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Here we studied the patterns of generation of neutralizing antibodies (NAbs) and virus escape during non-B subtype HIV-1 chronic infection among asymptomatic patients, and established whether a correlation exists between the generation of NAbs and the kinetics of CD4 T-cell decline. Therefore, sequential viruses and plasma obtained at 6 months to one year intervals over a three years period from ten HIV-1 group M subtype A, CRF02_AG, G, and H infected treatment-naive individuals were tested in neutralization assays. Overall, NAbs were present in all ten individuals, and had the capacity to neutralize autologous virus obtained six months earlier. Eight of the ten subjects showed an increasing capacity to neutralize early viruses and a low capacity to neutralize contemporaneous and later time-point viruses. The neutralizing activities within these individuals resulted in emergence of neutralization resistant viruses, and with the subsequent generation of more NAbs to the emerging resistant viruses. In the remaining two individuals, the capacity to neutralize early, contemporaneous, and later time-point viruses remained conserved. While the kinetics of CD4 T-cell decline varied among all ten individuals, there was no correlation with the capacity to generate NAbs in that, sequential plasmas from individuals with moderately or rapidly declining CD4 T-cells were capable of neutralizing early sequential viruses. We conclude from this study that in non-B subtype chronically infected asymptomatic patients with moderately and rapidly declining CD4 T-cells, potent NAbs are readily generated as the virus evolves to escape the effect of these antibodies.

Objective: To document infection with HIV type 1 (HIV-1) group M non-B subtypes in individuals living in New York City. Design: From October 1999 through April 2003, HIV-1-seropositive individuals were selected from 3 clinics in New York City based on having risk factors for infection with HIV-1 non-B subtypes. Methods: HIV-1 RNA was extracted from plasma samples, and partial gag, pol, or env genes were amplified by PCR analysis. The infecting HIV- 1 group M subtype was determined based on results of either heteroduplex mobility assay or sequencing and phylogenetic analysis. Results: Ninety-seven subjects were enrolled in the study. Of the 97 subjects, 91 (94%) were selected based on having emigrated from a non-European country, while 6 (6%) were native United States citizens. Subtypes were successfully determined in 53 (55%) of the 97 plasma samples tested. The subtypes in 2 plasma samples were unclassifiable. HIV-1 infections were classified as those due to the following group M subtypes: A (n = 4; 7%), B (n = 12; 22%), C (n = 8; 15%), F (n = 2; 4%), CRF01―AE-like (n = 7; 13%), CRF02―AG-like (n = 19; 34%), an intersubtype recombinant form G gag /A env (n = 1; 2%), and unclassifiable viruses (n = 2; 4%). Conclusion: This study reveals infection with a broad variety of HIV-1 group M subtypes mostly in the immigrant population of New York City as well as how several non-B subtypes are being introduced into the United States.

Objective: To investigate the genetic diversity of the HIV-1 circulating in Shanghai and to analyze the mutations in the protease (PR) gene associated with resistance to protease inhibitors (PIs). Design: The genetic diversity of HIV-1 and PI resistance–associated mutations was studied in 40 Shanghai HIV-1-seropositive treatment-naive residents. The patients studied were exposed to the infection mainly through contaminated blood products (hemophiliacs) (n = 17) and sexual contacts (n = 19). Samples from 2 injecting drug users (IDUs) and 2 children born to HIV-1 infected mothers were also analyzed. Methods: HIV-1 partial gag pol and env genes in infected plasma samples were amplified by reverse transcriptase polymerase chain reaction sequenced and phylogenetically analyzed. Analysis of PI resistance –associated amino acid substitution in PR was performed. Results: HIV-1 genes in 38 of the 40 plasma samples were successfully amplified and analyzed. Polymerase chain reaction amplification was successful for 16/17 hemophilia patients and 18/19 sexually infected individuals. While all the 16 hemophilia patients infected through contaminated blood products were infected with subtype B’ the 18 patients infected through sexual contact were infected with several subtypes including subtype A (n = 2) B (n = 4) B’ (n = 1) C (n = 2) CRF08_BC (n = 1) CRF01_AE (n = 7) and intersubtype recombinant CRF01_AE/B (n = 1). The 2 IDUs were infected with CRF08_BC and the 2 children born to HIV-1 infected mothers were infected with subtype B’ and CRF01_AE. PI resistance–associated amino acid substitutions were found at 1 codon in primary and 7 codons in secondary regions of the PR gene. Amino acid substitutions were more frequently found in the B/B’ sequences (69%) than in the non-B sequences (31%). Substitutions characteristic with the subtype B/B’ sequences mainly among hemophiliacs included L63P (87%) A71V/T (27%) and V77I (93%) while those that characterized the non-B sequences mainly found among heterosexuals included M36I (69%) and K20R (19%). Conclusion: This study reveals the presence of multiple HIV-1 subtypes and recombinants infecting Shanghai residents. The broad HIV-1 diversity is being introduced into this city through heterosexual contacts. This study also reveals that viruses infecting these treatment- naive patients have acquired both primary or secondary mutations in their PR genes. These studies should provide the basis for further epidemiologic surveys of HIV-1 subtypes and set strategies for treatment intervention and vaccine programs. (authors)

An array of CRFs have been identified in Cameroon, the most notable being CRF02_AG. HIV-1 in the East Province of Cameroon is particularly diverse: in a recent study, we found a high proportion of unique recombinant forms (URFs). Herein we describe the analysis of the full-length sequences of two of these URFs, which, after preliminary analysis of gag, pol, and env fragments, appeared to be a novel CRF. This novel strain, CRF36_cpx, contains fragments that can be assigned to the CRF01_AE, CRF02_AG, and subtype A and G radiations. Forty percent of the genome can be classified as CRF02_AG, including regions in gag, pol, env, and the accessory genes. Twenty-seven percent is CRF01_AE, comprising the majority of gag, the beginning of env, and the end of env into the 3' LTR. Twenty percent of the genome can be assigned to subtype A, with segments in pol and env. The remaining 13% of the sequence is classifiable as subtype G, in pol and vpu. The subtype A and G lineages formed by the CRF36_cpx sequences are unique and appear ancestral in nature. CRF36_cpx is both the first to combine more than one CRF and the first to include fragments of CRF02_AG. The ancestral sequences present in CRF36_cpx represent a link to extinct strains, and, potentially, insight into the evolution of HIV-1.

HIV-1 in Cameroon is genetically diverse, but is predominated by the circulating recombinant form (CRF) 02_AG, which cocirculates among an array of other CRFs, unique recombinant forms (URFs), and all group M subtypes. In particular, our studies of HIV-1 diversity in the East Province found a high proportion of URFs and second generation recombinants (SGRs), suggesting this region of Cameroon may be a breading ground for new CRFs. Herein we present the full-length sequence analysis of one such CRF, composed primarily (66%) of unique, distant lineages of subtypes A and G in alternating regions throughout the genome. This CRF also combines segments in pol and env genes possessing intrasubtype distance (

HIV-1 circulating recombinant form (CRF) 02_AG is responsible for greater than 65% of HIV-1 infections in Cameroon and is widespread across West and West-Central Africa. The parental subtypes A1 and G cocirculate in this part of Africa, and high rates of infection predispose to the generation of AG unique recombinant forms (URFs). Little is known as to whether A1 and G can recombine and thrive in vivo with breakpoints other than those characteristic of CRF02_AG. In this study, six unique recombinant viruses of subtypes A1 and G were identified in two individuals in Cameroon. A 1.5 kb fragment of the reverse transcriptase (RT) region of pol (HXB2 location 2,612–4,159) and the entire env gene (HXB2 location 6,202–9,096) were evaluated by phylogenetic and breakpoint analyses. Each URF was found to have breakpoints different than CRF02_AG, indicating that A and G gene segments are functionally compatible with more than one pattern of recombination. Furthermore, contemporaneous, cultured viruses from these individuals were analyzed, revealing different proportions of URFs compared to those found in plasma, possibly indicating compart mentalization and/or phenotypic variation among the URFs. CRF02_AG emerged from West-Central Africa to become a highly successful viral strain. As such, monitoring the spread of newly emerging AG recombinants is critical not only for understanding the epidemiology of HIV-1, but also in the design of future therapeutics and vaccines appropriate to this part of Africa, and globally. J. Med. Virol. 79:1270–1285, 2007. © Wiley-Liss, Inc.

The majority of global human immunodeficiency virus infections are caused by viruses characterized by a GPGQ motif at the tip of the V3 loop. Characterization of anti-V3 monoclonal antibodies (MAbs) that neutralize isolates with the GPGQ V3 motif is an important step in designing vaccines that will induce such Abs. Consequently, seven human anti-V3 MAbs derived from the cells of individuals infected with non-B-subtype viruses (anti-V3non-BMAbs) were generated from the cells of individuals from Africa infected with circulating recombinant forms CRF02_AG, CRF09_cpx, and CRF13_cpx, each of which contains a subtype Aenvgene. Sequence analysis of plasma viruses revealed a GPGQ motif at the apex of the V3 loop from six of the seven subjects and a GPGR motif from one subject. The MAbs were selected with fusion proteins (FP) containing V392UG037.8or V3JR-CSFfrom subtype A or B, respectively. In virus binding assays, five of the seven (71%) anti-V3non-BMAbs bound to V3-FPs from both subtype A and subtype B, while only four of the nine (44%) anti-V3BMAbs recognized both V3-FPs. Using two neutralization assays, both the anti-V3non-Band the anti-V3BMAbs neutralized subtype B viruses with similar activities, while the anti-V3non-BMAbs exhibited a tendency toward both increased potency and breadth of neutralization against non-B viruses compared to anti-V3BMAbs. Statistical significance was not achieved, due in large measure to the sizes of the MAb panels, but the overall pattern of data strongly suggests that viruses with the GPGQ motif at the tip of the V3 loop induce anti-V3 Abs with broader cross-neutralizing activity than do viruses with the GPGR motif.

Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 02_AG is the predominant subtype in Cameroon, even more prevalent than the parental subtypes A and G. An important question that needs to be addressed is whether recombination in HIV-1 infection can lead to the emergence of viruses with biological advantages. The replicative capacity was investigated in peripheral blood mononuclear cells (PBMCs) of 13 R5-tropic primary HIV-1 isolates, including 5 CRF02_AG, 4 subtype A, and 4 subtype G viruses. HIV-1 subtype identity was defined by phylogeny either of the full-length genome or analysis of a combination of segments of the gag, pro, pol, and env genes followed by recombination breakpoint analysis. All viruses were grown on PBMCs for 11 days and culture supernatant was analyzed for reverse transcriptase (RT) activity and p24 production. On day 11 post-infection, CRF02_AG strains had a 1.4-1.9 times higher RT activity and reached a significantly higher level of p24 production than the parental subtypes A and G. Furthermore, the replication rate as measured by p24 production was 1.4 times higher for CRF02_AG strains compared to the subtypes A and G. This study suggests that the recombination event that led to CRF02_AG resulted in a variant with a better replicative capacity than its progenitors. This adaptation could contribute to the broader spread of HIV-1 CRF02_AG leading to its predominance in West Central Africa compared to the lower prevalence of its parental subtypes A and G.

This study describes the HIV-1 genetic diversity that currently circulates in Bamenda, the provincial capital of the North West province of Cameroon. Phylogenetic analysis of the protease (pro) gene of 20 HIV-1-seropositive individuals identified 11 (55%) CRF02_AG, one D, one F2, one J, and four (20%) unclassifiable strains. Interestingly, the remaining two (10%) samples, 02CMNYU3072 and 03CMNYU3224, originating from epidemiologically unlinked individuals, were classified as CRF09_cpx, representing the first reported cases of this complex circulating recombinant form (CRF) in Cameroon. Additional analysis of the C2V5 portion of the envelope (env) gene confirmed the CRF09_cpx identity of these isolates and classified the remaining isolates as CRF02_AG (n = 12, 63%), subtype D (n = 2, 11%), subtype F2 (n = 2, 11%), and subtype A1 (n = 1). In combination, the pro and env subtyping results revealed three (16%) isolates with discordant subtypes including J( pro )CRF02_AG( env ), CRF02_AG( pro )D( env ), and CRF02_AG( pro )F2( env ). In conclusion, this study highlights the presence of HIV-1 CRF09_cpx in Cameroon and identifies three possible intersubtype recombinants (ISRs) containing CRF02_AG in a town where CRF02_AG infections predominate, and stresses the commonness of HIV-1 recombinant strains in a region where broad genetic diversity exists.

We describe the resistance-associated substitutions that are present in the reverse transcriptase (RT) genes of HIV-1 CRF02_AG strains infecting drug-naive villagers of Cameroon. The 11 sequences analyzed were previously subtyped as CRF02_AG in the gag, pro, and env genes, and this work revealed that most (10/11) had a concordant subtype (CRF02_AG) in the pol gene, while one sequence had discordant subtype (A1) in the pol gene. Classification of the CRF02_AG sequences was further confirmed by recombination breakpoint analysis, which revealed a mosaic composition similar to the reference strain IbNG. Analysis of the RT genes for resistance-associated substitutions revealed two sequences containing a V118I substitution. Even though no other resistance-associated substitutions were found, the presence of V118I, which is implicated in resistance to reverse transcriptase inhibitors, in CRF02_AG strains infecting drug-naive individuals should be considered when introducing these antiretrovirals in areas where CRF02_AG is the predominant subtype, such as Cameroon.

To describe the presence of protease inhibitor (PI) resistance-associated mutations and subtype distribution in drug-naive villagers of six provinces of Cameroon, we sequenced the protease (PR) gene (297 bp) of 128 viruses. Secondary PI resistance-associated mutations were identified at five sites: L10I/V (16%), K20R (8%), M36I (98%), L63P (13%), and V77I (6%). No primary mutation in the PR was identified. Of the 128 specimens analyzed, subtypes A (11%), C(2%), D (6%), F2 (3%), G (6%), H (0.8%), J (6%), and CRF02_AG (60%) were identified. The mutations identified were not characteristic to any particular subtype. The absence of primary mutations, in addition to the few secondary mutations, gives good perspectives for PI treatment interventions in these rural areas.