showing the complex mosaic structure of the 06FR-CRN strain (9684bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8116 unambigously aligned base pairs). (b) Bootscan plots with B and C references performed to better characterize the geographic origin of the 06FR-CRN strain.

Mentions: The bootscan analysis of 06FR-CRN (Fig. 4a) showed that the majority of the genome is subtype C except two small regions in pol: the first one included part of the RT gene and clustered with subtype B; the second one (5'end of the integrase gene) clustered with the common branch for B and D subtypes (region 4). The 3'end of the nef gene and LTR were subtype B. Figure 4b shows a more detailed bootscan analysis of 06FR-CRN against 10 subtype C reference strains, isolated from different regions over the world and illustrates that 06FR-CRN "C" regions strongly clustered with 98BR-BR004, isolated in Brazil [25]. Despite iterative bootscan analysis including additional B and D reference strains or with BLAST analysis, the region 4 remained undetermined. The subtype identifications of the various genomic regions were all confirmed by phylogenetic tree analysis of the corresponding fragments (Figure 5). We included reference sequences of CRF31_BC strains in these trees to illustrate the differences between this previously described CRF and 06FR-CRN, which both resulted from the recombination between a Brazilian C strain and a B virus. Figure 3b shows the overall mosaic structure of the new B/C/U 06FR-CRN strain.


New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study.

Frange P, Galimand J, Vidal N, Goujard C, Deveau C, Souala F, Peeters M, Meyer L, Rouzioux C, Chaix ML - Retrovirology (2008)

Analysis of the recombinant structure of 06FR-CRN strain. Bootscan plots (a) showing the complex mosaic structure of the 06FR-CRN strain (9684bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8116 unambigously aligned base pairs). (b) Bootscan plots with B and C references performed to better characterize the geographic origin of the 06FR-CRN strain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553414&req=5

Figure 4: Analysis of the recombinant structure of 06FR-CRN strain. Bootscan plots (a) showing the complex mosaic structure of the 06FR-CRN strain (9684bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8116 unambigously aligned base pairs). (b) Bootscan plots with B and C references performed to better characterize the geographic origin of the 06FR-CRN strain.
Mentions: The bootscan analysis of 06FR-CRN (Fig. 4a) showed that the majority of the genome is subtype C except two small regions in pol: the first one included part of the RT gene and clustered with subtype B; the second one (5'end of the integrase gene) clustered with the common branch for B and D subtypes (region 4). The 3'end of the nef gene and LTR were subtype B. Figure 4b shows a more detailed bootscan analysis of 06FR-CRN against 10 subtype C reference strains, isolated from different regions over the world and illustrates that 06FR-CRN "C" regions strongly clustered with 98BR-BR004, isolated in Brazil [25]. Despite iterative bootscan analysis including additional B and D reference strains or with BLAST analysis, the region 4 remained undetermined. The subtype identifications of the various genomic regions were all confirmed by phylogenetic tree analysis of the corresponding fragments (Figure 5). We included reference sequences of CRF31_BC strains in these trees to illustrate the differences between this previously described CRF and 06FR-CRN, which both resulted from the recombination between a Brazilian C strain and a B virus. Figure 3b shows the overall mosaic structure of the new B/C/U 06FR-CRN strain.

Bottom Line: Others PHI were further observed in 2006-2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France.Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.

View Article: PubMed Central - HTML - PubMed

Affiliation: EA 3620, Université Paris - Descartes, Laboratoire de Virologie, Hôpital Necker - Enfants Malades, AP-HP, Paris, France. pierre.frange@nck.aphp.fr

ABSTRACT

Background: Prevalence of HIV-1 non-B subtypes has increased overtime in patients diagnosed at the time of primary infection (PHI) in France. Our objective was to characterize in detail non-B strains which could not be genetically classified into the known subtypes/Circulating Recombinant Forms (CRFs).

Methods: Among 744 patients enrolled in the ANRS PRIMO Cohort since 1996, 176 (23.7%) were infected with HIV-1 non-B strains. The subtype/CRF could not be identified in RT for 15 (2%). The V3-V5 env region was sequenced and 3 strains (04FR-KZS, 06FR-CRN, 04FR-AUK) were full-length sequenced. Phylogenetic and bootscan analyses were used to characterize the mosaic structures.

Results: Among V3-V5 sequences, 6 were divergent A, 2 distantly related to E or D, 2 C, 1 B and 2 remained unclassified. 04FR-KZS, isolated in a Congolese woman infected in France, clustered with 2 previously described viruses from the Democratic Republic of Congo. They represent CRF27_cpx involving A/E/G/H/J/K/U subtypes. 06FR-CRN, isolated in a homosexual Caucasian patient, was a B/C/U recombinant involving a Brazilian C strain. 04FR-AUK, isolated in a Congolese patient infected in France, was a A/K/CRF09/U recombinant clustering from gag to vif with HIV-1 MAL. Others PHI were further observed in 2006-2007 with 1 KZS and 5 CRN-like viruses, suggesting their spread in France.

Conclusion: This study illustrates the increasing HIV-1 diversity in France associating new (06FR-CRN) and old (CRF27_cpx and "MAL-like" 04FR-AUK) strains, which are rare in their region of origin but may have a possible founder effect in France. Our results strengthen the French guidelines recommending viro-epidemiological surveillance of HIV-1 diversity.

Show MeSH
Related in: MedlinePlus