The impact of immigration on env HIV-1 subtype distribution among heterosexuals in the Netherlands: influx of subtype B and non-B strains

Travelling with HIV in the XXI century: Case report and narrative review

The number of migrants and travellers has grown in recent decades. This phenomenon is also true of people living with HIV, given their much-improved life expectancy and quality of life. A significant number of travellers with HIV are migrants returning to their home countries to visit friends and relatives (VFRs). This population constitutes a high-risk group because they travel for longer and often to rural and remote areas and have closer contact with the local population. In this review we discuss the sociodemographic characteristics of travellers with HIV, the differences between conventional travellers and VFRs, and the risks of HIV acquisition and transmission during travel. We also present the most relevant travel-associated illnesses and highlight the particularities of pre-travel advice given to this population, including immunosuppression, responses to vaccines, high incidence of comorbidities, drug interactions, legal and language barriers. The need to integrate these factors based on far less evidence than that available for the general population makes pre-travel advice for travellers with HIV genuinely challenging.

HIV-1 Genetic Diversity and Drug Resistance Mutations Among Treatment-Naive Adult Patients in Suriname

The molecular epidemiologic profile of HIV-1 in Suriname was determined through protease (PR) and reverse transcriptase (RT) sequences obtained from HIV-1 strains collected from 100 drug-naive HIV-1-infected persons. Subtype determination revealed that most viruses were of subtype B (94.9%) in both PR and RT genomic regions, followed by B/D recombinants (5.1%). Analysis of drug resistance mutations showed only one transmitted dug resistance mutation (TDRM) (V75M) in a single strain. The genetic data obtained can serve as a baseline for Suriname to monitor emerging mutations. This study reveals that the HIV-1 epidemic in Suriname is still characterized by a low TDRM rate (1%) and a low level of subtype diversity. However, both genes display a high genetic polymorphism. This high polymorphism may ultimately lead to drug resistance. Continuous monitoring of the baseline resistance is therefore a prerequisite to safeguard effective long-term treatment for people living with HIV-1 in Suriname.

Acquisition of HIV by African-born residents of Victoria, Australia: insights from molecular epidemiology

African-born Australians are a recognised "priority population" in Australia's Sixth National HIV/AIDS Strategy. We compared exposure location and route for African-born people living with HIV (PLHIV) in Victoria, Australia, with HIV-1 pol subtype from drug resistance assays and geographical origin suggested by phylogenetic analysis of env gene. Twenty adult HIV positive African-born Victorian residents were recruited via treating doctors. HIV exposure details were obtained from interviews and case notes. Viral RNA was extracted from participant stored plasma or whole blood. The env V3 region was sequenced and compared to globally representative reference HIV-1 sequences in the Los Alamos National Library HIV Database. Twelve participants reported exposure via heterosexual sex and two via iatrogenic blood exposures; four were men having sex with men (MSM); two were exposed via unknown routes. Eight participants reported exposure in their countries of birth, seven in Australia, three in other countries and two in unknown locations. Genotype results (pol) were available for ten participants. HIV env amplification was successful in eighteen cases. HIV-1 subtype was identified in all participants: eight both pol and env; ten env alone and two pol alone. Twelve were subtype C, four subtype B, three subtype A and one subtype CRF02_AG. Reported exposure location was consistent with the phylogenetic clustering of env sequences. African Australians are members of multiple transnational social and sexual networks influencing their exposure to HIV. Phylogenetic analysis may complement traditional surveillance to discern patterns of HIV exposure, providing focus for HIV prevention programs in mobile populations.

Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013

An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.

Transmission of risk-group specific HIV-1 strains among Dutch drug users for more than 20 years and their replacement by nonspecific strains after switching to low-harm drug practices

OBJECTIVES

To characterize HIV-1 epidemiological networks of men having sex with men (MSM) and drug users (DUs) in the Netherlands for >30 years.

DESIGN AND METHODS

Previously, we demonstrated different origin of the HIV-1 epidemics in Dutch MSM and DUs. To achieve the study objectives, risk group-specific genetic markers in the pol gene were examined in 315 participants of the Amsterdam Cohort Studies on HIV/AIDS who were registered as HIV-1 infected in 1981-2011.

RESULTS

Phylogenetic analysis demonstrated circulation of distinct virus strains in the 2 networks, with 98% of viruses of MSM clustering together and apart from strains of 73% DUs. Nine genetic markers that significantly distinguished virus strains specific for DUs were identified, of which 3 were ≥90% conserved. Over the total observation period, only 6% of viruses (4 of MSM and 14 of DUs) clustered with those of the other risk group. Among these sequences, the 3 most conserved genetic markers of that other risk group were 87% conserved.All 4 cases of DU-specific viruses among MSM occurred in 1980s-early 1990s. Viruses nonspecific for DUs were causing new infections among DUs at the rate of 20% till 2002 and replaced DU-specific strains among new infections thereafter, coinciding with switching of DUs to low-harm drug practices.

CONCLUSIONS

Dutch MSM and DUs have remained separate epidemiological networks for decades, despite their geographical and behavioral overlap. Switching to low-harm drug practices among DUs resulted in new infections caused by HIV-1 strains originating from other risk groups.

Characterizing viral subtypes to assess patterns of HIV transmission

We characterized HIV-1 subtypes among 204 persons newly diagnosed with HIV in Ontario from 2003 to 2005 using samples from the Canadian HIV Strain and Drug Resistance Surveillance Program. We examined HIV-1 subtype by demographic characteristics and exposure category, and determined independent predictors of infection with a non-B HIV subtype using multivariate logistic regression. The distribution of HIV subtypes was: B 77.0%, C 10.3%, AG 4.9%, A 2.5%, AE 2.5% and others 3.0%. Overall, 23.0% were non-B, greater in women than in men (62.8% versus 12.4%, P < 0.0001) and persons under 35 years (31.1% versus 18.5% in those ≥35, P = 0.04). Non-B subtype was predominant (78.9%) among persons from HIV-endemic regions and considerable (28.6%) among other persons infected heterosexually. In multivariate modelling adjusted for gender, non-B subtype was significantly associated with birth in an HIV-endemic region (adjusted odds ratio [aOR] 59.2, P < 0.0001) and heterosexual exposure (aOR 6.3, P = 0.02). Additionally, compared with men who had sex with men, non-B subtype was greater among heterosexual women (aOR 17.8, P < 0.001) and women who injected drugs (injection drug use, aOR 13.4, P = 0.01). We found a non-negligible proportion of non-B subtypes among women infected heterosexually not from HIV-endemic countries, providing interesting insights into HIV transmission patterns.

Implications of HIV diversity for the HIV-1 pandemic

HIV-1 genetic variability within individuals and populations plays a central role in the HIV pandemic. Multiple zoonotic transmissions of SIV to humans have resulted in distinct HIV lineages in humans which have further diversified within the population over time. High rates of mutation and recombination during HIV reverse transcription create a genetic diversity in the host which is subject to selection pressures by the immune response and antiretroviral treatment. The global distribution of HIV genetic variants and the impact of HIV diversity on pathogenesis, transmission and clinical management are reviewed. Finally, the key role of escape mutations in the immune response to HIV is discussed as well as the major challenge which HIV-1 diversity poses to HIV vaccine development.

Can migrants from high-endemic countries cause new HIV outbreaks among heterosexuals in low-endemic countries?

OBJECTIVES

To investigate how the sexual behaviour of migrants originating from HIV-endemic countries affects the spread of HIV among heterosexuals in low-endemic countries.

METHODS

A mathematical model is developed describing the transmission of HIV in heterosexual partnerships between African migrants, Caribbean migrants, and local natives. The model accounts for infection of migrants before migration and during trips to their home country. The model is parameterized using data from the Netherlands.

RESULTS

Among new and newly imported, heterosexually acquired, infections in 2010 in the Netherlands, the individual acquiring HIV is an African in 53% of cases, a Caribbean in 26% of cases, and a Dutch native in 21% of cases. The percentage of new infections acquired outside the Netherlands is 40% among African migrants and 32% among Caribbean migrants; these are mostly acquired before migration to the Netherlands. The prevalence of HIV in the Netherlands is hardly affected by changes in risk behaviour of migrants during trips to their home country after migration. If migrants mix more with the Dutch in forming partnerships, then HIV prevalence among migrants will decrease. The more initiating antiviral therapy is delayed among migrants, the higher the resulting prevalence in their own ethnic group and among the Dutch.

CONCLUSION

The serostatus of individuals migrating to low-prevalence countries as well as their sexual behaviour in the country of residence affect considerably the spread of HIV. Preventive measures should focus on targeted interventions, promoting safe sex practices, HIV testing, and entry to specialized HIV care among migrants.

Two independent epidemics of HIV in Maryland

BACKGROUND

HIV-1 subtype B virus is the predominant subtype in HIV-infected individuals in the United States. However, increasing evidence suggests that prevalence of non-B subtypes may be on the rise in the West, and this may have implications for HIV-1 disease surveillance and treatment. The state of Maryland currently has the fourth highest AIDS case report rate in the United States. The goal of this study was to evaluate the prevalence of HIV-1 non-B subtypes in Maryland. The study population included individuals diagnosed with HIV in 2007 through the voluntary counseling and testing sites at the Maryland Department of Health and Mental Hygiene and HIV-infected patients who had genotyping performed at the University of Maryland Medical Center.

RESULTS

At the Department of Health and Mental Hygiene sites, 47 unique non-B subtype strains were identified representing a non-B prevalence of 12.9%. These non-B subtypes included CRF02_AG (n = 20), C (n = 11), A (n = 7), G (n = 5), D (n = 1), and unique recombinant forms (n = 3). The non-B patients were predominantly non-Hispanic black (95.7%) with 63.8% female. Although the majority of the HIV subtype B cases (65.3%) were identified from the Baltimore metropolitan area, most (80.9%) of the non-B cases were from the Maryland suburbs of Washington, DC. Among University of Maryland Medical Center patients, there were 30 non-B subtypes, representing a non-B prevalence of 1.9%. The non-B subtypes detected were CRF02_AG (n = 14), C (n = 6), A (n = 6), G (n = 2), D (n = 1), and unique recombinant forms (n = 1). Phylogenetic analysis of the non-B subtypes revealed that viral sequences from both sources were intermixed, confirming that both sampling frames were drawing from the same overall population.

CONCLUSIONS

Multiple HIV-1 subtypes exist in the Baltimore-Washington metropolitan area with a significant non-B-infected population in the Maryland suburbs of Washington, DC, suggesting 2 independent epidemics of HIV in Maryland. Population-based surveillance inclusive of groups at higher risk of non-B strains is essential to monitor the prevalence and variations of HIV subtypes in Maryland and the United States.

Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach

BACKGROUND

The prevalence and the origin of HIV-1 subtype B, the most prevalent circulating clade among the long-term residents in Europe, have been studied extensively. However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced.

RESULTS

In the current study we inferred the migration history of HIV-1 subtype B by way of a phylogeography of viral sequences sampled from 16 European countries and Israel. Migration events were inferred from viral phylogenies by character reconstruction using parsimony. With regard to the spatial dispersal of the HIV subtype B sequences across viral phylogenies, in most of the countries in Europe the epidemic was introduced by multiple sources and subsequently spread within local networks. Poland provides an exception where most of the infections were the result of a single point introduction. According to the significant migratory pathways, we show that there are considerable differences across Europe. Specifically, Greece, Portugal, Serbia and Spain, provide sources shedding HIV-1; Austria, Belgium and Luxembourg, on the other hand, are migratory targets, while for Denmark, Germany, Italy, Israel, Norway, the Netherlands, Sweden, Switzerland and the UK we inferred significant bidirectional migration. For Poland no significant migratory pathways were inferred.

CONCLUSION

Subtype B phylogeographies provide a new insight about the geographical distribution of viral lineages, as well as the significant pathways of virus dispersal across Europe, suggesting that intervention strategies should also address tourists, travellers and migrants.

Description of the first full-length HIV type 1 subtype F1 strain in Argentina: implications for the origin and dispersion of this subtype in South America

HIV-1 subtype F1 in South America is mainly found as part of diverse BF1 recombinant forms and only five full-length "pure" F1 strains from Brazil were characterized to date. In the present study we describe the first near full-length sequence of a nonrecombinant F1 HIV-1 strain from Argentina, and explore the epidemiological history of this subtype in South America. Three separate phylogenetic analyses were carried out: with all available F1 full-length sequences, with concatenated F1 sequences contained in F1 and BF1 strains, and with partial F1 env sequences derived from worldwide strains. All analyses were consistent in showing a local origin of the newly reported Argentine subtype F1 strain, and a common ancestry of the South American subtype F1 sequences, present either in pure or recombinant genomes. By coalescent analysis, the onset date of the HIV-1 subtype F1 epidemic in South America was estimated to be around the late 1970s. The results indicate for the first time that nonrecombinant F1 HIV-1 strains are present in Argentina, and suggest that the subtype F1 epidemic in South America was initiated by the introduction of a very small group of genetically related viruses during late 1970s.

Introduction of non-B subtypes among Spaniards newly diagnosed with HIV type 1 in the Canary Islands

The Spanish Canary Islands face the northwest coast of Africa, being one gate of entrance of African immigrants into Europe and of HIV-1 non-B strains, prevalent in most African regions. The presence and nature of HIV-1 non-B subtypes were examined in Spanish natives newly diagnosed with HIV-1 infection from 1998 to 2004 in a reference hospital located in one of the largest islands of the archipelago. Subtyping of HIV-1 pol genes was performed in 139 out of 429 individuals found to be HIV-1 positive during that period. Non-B strains infected 40 (28.8%) subjects, 12 (13.7%) out of 87 native Spaniards and 28 (53.8%) out of 52 immigrants (75% Africans) (p < 0.01). HIV-1 non-B subtypes, mostly recombinant forms, were present in Spaniards at least since 1998. HIV-1 non-B subtypes are frequently recognized in HIV+ Africans arriving in the Canary islands and continuously introduced into the newly diagnosed HIV-1+ native population living in the archipelago.

Characterization of an HIV-1 group M variant that is distinct from the known subtypes

We identified an HIV-1 variant that belongs to the M group, with limited similarity of short genetic regions (100-200 nt) to subtype K, but the remainder of the genome is unrelated to any established HIV-1 subtype. The isolate was obtained from an HIV-1-positive male, living in the Netherlands, who encountered the virus before 1989, most probably via heterosexual contact in Africa. We describe the full-length genome sequence of four biological clones that were obtained from two samples collected 5 years apart. At both time points all open reading frames were intact. Within the 5-year interval, the person received antiretroviral therapy with zalcitabine and zidovudine for almost 4 years. Evolution of drug-resistant variants is likely given the increase in viral RNA load to +/-10,000 copies/ml during the last year of treatment. Surprisingly, the only regular RT mutation acquired during this period was K70R, which suggests that the genetic background of this variant is perhaps not suitable for the generation of the standard 41L, 67N, and 215Y/F mutations that typically arise during prolonged, nonsuccessful, zidovudine treatment. Awaiting the discovery of at least two additional, epidemiologically unrelated patients with a phylogenetically related HIV-1 variant, we can designate this variant a new HIV-1 subtype, or a distinct branch of subtype K.

Molecular and epidemiological characteristics of blood-borne virus infections among recent immigrants in Spain

The increased immigration from developing regions to Western countries raises public health concerns related to blood-borne viruses. The prevalence of human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), and human T-lymphotropic virus (HTLV) infections among recent immigrants attending several Spanish diagnostic centers in years 2002 and 2003 was examined. Genetic characterization of viral subtypes and its relationship with distinct at-risk populations was carried out. A total of 1,303 immigrants were identified. They originated in Latin America (46.9%), Sub-Saharan Africa (23.7%), Eastern Europe (9.4%), and the Maghreb (9.2%). Seroprevalence rates were as follows: HIV-1 4.2%, HBV 4.1%, HCV 2.9%, and HTLV-1 0.8%. All patients with HIV-1 non-B subtypes, HBV genotypes E and A3, and HCV genotype 4 were sub-Saharan Africans, and had been infected mainly through heterosexual contacts. In contrast, Latin American homo/bisexual men carried HIV-1 subtype B most likely acquired after their arrival to Spain. In conclusion, while Sub-Saharan Africans carry wide diverse genetic variants of blood-borne viruses, the absence of high-risk practices in most cases could limit the spread of these variants. In contrast, Latin Americans with high-risk sexual practices may be a particularly vulnerable collective to acquire blood-borne viruses in the receptor country.

Performance of the automated Abbott RealTime™ HIV-1 assay on a genetically diverse panel of specimens from London: Comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx® HIV RNA Quantitative assays

Automated RNA extraction and quantitation of HIV-1 by real-time PCR offer potential advantages of efficient sample processing, improved sensitivity, expanded dynamic range and reduced contamination risk. In this study, plasma was collected from 100 HIV-1 infected patients visiting The Courtyard Clinic of St. George's Hospital in London, United Kingdom (UK). Viral loads measured using the automated Abbott RealTime HIV-1 assay (m2000sp sample preparation and m2000rt amplification and detection instruments) were compared to results obtained with Versant HIV-1 RNA 3.0 (bDNA), AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) and LCx HIV RNA Quantitative (LCx HIV) assays. Based on gag p24, pol integrase, and env gp41 sequences, the panel included 26 subtype A, 20 B, 27 C, 10 D, 1 CRF01_AE, 3 CRF02_AG and 13 recombinant viruses. RealTime HIV-1, bDNA, Monitor v1.5 and LCx HIV quantitated 82, 74, 82, and 83% of samples, respectively, with 82, 71, 69 and 80 of the 100 samples measured within the dynamic ranges. Viral loads were highly correlated with 99% of values within 1 log(10) copies/ml between tests. The automated m2000 system and RealTime HIV-1 assay can increase laboratory throughput, enhance overall efficiency and reduce operator-associated errors while providing reliable quantitation of genetically diverse strains of HIV-1.

A diversidade do HIV-1: uma ferramenta para o estudo da pandemia

Uma das características mais marcantes do HIV-1 é a imensa diversidade observada entre as cepas que compõem a pandemia de HIV/AIDS. Na última década, a classificação das variantes do vírus em grupos, subtipos e formas recombinantes circulantes (CRF) e a observação de padrões específicos de mutação têm provado serem ferramentas poderosas para os estudos da dinâmica molecular do vírus. O acompanhamento da distribuição mundial da diversidade do HIV-1 tem sido empregado, por exemplo, em programas de vigilância epidemiológica, bem como na reconstrução da história de epidemias regionais. Além disto, a observação de padrões específicos de distribuição espacial do vírus sugere a existência de diferenças na patogenia e transmissibilidade entre os diversos subtipos. A análise molecular das seqüências do vírus também permite a estimativa do tempo de divergência entre as variantes e das forças dinâmicas que modelam as árvores filogenéticas.

Sexual risk behaviour among Surinamese and Antillean migrants travelling to their countries of origin

OBJECTIVES

To examine travel related sexual risk behaviour among migrants living in Amsterdam.

METHODS

People originating from Surinam (n = 798) and the Netherlands Antilles (n = 227) were recruited in order to study the heterosexual spread of HIV within ethnic groups. Log binomial regression was used to study determinants for homeland travel over the past 5 years; logistic regression was used to study determinants of unprotected sex on these visits.

RESULTS

Of the migrants, 38% of men and 42% of women visited their homeland. Visits were most likely among men who had lived > or =7 years in the Netherlands, were employed, had a high educational level and were/had been married. For women, visiting was associated with older age and living in the Netherlands for > or =8 years. Of migrants visiting their homeland, 47% of men and 11% of women acquired a local sexual partner. For male travellers, Surinamese origin (adjusted OR 10.66; 95% CI 1.72 to 104.48) and a history of > or =1 sexually transmitted infection (STI) (adjusted OR 12.51; 95% CI 3.75 to 46.95) were associated with having unprotected sex with local partners. For women, having >1 partner in the past 5 years (OR 13.57; 95% CI 2.57 to 250.28) was associated with unprotected sex with local partners.

CONCLUSION

Migrants are at substantial risk for HIV and STIs while visiting their homeland. It is important to reach migrants, who are likely to engage in unprotected sex during visits, for pretravel health education. Additional research on risk behaviour in the homeland and the Netherlands is needed to identify migrants with high risk behaviour.

Heterogeneous nature of HIV-1 recombinants spreading in Spain

HIV-1 infections due to non-B subtypes are increasing rapidly in number and spreading across Europe. The genetic nature of HIV-1 non-B variants containing subtype G sequences at the protease (PR)-coding region are described from 48 unrelated subjects living in Spain. Phylogenetic analyses of the HIV-1 reverse transcriptase (RT) and envelope (env) genes (including the V3 loop) were performed. Up to 32 (66.6%) of samples carried inter-subtype recombinant viruses. Although double recombinants were found most frequently (G/A in 20; G/B in 8; G/K in 2), two individuals harbored triple recombinant viruses (GPR/BRT/Aenv and GPR/KRT/Aenv, respectively). Only 33 (68.7%) and 9 (18.7%) sequences clustered with clade G when examining the RT and env genes, respectively. Nearly 70% of samples with pol sequences (PR/RT) belonging to subtype G harbored env sequences ascribed to other clades: A (55.6%), B (11.1%), or K (3.7%). Of note, most recombinant viruses clustered with CRF02_AG, although CRF14_BG recombinants were also found. This study demonstrates that most viruses circulating in Spain with clade G sequences at the pol-coding region are in fact inter-subtype recombinants, with CRF02_AG being the most prevalent virus.

Impact of frequent natural polymorphisms at the protease gene on the in vitro susceptibility to protease inhibitors in HIV-1 non-B subtypes

BACKGROUND

Naturally-occurring polymorphisms at the human immunodeficiency virus type 1 (HIV-1) protease which have been associated to resistance to protease inhibitors (PIs) in clade B viruses are frequently found in non-B subtypes, with unknown clinical significance.

OBJECTIVE

To assess the susceptibility of non-B viruses to different PIs.

STUDY DESIGN

Plasma samples from 58 drug-naive individuals infected with HIV-1 non-B subtypes (2A, 22C, 2D, 1F, 29G and 2J) defined by phylogenetic analyses of the protease gene were tested using a phenotypic assay (PhenoSense, ViroLogic, South San Francisco, CA, USA). Twenty of them were further analyzed with another assay (Antivirogram, Virco, Mechelen, Belgium). All 58 non-B viruses harbored amino acid substitutions associated with reduced PI susceptibility in clade B (positions 10, 20, 36, 63, 70, 77 and 82).

RESULTS

Using PhenoSense-HIV assay, all but two individuals harbored viruses completely susceptible to all six PIs tested (indinavir (IDV), ritonavir (RTV), saquinavir (SQV), nelfinavir (NFV), amprenavir (APV), lopinavir (LPV)). The two viruses with reduced susceptibility belonged to clade G. The first virus, which had K20I, M36I and V82I, showed 2.9-fold decreased susceptibility to APV, while the second virus showed 3.9-fold decreased susceptibility to both NFV and RTV, with amino acid substitutions K20I, M36I, L63P and V82I. Of note, several other viruses displayed the same constellation of mutations but without showing any reduced susceptibility, suggesting that these polymorphisms per se do not affect PI susceptibility.

CONCLUSION

PI susceptibility in HIV-1 non-B viruses seems to be preserved despite the presence of polymorphic changes which have been associated to PI resistance in clade B viruses.

Measurement of HIV RNA in patients infected by subtype C by assays optimized for subtype B results in an underestimation of the viral load

Quantitation assays of HIV-1 RNA used currently were designed and optimized for subtype B viruses. However, infection with non-B HIV viruses has become more common worldwide. Unfortunately, little information is available regarding the suitability of these assays for measurement of viral load in specific non-B subtypes. The performance of two commercial HIV-1 RNA quantitation assays was evaluated in 82 HIV subtype C-infected patients and in 43 HIV-1 subtype B-infected patients. Blood samples were tested by the Amplicor HIV-1 Monitor Assay, Version 1.5, and by the nucleic acid sequence-based amplification HIV-1 assay (NucliSens). The results were compared by using a paired, two-tailed Student's t-test; the difference between the assays was found to be significant only for subtype C. Discordant results (>0.5 log difference) between the two assays were detected in 39% of subtype C samples, compared to 23.2% of subtype B samples. In all cases in which a discordant result was detected, the lower results were obtained by the NucliSens assay. Discordant results between CD4 and viral load (CD4 < 200 cells/ml with a viral load <5,000 copies/ml) were observed in eight of the subtype C-infected patients when a viral load was measured by NucliSens (9.7%), compared to three patients (3.6%) when measured by the Amplicor assay. In conclusion, in patients with HIV subtype C infection, measurement of HIV RNA by the NucliSens assay resulted in a significant underestimation of the viral load as compared to the Amplicor assay. As a consequence, such an underestimation may result in sub-optimal care of patients infected with HIV subtype C.

High prevalence of M184 mutation among patients with viroimmunologic discordant responses to highly active antiretroviral therapy and outcomes after change of therapy guided by genotypic analysis

Whether highly active antiretroviral therapy (HAART) should be modified in patients with persistent increases in CD4(+) T cells despite detectable viral loads is an unresolved question. Forty-three heavily pretreated human immunodeficiency virus (HIV)-infected patients with virologic failure during HAART were studied before a change of therapy guided by genotypic analysis and during follow-up. Patients with an increase in CD4(+) cell count (>100 cells/ml) over pre-HAART values were considered to be discordant patients (20 individuals), whereas patients with a lower increase or no increase in CD4(+) cell count were considered failing patients (23 individuals). Based on univariate analysis, a high CD4(+) cell count before antiretroviral treatment, homosexual behavior as a risk factor for HIV infection, reduced drug exposure to nonnucleoside reverse transcriptase inhibitors, low replicative capacity of HIV isolates, and more frequent detection of HIV isolates with a non-B subtype, an R5 biological phenotype, and M184V and T215Y/F mutations were factors associated with a discordant response to HAART. Based on multivariate analysis, only the M184V mutation remained significantly associated with a viroimmunologic discordant response (odds ratio, 25.48; 95% confidence interval, 1.43 to 453.93). No difference in lamivudine exposure was found between discordant (95%) and failing (91%) patients. Twelve months after the genotypic analysis-guided change of therapy, 3 discordant (15%) and 6 failing patients (26%) achieved undetectable viral loads (<50 copies/ml), whereas in patients with HIV RNA loads of >500 copies/ml, discordant responses were observed in 5 out of 15 discordant patients and in 4 out of 16 failing patients. A relationship between the M184V mutation and a viroimmunologic discordant response to HAART was found. After the genotypic analysis-driven change of therapy, similar rates of virologic suppression were detected in the two groups.

Plasma RNA quantification and HIV-1 divergent strains

The diversity of HIV complicates viral load measurement for patient management and treatment monitoring. Numerous studies have shown that non-B group M variants can be underestimated and that group O strains are not detected by commercial tests. More recent versions of the kits used for previous studies have improved the quantification of non-B variants but are still unable to detect or correctly quantify group O strains. In this study, the authors evaluated the new Abbott LCx HIV RNA Quantitative viral load kit with a large collection of samples from Europe and central Africa. One hundred thirty-three group M samples, including 69 from patients infected with non-B variants, and 70 group O samples were tested. The LCx system was compared with the Cobas Amplicor HIV-1 Monitor v1.5 test and with a quantitative real-time polymerase chain reaction method based on LightCycler technology. The LCx and Cobas tests had similar quantification ranges for group M samples and a high degree of linearity (r2 = 0.9582). The LCx method quantified group O variants (31 of the 48 patients were quantifiable) and gave values within the range of those obtained with the LightCycler assay. The two assays were sensitive but showed only moderate linearity (r2 = 0.6195), probably because of higher diversity of group O strains and the use of primers and probes in different regions. In conclusion, the authors showed that the LCx kit allowed quantification of the large group M diversity and group O variants.

Introduction of HIV type 1 non-B subtypes into Eastern Andalusia through immigration

A study of the distribution of HIV-1 subtypes in the native and immigrant populations of Eastern Andalusia (Southern Spain) was conducted to determine any changes between 1983 and 2001 and to identify antiretroviral resistance mutations in non-B subtype strains among the immigrant population. The study included 111 native patients from Eastern Andalusia: 94 infected with HIV before 1996 and 17 infected since 1996. A parallel study was conducted on 26 HIV-positive immigrants from Africa. Subtyping was done with the heteroduplex mobility assay. Resistance mutations were determined by line probe assay. A total of 137 patients were studied: 9.2% had subtype A (n = 12), 80.8% subtype B (n = 105), and 1.5% subtype C (n = 2). Among the Eastern Andalusia population infected before 1996, 10.9% had non-B subtypes, compared with 23.5% of those infected after that year. The greatest percentage of non-B subtypes (52.4%) was found among the immigrant population. Resistance mutation K70R was detected in one of the six immigrants with non-B subtype and M41L in another. There has been a slight increase in the diversity of HIV-1 subtypes in Eastern Andalusia over the past few years, possibly influenced by non-B subtypes introduced by immigrants from sub-Saharan Africa.

High Incidence of Non-B and Recombinant HIV-1 Strains in Newly Diagnosed Patients in Galicia, Spain: Study of Genotypic Resistance

The objectives of this study are to describe the incidence of non-B and recombinant HIV-1 strains in newly diagnosed HIV-1 infections in Galicia, northwest of Spain, during a 2-year period (May 2000 to June 2002), and the frequency of resistance-associated mutations in reverse transcriptase (RT) and protease (PR) genes, analysing the polymorphisms more frequently detected in non-B and recombinant viruses. All newly diagnosed HIV-1-infected patients attending the nine public hospitals of the seven main cities of Galicia were included in this study. RT, PR and V3 regions from HIV-1 RNA plasma were amplified and sequenced, being the corrected sequences sent to the Stanford HIV RT and Protease Sequence Database. Nineteen of 85 patients (22.3%) were infected by non-B or recombinant viruses: three subtype C, two G, one F1, one Dpol/A1V3, five CRF02_AG, one CRF14_BG, five BGpol/BV3 and one UKpol/UV3 (U, unknown fragment). Eleven of these 19 patients (57.9%) were foreign individuals living in Galicia infected through heterosexual contact, and the other eight (42.1%) were Spanish intravenous drug users who had shared injection equipment. Five of 85 patients (5.9%), all infected with B subtype viruses, showed resistance-associated mutations in RT (M184V, M41L, L210W, T215Y/D and K219Q). In one patient (1.2%) infected with a subtype G strain, resistance-associated mutations in PR (K20I+M36I+M46I+V82I) were detected. In subtype B viruses resistance mutations in PR were not detected. Several polymorphisms in RT: D123S, Q174K, D177E, T200A, V245Q, and PR: I13V, K20I, M36I, R41K, H69K, L89M were detected more frequently in non-B and recombinants than in B strains ( P<0.01 to P<0.001). This study reports a high incidence (22.3%) of newly diagnosed patients infected by different non-B and recombinant HIV-1 strains, in a geographical area of Spain, showing also a high frequency of polymorphisms in RT and PR genes.

Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes B and C

Continual human immunodeficiency virus type 1 (HIV-1) evolution and expansion within the human population have led to unequal distribution of HIV-1 group M subtypes. In particular, recent outgrowth of subtype C in southern Africa, India, and China has fueled speculation that subtype C isolates may be more fit in vivo. In this study, nine subtype B and six subtype C HIV-1 isolates were added to peripheral blood mononuclear cell cultures for a complete pairwise competition experiment. All subtype C HIV-1 isolates were less fit than subtype B isolates (P < 0.0001), but intrasubtype variations in HIV-1 fitness were not significant. Increased fitness of subtype B over subtype C was also observed in primary CD4(+) T cells and macrophages from different human donors but not in skin-derived human Langerhans cells. Detailed analysis of the retroviral life cycle during several B and C virus competitions indicated that the efficiency of host cell entry may have a significant impact on relative fitness. Furthermore, phyletic analyses of fitness differences suggested that, for a recombined subtype B/C HIV-1 isolate, higher fitness mapped to the subtype B env gene rather than the subtype C gag and pol genes. These results suggest that subtype B and C HIV-1 may be transmitted with equal efficiency (Langerhans cell data) but that subtype C isolates may be less fit following initial infection (T-cell and macrophage data) and may lead to slower disease progression.

HIV type 1 diversity in France, 1999-2001: molecular characterization of non-B HIV type 1 subtypes and potential impact on susceptibility to antiretroviral drugs

Non-B HIV-1 samples collected in France between 1999 and 2001 were sequenced in the env, reverse transcriptase (RT), and protease genes (1) to characterize further the non-B strains circulating in the country, (2) to assess the importance of recombination, and (3) to describe the polymorphism of RT and protease genes and appreciate a possible impact on susceptibility to antiretroviral (ARV) drugs. The results show that, within a background of CRF02_AG predominance, there is a high genetic diversity of non-B isolates, including intersubtype recombinants. There is an extensive polymorphism of protease and RT genes compared with B consensus sequences; we have so far no data indicating that these non-B isolates may have reduced sensitivity to ARV drugs.

Rapid detection of human immunodeficiency virus type 1 subtype e infection by PCR

The CRF01_AE (subtype E) strain of human immunodeficiency virus type 1 (HIV-1), originally reported in Thailand, spread rapidly to and showed prevalence in several countries in Southeast Asia, including Taiwan. This strain was also found in other regions of the world. Based on sequence analysis of the vpu gene, a nested PCR assay including an outer primer pair and a subtype E-specific inner primer pair was developed in this study for rapid detection of subtype E viruses. It was tested with 397 HIV-1-positive samples of known subtypes. For these samples, the sensitivity of detection of subtype E viruses was 100% (127 of 127), and the specificity was 97.8% (264 of 270). Although six samples of either subtype A or G showed a positive PCR, most of the cross-reactivity could be reduced by raising the annealing temperature from 54 degrees C to 63 degrees C. When tested with 195 HIV-positive samples of unknown subtypes, the assay had a sensitivity of 98.0% and a specificity of 98.6%. This is a simple, convenient, and sensitive method for rapid detection of subtype E viruses, especially in regions in which viruses of subtypes B and E are predominant.