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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 04FR-AUK strain. Bootscan plots (a) showing the complex mosaic structure of the AUK strain (9680bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8051 unambigously aligned base pairs). The same analysis was then performed in the undetermined region 10 by adding CRF09_cpx reference sequences (in doted lines). Bootscan plots showing the mosaic structure of the previously reported MAL [23] (b) and NOGIL [24] (c) strains.
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Figure 6: Analysis of the recombinant structure of 04FR-AUK strain. Bootscan plots (a) showing the complex mosaic structure of the AUK strain (9680bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8051 unambigously aligned base pairs). The same analysis was then performed in the undetermined region 10 by adding CRF09_cpx reference sequences (in doted lines). Bootscan plots showing the mosaic structure of the previously reported MAL [23] (b) and NOGIL [24] (c) strains.

Mentions: Although subtype A and K predominate, the complexity of the new 04FR-AUK strain was readily apparent from the similarity plots (data not shown) and the bootscan analyses (Fig 6a). The LTR, gag, vif, vpr and nef genes and the majority of pol and env were subtype A (regions 1, 7, 9, 11). A short region, located at the 5'end of the RT, clustered with the common branch for F1 and F2 sub-subtypes in the phylogenetic analysis although not with a significant boostrap value (region 2). Therefore we classified this region as "undetermined" (U1), but it might represent an "F" variant. The pol gene included two regions (regions 3 and 5) which were clearly subtype K. A small region between them (region 4) was not well defined in the bootscan analysis and was therefore named "undetermined" (U2). However, 04FR-AUK clustered with subtype K in the phylogenetic tree analysis of this region, and may be considered as a divergent "K". In the 5' end of the integrase, a small region could not be clearly defined in the bootscan and phylogenetic tree analyses and was therefore classified as undetermined (region 6 = U3). The 3' end of the accessory gene region, including the entire vpu gene, was subtype K (region 8). On the boostrap and similarity plots, a 350 bp region at the 3'end of the env gene seemed difficult to classify (region 10 = U4). To better characterize the undetermined regions, we performed a BLAST search. The best match (94%) was found with an "undetermined" fragment of CRF09_cpx in region 10 only. We included in the bootscan analysis (figure 6a) of this region CRF09 strains and subsequent phylogenetic tree analysis, confirmed that this 04FR-AUK clustered significantly with the U fragment from CRF09. Figure 3c shows the overall mosaïc structure of the new 04FR-AUK strain. Finally, this complex A/K/CRF09/U virus strongly clustered with MAL and NOGIL viruses from gag to vif in the phylogenetic tree analyses. The MAL/NOGIL and MAL/04FR-AUK divergence breakpoints were located at the same place in the vif gene, while the NOGIL/04FR-AUK divergence breakpoints were located in the vpr gene, as shown in the bootscan analyses of MAL and NOGIL (Fig. 6b and 6c). In the 3'end of the nef gene and the LTR, NOGIL was subtype H but 04FR-AUK and MAL clustered together again in subtype A. Overall, it can be stated that the 5'end of the MAL/NOGIL/04FR-AUK strains have a common parental ancestor.


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 04FR-AUK strain. Bootscan plots (a) showing the complex mosaic structure of the AUK strain (9680bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8051 unambigously aligned base pairs). The same analysis was then performed in the undetermined region 10 by adding CRF09_cpx reference sequences (in doted lines). Bootscan plots showing the mosaic structure of the previously reported MAL [23] (b) and NOGIL [24] (c) strains.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Analysis of the recombinant structure of 04FR-AUK strain. Bootscan plots (a) showing the complex mosaic structure of the AUK strain (9680bp). The full-length sequence was aligned with HIV-1 subtype and subsubtype reference sequences (gaps were stripped from the 8051 unambigously aligned base pairs). The same analysis was then performed in the undetermined region 10 by adding CRF09_cpx reference sequences (in doted lines). Bootscan plots showing the mosaic structure of the previously reported MAL [23] (b) and NOGIL [24] (c) strains.
Mentions: Although subtype A and K predominate, the complexity of the new 04FR-AUK strain was readily apparent from the similarity plots (data not shown) and the bootscan analyses (Fig 6a). The LTR, gag, vif, vpr and nef genes and the majority of pol and env were subtype A (regions 1, 7, 9, 11). A short region, located at the 5'end of the RT, clustered with the common branch for F1 and F2 sub-subtypes in the phylogenetic analysis although not with a significant boostrap value (region 2). Therefore we classified this region as "undetermined" (U1), but it might represent an "F" variant. The pol gene included two regions (regions 3 and 5) which were clearly subtype K. A small region between them (region 4) was not well defined in the bootscan analysis and was therefore named "undetermined" (U2). However, 04FR-AUK clustered with subtype K in the phylogenetic tree analysis of this region, and may be considered as a divergent "K". In the 5' end of the integrase, a small region could not be clearly defined in the bootscan and phylogenetic tree analyses and was therefore classified as undetermined (region 6 = U3). The 3' end of the accessory gene region, including the entire vpu gene, was subtype K (region 8). On the boostrap and similarity plots, a 350 bp region at the 3'end of the env gene seemed difficult to classify (region 10 = U4). To better characterize the undetermined regions, we performed a BLAST search. The best match (94%) was found with an "undetermined" fragment of CRF09_cpx in region 10 only. We included in the bootscan analysis (figure 6a) of this region CRF09 strains and subsequent phylogenetic tree analysis, confirmed that this 04FR-AUK clustered significantly with the U fragment from CRF09. Figure 3c shows the overall mosaïc structure of the new 04FR-AUK strain. Finally, this complex A/K/CRF09/U virus strongly clustered with MAL and NOGIL viruses from gag to vif in the phylogenetic tree analyses. The MAL/NOGIL and MAL/04FR-AUK divergence breakpoints were located at the same place in the vif gene, while the NOGIL/04FR-AUK divergence breakpoints were located in the vpr gene, as shown in the bootscan analyses of MAL and NOGIL (Fig. 6b and 6c). In the 3'end of the nef gene and the LTR, NOGIL was subtype H but 04FR-AUK and MAL clustered together again in subtype A. Overall, it can be stated that the 5'end of the MAL/NOGIL/04FR-AUK strains have a common parental ancestor.

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