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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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Phylogenetic tree analysis of the 3 full-length sequenced strains (04FR-KZS, 06FR-CRN, 04FR-AUK).The sequences were aligned with HIV-1 subtype and subsubtype references, as well as CRF01_AE, MAL, NOGIL, 97CD-KTB49 and 02CD-LBR024 [19] sequences.
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Figure 2: Phylogenetic tree analysis of the 3 full-length sequenced strains (04FR-KZS, 06FR-CRN, 04FR-AUK).The sequences were aligned with HIV-1 subtype and subsubtype references, as well as CRF01_AE, MAL, NOGIL, 97CD-KTB49 and 02CD-LBR024 [19] sequences.

Mentions: To study more in detail these divergent HIV-1 strains, we characterized the full-length genome for 04FR-KZS, 06FR-CRN and 04FR-AUK strains. They were chosen for different reasons: 04FR-KZS strongly clustered with a previously described complex recombinant virus (97CD-KTB49 [18]); 06FR-CRN was undetermined in RT phylogenetic analysis but strongly clustered in the subtype C in V3-V5 analysis; 04FR-AUK displayed extensive similarity in the RT region with one of the earliest African HIV-1 strains, MAL, previously described as an A/D/K/U recombinant virus [23]. Moreover these 3 strains circulated in France between 2004 and 2006. The patients infected with these strains were diagnosed soon after infection with an acute retroviral syndrome (estimated delay from infection: 20, 24 and 22 days, respectively). Two of them (04FR-KZS and 06FR-CRN) presented with a very low CD4 cell count and a high viral load; the third one (04FR-AUK) had a moderate CD4 cell count decrease associated with a spontaneously low viral load (Table 1). The 3 new full-length sequences were compared with representatives of all subtypes, sub-subtypes, CRFs available in the HIV database and with other unpublished and published URFs. The phylogenetic tree analysis (Figure 2) showed that 06FR-CRN formed a well supported cluster with subtype C. The 04FR-AUK strain did not cluster with any known sequence but seemed to be related to the previous reported complex recombinant strains from central African origin: MAL [23] and NOGIL (A/K/H/U) [24] which have a common A/K/U structure in gag-pol.


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)

Phylogenetic tree analysis of the 3 full-length sequenced strains (04FR-KZS, 06FR-CRN, 04FR-AUK).The sequences were aligned with HIV-1 subtype and subsubtype references, as well as CRF01_AE, MAL, NOGIL, 97CD-KTB49 and 02CD-LBR024 [19] sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Phylogenetic tree analysis of the 3 full-length sequenced strains (04FR-KZS, 06FR-CRN, 04FR-AUK).The sequences were aligned with HIV-1 subtype and subsubtype references, as well as CRF01_AE, MAL, NOGIL, 97CD-KTB49 and 02CD-LBR024 [19] sequences.
Mentions: To study more in detail these divergent HIV-1 strains, we characterized the full-length genome for 04FR-KZS, 06FR-CRN and 04FR-AUK strains. They were chosen for different reasons: 04FR-KZS strongly clustered with a previously described complex recombinant virus (97CD-KTB49 [18]); 06FR-CRN was undetermined in RT phylogenetic analysis but strongly clustered in the subtype C in V3-V5 analysis; 04FR-AUK displayed extensive similarity in the RT region with one of the earliest African HIV-1 strains, MAL, previously described as an A/D/K/U recombinant virus [23]. Moreover these 3 strains circulated in France between 2004 and 2006. The patients infected with these strains were diagnosed soon after infection with an acute retroviral syndrome (estimated delay from infection: 20, 24 and 22 days, respectively). Two of them (04FR-KZS and 06FR-CRN) presented with a very low CD4 cell count and a high viral load; the third one (04FR-AUK) had a moderate CD4 cell count decrease associated with a spontaneously low viral load (Table 1). The 3 new full-length sequences were compared with representatives of all subtypes, sub-subtypes, CRFs available in the HIV database and with other unpublished and published URFs. The phylogenetic tree analysis (Figure 2) showed that 06FR-CRN formed a well supported cluster with subtype C. The 04FR-AUK strain did not cluster with any known sequence but seemed to be related to the previous reported complex recombinant strains from central African origin: MAL [23] and NOGIL (A/K/H/U) [24] which have a common A/K/U structure in gag-pol.

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