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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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Mentions: To determine to what extend previously reported strains were related to MAL, NOGIL or 04FR-AUK strains, blast searches were done by cutting the full-length sequence into several fragments (about 1200–1300 bp), because an initial blast analysis with the complete genome sequence did not provide any significant information. We identified four strains from DRC (97CD-MBFE185, 97CD-MBS30, 02CD-KP061 and 02CD-KP097), one from Cameroon (97CM-MP814) and one from Senegal (98SN-40HALD) [26,27] for which partial pol sequences (1500 bp, protease and RT) clustered with 91% bootstrap values with 04FR-AUK/MAL/NOGIL and which displayed the same recombinant structure in that part of the genome as shown by additional bootscan and simplot analysis. Some of these strains had also been sequenced in other genomic regions such as the V3-V5 env or p24 gag region. Similarly as for 04FR-AUK, the following strains 97CD-MBFE185, 97CD-MBS30, 02CD-KP061 and 02CD-KP097 were also subtype A in the V3-V5 region, and 97CD-MBFE185, 97CD-MBS30 and 97CM-MP814 were also subtype A in gag p24. Moreover, other sequences from Gabon (97GA-G15, 97GA-ME56, 97GA-PP98, 97GA-TB64, 00GA-GAB22S, 97GA-G32, 97GA-TB45) [28], Congo (CgARV64 and CgARV64) [29] and Senegal (97SN-1055) [30] formed a subcluster with MAL/NOGIL/04FR-AUK supported by 78% bootstrap within subtype A. (See figures 7 and 8


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)

Part 2
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Part 2
Mentions: To determine to what extend previously reported strains were related to MAL, NOGIL or 04FR-AUK strains, blast searches were done by cutting the full-length sequence into several fragments (about 1200–1300 bp), because an initial blast analysis with the complete genome sequence did not provide any significant information. We identified four strains from DRC (97CD-MBFE185, 97CD-MBS30, 02CD-KP061 and 02CD-KP097), one from Cameroon (97CM-MP814) and one from Senegal (98SN-40HALD) [26,27] for which partial pol sequences (1500 bp, protease and RT) clustered with 91% bootstrap values with 04FR-AUK/MAL/NOGIL and which displayed the same recombinant structure in that part of the genome as shown by additional bootscan and simplot analysis. Some of these strains had also been sequenced in other genomic regions such as the V3-V5 env or p24 gag region. Similarly as for 04FR-AUK, the following strains 97CD-MBFE185, 97CD-MBS30, 02CD-KP061 and 02CD-KP097 were also subtype A in the V3-V5 region, and 97CD-MBFE185, 97CD-MBS30 and 97CM-MP814 were also subtype A in gag p24. Moreover, other sequences from Gabon (97GA-G15, 97GA-ME56, 97GA-PP98, 97GA-TB64, 00GA-GAB22S, 97GA-G32, 97GA-TB45) [28], Congo (CgARV64 and CgARV64) [29] and Senegal (97SN-1055) [30] formed a subcluster with MAL/NOGIL/04FR-AUK supported by 78% bootstrap within subtype A. (See figures 7 and 8

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