Fabienne De Oliveira

A new human immunodeficiency virus derived from gorillas.

We have identified a new human immunodeficiency virus in a Cameroonian woman. It is closely related to gorilla simian immunodeficiency virus (SIVgor) and shows no evidence of recombination with other HIV-1 lineages. This new virus seems to be the prototype of a new HIV-1 lineage that is distinct from HIV-1 groups M, N and O. We propose to designate it HIV-1 group P.

HIV-1 group N: travelling beyond Cameroon.

On Jan 21, 2011, a 57-year-old man living in France attended our emergency unit with fever, rash, lymphadenopathy, and genital ulceration, 8 days after returning from Togo. He reported sexual contact with a Togolese partner, and HIV primary infection was suspected. Fourth-generation ELISA (ARCHITECT HIV Ag/Ab Combo, Abbott, Chicago, IL) was weakly positive, and HIV-1 western blot (New Lav Blot I, Biorad, Paris, France) showed weak reactivity with the p55 and p24 antigens. On Feb 1, 2011, his HIV-1 RNA load was 4∙2 log10 copies per mL (Cobas TaqMan HIV-1 v2.0 assay, Roche Molecular Systems, Branchburg, NJ, USA). On Feb 9, 2011, he developed facial paralysis. At this time his CD4 cell count was 219 per μL and his plasma and CSF HIV-1 RNA concentrations were 4∙4 log10 and 4∙5 log10 copies per mL, respectively. In keeping with French guidelines on new cases of HIV infection, we undertook resistance genotyping before starting treatment. We were surprised that we could not amplify the reverse transcriptase and protease genes with the ViroSeq HIV-1 genotyping assay (Abbott, Chicago, IL, USA) and the French National Agency for AIDS Research consensus primers, despite the high viral load. This fi nding prompted us to serotype the samples. Clear reactivity against group-N-specifi c antigens was obtained and we therefore did full-length genome sequencing. Phylogenetic analysis confi rmed that the new sequence clustered strictly within available group-N sequences (sequence designated N1.FR.2011, GenBank accession number JN572926). When last seen for followup after 4 weeks of antiretroviral combination therapy with tenofovir, emtricitabine, darunavir/ritonavir, raltegravir, and maraviroc, our patient’s plasma HIV-1 RNA load was below 20 copies per mL and his CD4 cell count was 483 per μL. HIV-1 group N (non-M, non-O) was fi rst identifi ed in 1998 in a Cameroonian woman with AIDS. This highly divergent HIV variant is more closely related to SIV isolated from wild chimpanzees than to HIV-1 groups M (major), O (outlier), and P. Group-N infection has previously been reported only in HIV-infected patients living in Cameroon. More than 12 000 HIVinfected patients living in Cameroon have been tested for group-N infection, but only 12 cases, including two couples infected by the same strains, have been identifi ed. Although our patient was diagnosed in Paris, the infection was probably acquired in Togo, which suggests that group-N viruses are now circulating outside Cameroon. This case of primary HIV-N infection is particularly important because of the severe clinical manifestations and early decline in the CD4 cell count. A fi ve-drug antiretroviral com bination showed good initial effi cacy, but longer-term immunological and virological follow-up is needed. The viral load of this HIV-N infected patient was positive during the primary infection as assessed by the Cobas TaqMan HIV-1 v2.0 assay, but the validity of the quantitative result is uncertain. The viral load was also assessed using the Abbott RealTime HIV-1 assay (Chicago, IL, USA), but was under-quantifi ed by about 1 log10. Whether other commercial assays can quantify these variants remains to be shown. Standard resistance genotyping methods used for group M failed to amplify the group-N virus, as happened with the fi rst case of group-P virus detected in 2009. Discrepancies between the results of HIV viral load assays and molecular tests should alert clinicians and virologists to the possibility of infection by a variant virus, which has important implications for management of the patient. This case of HIV-1 group-N primary infection indicates that this rare group is now circulating outside Cameroon, which emphasises the need for rigorous HIV epidemiological monitoring.

A New Real-Time Quantitative PCR for Diagnosis and Monitoring of HIV-1 Group O Infection

ABSTRACT The correct diagnosis and monitoring of HIV-1 group O (HIV-O) infection are essential for appropriate patient management, for the prevention of mother-to-child transmission, and for the detection of dual HIV-M/HIV-O infections. HIV-O RNA quantification is currently possible with two commercial kits (from Abbott and Roche), which quantify HIV-M and HIV-O strains indifferently; therefore, they cannot be used for the specific identification of HIV-O infection. We designed a new real-time quantitative reverse transcription PCR (RT-qPCR assay) (INT-O), which we compared with our previous version, LTR-O, and with the Abbott RealTime HIV-1 kit. Specificity was assessed with 27 HIV-1 group M strains and the prototype strain of group P. Clinical performances were analyzed by using 198 stored plasma samples, representative of HIV-O genetic diversity. Analytical sensitivity, repeatability, and reproducibility were also determined. The detection limit of the INT-O assay was 40 copies/ml, and its specificity was 100%. The repeatability and reproducibility were excellent. Analysis of clinical samples showed a good correlation between the INT-O and LTR-O assays (r = 0.8240), with an improvement of analytical sensitivity. A good correlation was also obtained between the INT-O and Abbott assays (r = 0.8599) but with significantly higher values (0.19 logs) for the INT-O method, due to marked underquantifications for some patients. These results showed that HIV-O genetic diversity still has an impact on RNA quantification. The new assay, INT-O, allows both the specific diagnosis of HIV-O infection and the quantification of diverse HIV-O strains. Its detection limit is equivalent to that of commercial kits. This assay is cheap and suitable for use in areas in which strains of HIV-1 groups M and O cocirculate.

Field evaluation of the Abbott ARCHITECT HIV Ag/Ab Combo immunoassay

BACKGROUND Fourth generation assays for HIV diagnosis are progressively being introduced into routine services, due to their improvement of diagnosis. In spite of this, HIV diagnosis remains a challenge in sub-Saharan Africa, due to false positive reactivity. There is a continuous need for field evaluations and routine validations of fourth generation HIV tests in African populations. OBJECTIVES Evaluate the performances of the ARCHITECT HIV Ag/Ab kit (Abbott) in a population living in an African setting-Cameroon compared to a population living in a European setting-France. STUDY DESIGN 645 HIV samples from both France and Cameroon were evaluated. The positive panel (378 samples) included a diverse series of HIV-1 variants (groups M, N, O, and P) as well as HIV-2 samples. Results were compared to original diagnosis done with other 4th generation assays (AxSYM HIV Ag/Ab (Abbott) and Vidas HIV DUO QUICK) (bioMérieux). RESULTS Sensitivity of the ARCHITECT was 100% in both sites. It diagnosed all variants of the panel with different reactivity profiles following strain diversity. A wider range of reactivity was observed for group O. Specificity was slightly lower (97.6%) in Cameroon than in France (98.6%), probably due to a higher rate of false positive reactivity. ARCHITECT HIV Ag/Ab assay had high performances in clinical sensitivity and specificity and is adapted to the wide genetic diversity of viruses circulating in West Central Africa. CONCLUSION Our results further highlight the need to evaluate HIV diagnostic tests before introduction into routine diagnostic services both in the North and in the South.

Rapid Discrimination between Human Immunodeficiency Virus Type 2 Groups A and B by Real-Time PCR

ABSTRACT We studied the feasibility of genotyping human immunodeficiency virus (HIV) type 2 groups A and B by real-time PCR. Two group-specific PCRs were developed. Real-time genotyping of 22 samples of genotype A, 10 samples of genotype B, and the isolate of new group H were compared to genotyping by sequencing and phylogeny. The group-specific PCRs specifically identified 84.3% of group A or B samples; isolate H was not detected. This method allowed rapid and specific discrimination between HIV-2 groups A and B and could be a useful tool for molecular epidemiological studies.

The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon

Unlike the pandemic form of HIV-1 (group M), group O viruses are endemic in west central Africa, especially in Cameroon. However, little is known about group O’s genetic evolution, and why this highly divergent lineage has not become pandemic. Using a unique and large set of group O sequences from samples collected from 1987 to 2012, we find that this lineage has evolved in successive slow and fast phases of diversification, with a most recent common ancestor estimated to have existed around 1930 (1914–1944). The most rapid periods of diversification occurred in the 1950s and in the 1980s, and could be linked to favourable epidemiological contexts in Cameroon. Group O genetic diversity reflects this two-phase evolution, with two distinct populations potentially having different viral properties. The currently predominant viral population emerged in the 1980s, from an ancient population which had first developed in the 1950s, and is characterized by higher growth and evolutionary rates, and the natural presence of the Y181C resistance mutation, thought to confer a phenotypic advantage. Our findings show that although this evolutionary pattern is specific to HIV-1 group O, it paralleled the early spread of HIV-1 group M in the Democratic Republic of Congo. Both viral lineages are likely to have benefited from similar epidemiological contexts. The relative role of virological and social factors in the distinct epidemic histories of HIV-1 group O and M needs to be reassessed.

Performance of the Liaison XL Murex HIV Ab/Ag Test on Clinical Samples Representing Current Epidemic HIV Variants

ABSTRACT Screening for HIV infection has improved since the first immunoassays. Today, diagnosis of HIV infection can be performed with fourth-generation tests that track both the patients antibodies and HIV antigen. The objective of this study was to evaluate the clinical sensitivity and specificity of the new DiaSorin Liaison XL Murex HIV Ab/Ag assay compared to another fourth-generation assay, the Abbott Architect HIV Ag/Ab Combo kit. This work was performed on a large panel of 900 samples, including negative samples (n = 493) and HIV-positive (n = 407) representatives of HIV-1 group M subtypes and circulating recombinant forms (CRFs), HIV-1 group O, and HIV-2 variants. The results highlight the high specificity (98.9%) and sensitivity (100%) of this new fourth-generation assay, which are consistent with its use for the screening and diagnosis of HIV infections with the current circulating strains.

A Multiplex PCR Approach for Detecting Dual Infections and Recombinants Involving Major HIV Variants

ABSTRACT The cocirculation of different HIV types and groups can lead to dual infections and recombinants, which hinder diagnosis and therapeutic management. We designed two multiplex PCRs (mPCRs) coupled with capillary electrophoresis to facilitate the detection of such infections. The first, MMO2, targets three variants (HIV-1/M, HIV-1/O, and HIV-2), and the second, MMO, targets HIV-1/M and HIV-1/O. These mPCRs were validated on DNA and RNA extracts from 19 HIV-1/M, 12 HIV-1/O, and 13 HIV-2 cultures and from mixtures simulating dual infections. They were then assessed with DNA and RNA extracts from samples of 47 clinical monoinfections and HIV-1/M+O dual infections or infections with HIV-1/MO recombinants. Both mPCRs had excellent specificity. Sensitivities ranged from 80 to 100% for in vitro samples and from 58 to 100% for clinical samples, with the results obtained depending on the material used and the region of the genome concerned. Sensitivity was generally lower for DNA than for RNA and for amplifications of the integrase and matrix regions. In terms of global detection (at least one target gene for each strain), both mPCRs yielded a detection rate of 100% for in vitro samples. MMO2 detected 100% of the clinical strains from DNA and 97% from RNA, whereas MMO detected 100% of the strains from both materials. Thus, for in vitro and clinical samples, MMO2 was a useful tool for detecting dual infections with HIV-1 and HIV-2 (referred to as HIV-1+HIV-2) and HIV-1/M+O, and MMO was useful for detecting both MO dual infections and MO mosaic patterns.

Misidentification of recombinant hepatitis C virus leading to treatment failure with direct acting antivirals

The use of new Direct Acting Antivirals, specific of HCV, has greatly improved the HCV treatment. Most of the DAA are specific of HCV genotypes. Genotyping methods may target different regions of the HCV genome, though only the whole genome sequencing could confirm the correct genotype. The present study describes the virological investigation of a treatment failure due to the false identification of an unusual 2k/1b recombinant HCV form. It describes the sequencing methods, and the similarity analysis of the sequences to different genotype query sequences, to identify the recombination breakpoint.

Simian Immunodeficiency Virus seroreactivity in inhabitants from rural Cameroon frequently in contact with non-human primates

Central African tropical forests are home to several species of non-human primates (NHPs), infected by Simian Immunodeficiency Virus (SIV). It is well-known that HIV-1 epidemic is due to cross-transmission and adaptation of SIV to humans. The main goal of this work was to investigate if a NHP bite is a risk factor for SIV acquisition. A cross-sectional study was performed in rural Cameroon on 246 bitten individuals (mostly by adult NHPs), matched, according to sex, age, and ethnicity (Bantus and Pygmies), with an equal number of not-bitten subjects. Following a serological assay for a wide range of SIVs, we observed a high level of indeterminate seroreactivity (25.8%) in the total population, whereas 68.9% were sero-negative and 5.3% HIV-1 positive. Bites do not appear to be a risk factor for SIV seroreactivity, in contrast to Simian Foamy Virus and Simian T-Lymphotropic Virus type 1 in the same studied population.