Genetic diversity of env V3 loop sequences in HIV type 1-infected homosexuals, heterosexuals, intravenous drug users, and hemophilia patients in norway: high prevalence of subtype B and detection of subtype C

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.

Short communication: retrospective study to time the introduction of HIV type 1 non-B subtypes in Lyon, France, using env genes obtained from primary infection samples

Using blood samples from primary HIV-1 infection (PHI) patients obtained in Lyon, France, we characterized the newly transmitted HIV-1 variants in this area during the 1992-1996 period. As PHI samples allowed the precise timing of the transmission event, we were able to date the introduction of non-B subtypes or recombinant forms of the virus in Lyon. Genomic DNA from 18 HIV-1-positive patients at primary infection was used to amplify the full-length env gene by nested PCR; after cloning, the gene was sequenced for subsequent phylogenetic analysis. Several non-B subtypes and recombinant forms of HIV-1 were identified among the 18 patients studied (1 subtype F1, 1 CRF01-AE, 2 subtype G and 2 CRF02-AG). We also found a new J/K recombinant form transmitted in 1995 and never described until now. The introduction of CRF02-AG in Lyon, France, occurred prior to 1992 and six transmission events including non-B subtypes were documented in the following 4 years. Heterosexual contacts appeared as the main introduction pathway for non-B subtypes or recombinant forms. Nevertheless, as transmission of these viruses occurred not only during travel to endemic regions, but also in France or Germany, we conclude that non-B strains entered Europe before the studied period. This retrospective study showed that even if subtype B remained prevalent in the spreading HIV-1 infection in Lyon between 1992 and 1996, non-B subtypes and circulating recombinant forms represented a significantly growing part.

High prevalence of HIV-1 subtype G and natural polymorphisms at the protease gene among HIV-infected immigrants in Madrid

OBJECTIVES

Genetic characterization of HIV-1 subtypes among immigrants and natives infected overseas.

METHODS

Phylogenetic analysis of HIV-1 protease sequences obtained from 109 foreigners (mainly Africans) and 32 native individuals infected overseas attending a reference HIV/AIDS centre located in Madrid, Spain.

RESULTS

The overall rate of infection with HIV-1 non-B subtypes was 50.3% (71/141). Whereas 94.3% (67/71) belonged to immigrants (mostly Africans, 60/67), only 5.6% (4/71) were from native individuals (P < 0.05). The distribution of non-B subtypes was: 49 G, eight C, six A, four D, two F and two H. The high prevalence of subtype G was mainly related to individuals from west-central Africa. Interestingly, substitutions at three or more positions associated with protease inhibitor (PI) resistance were recognized in 52.6% of naive subjects carrying non-B subtypes, but only in 8% of those infected with B viruses (P < 0.05). The genotypes most frequently recognized among non-B and B subtypes occurred, respectively, at positions 36 (100 versus 12%), 20 (77.2 versus 0%), 63 (40.3 versus 64%), 82 (17.5 versus 0%), 10 (14 versus 12%), 77 (3.5 versus 34%), and 71 (0 versus 2%). Accordingly, changes I-36 and I-20 may be considered specific genetic markers for non-B, group M variants and subtype G infections, respectively.

CONCLUSION

Nearly two-thirds of foreigners with HIV-1 infection in Madrid carry non-B subtypes, subtype G (protease) being the most common among west-central African immigrants. The high rate of natural polymorphisms at the protease gene in non-B viruses may compromise the response to PI. Therefore, HIV subtyping should be considered in treatment guidelines.

HIV-1 diversity in France, 1996-1998. The AC 11 laboratory network

OBJECTIVE

To study the distribution of HIV-1 subtypes in France and to describe the characteristics of patients infected with non-B subtypes.

METHODS

All adults who tested HIV-1 positive on Western blot for the first time in one of the participating laboratories between September 1996 and March 1998 were eligible, whether or not they had been diagnosed previously elsewhere. Data on age, sex, country of birth, HIV-transmission group, dates of the last negative and first positive HIV test and clinical stage were collected. Serotyping was performed with a peptide subtype-specific enzyme immunoassay on each plasma sample and genotyping with heteroduplex mobility assay on each non-B serotype-infected patient. Patients characteristics were compared in B and non-B subtypes.

RESULTS

Of the 2168 HIV-positive patients included by 32 laboratories, subtype,results were available for 2042. Among those, 73.4% were men, 12.2% born in sub-Saharan Africa, 41.5% infected through heterosexual contact and 67.6% in CDC stage A. Among the 2042 patients, 1 725 (84.5%) were infected with B subtype. Among the 317 non-B subtypes, subtype A was predominant (66.9%); all other subtypes (C, D, E, F, G, H, O) were present. Factors independently associated with a non-B subtype were to be included in the Paris area [adjusted odds ratio (aOR), 1.6; 95% confidence interval (CI), 1.1-2.3], to be born in sub-Saharan Africa (aOR, 26.0; 95% CI, 17.5-37.8) and to be infected through heterosexual contact (aOR, 4.2; 95% CI, 2.8-6.4).

CONCLUSIONS

In France, although B subtype is still predominant, all non-B subtypes are now present. The diversity of HIV strains may affect diagnostic tests and clinical practice, especially viral load measurements. Moreover, the decreased susceptibility of non-B subtypes to antiretroviral drugs emphasizes the importance of surveillance of HIV diversity.

Silent mutation in the V3 region characteristic of HIV type 1 env subtype B strains from injecting drug users in the former Soviet Union

New independent states of the former Soviet Union are facing a rapidly growing epidemic of HIV-1 among injecting drug users (IDUs). This epidemic is caused by three HIV-1 populations, one belonging to HIV-1 subtype A (IDU-A), another to subtype B (IDU-B), and the third being a recombinant of the IDU-A and IDU-B viruses (IDU-A/B, gagA/envB). Each of these populations is characterized by a high level of genetic homogeneity. We identified a unique synonymous nucleotide substitution in the first isoleucine codon at the IHIGPGR motif (ATT), which was observed in the env subtype B V3 sequences derived from IDUs in Russia and the Ukraine. This substitution was observed in none of 179 sequences obtained from IDUs in western Europe, northern America, and Asia. Molecular epidemiological analysis of HIV-1 strains based on this sequence pattern could be useful for tracing the origin and spread of the IDU-B viruses to other countries and risk groups.

Genetic analysis of HIV-1 samples from Spain

To characterize the viruses responsible for the HIV-1 epidemic in Spain, we genetically characterized 79 samples obtained from Spanish patients with different risk practices (injecting drug users and male homosexuals) in two regions (Madrid and Navarra). Genetic characterization was carried out by nucleotide sequencing in the C2-V3-C3 region and by phylogenetic analysis. All samples were of subtype B except one that clustered with clade F. Because no segregation of samples was determined according to the risk group of patients nor to their geographic origin, the Spanish samples analyzed constitute a single group of viruses. These data, along with the starlike topology of the phylogenetic tree, support the existence of a single introduction of HIV-1 subtype B in Spain. The mean genetic distance among subtype B sequences was of 13.9%+/-0.06% (range, 5%-25%), suggesting an epidemic of long evolution. Analysis of sequences in relation to isolation dates revealed an increase in the heterogeneity of the nucleotide sequences with time. According to these data, a divergence rate of 0.49%+/-0.11% per year was calculated for the Spanish samples during the period analyzed.

Molecular epidemiology of an HIV-1 subtype A subcluster among injection drug users in the Southern Ukraine

Phylogenetic characterization of primary isolates from 17 HIV-1-infected individuals within a recent epidemic in the city of Odessa, Ukraine was conducted. The isolates were drawn from two time periods, 1993 and 1996. The 1996 isolates coincided with the first apparent expansion of HIV-1 among injection drug users (IDU). Multi-locus phylogenetic analysis indicated that HIV-1 gag, env, tat, and long terminal repeat (LTR) sequences all conformed to the HIV-1 classification of a subcluster within subtype A. There was no evidence for intersubtype recombinants among these isolates. A number of potential signature sequences, particularly within env, were identified in these two time periods, possibly suggesting a selective pressure on viral evolution among IDU. Results of this study are consistent with a recent introduction and subsequent independent evolution of an HIV-1 subtype A subcluster among IDU in the Southern Ukraine. This study demonstrates a congruence of multi-locus phylogenetic analysis, and suggests that non-B genetic subtypes, such as HIV-1 subtype A, may become relevant to the study of IDU transmission in the future.

HIV-1 strains specific for Dutch injecting drug users in heterosexually infected individuals in The Netherlands

OBJECTIVE

To study the molecular epidemiology of HIV-1 subtype B amongst heterosexually infected individuals in The Netherlands.

DESIGN

The study population comprised 54 individuals infected by subtype B viruses through heterosexual contacts. Serum samples were collected between 1988 and 1996.

METHODS

Sequences of the gp120 V3 region were obtained from serum samples and analysed by using the signature pattern and phylogenetic methods.

RESULTS

In 22 (41%) out of 54 subtype B sequences from heterosexually infected individuals, the synonymous nucleotide substitution in the second glycine codon at the tip of the V3 loop (the GGC pattern), previously identified as specific for Dutch injecting drug users (IDU), was found. The other previously described IDU sequence patterns were observed significantly more often among GGC- than among non-GGC-containing sequences. In addition, we identified another amino-acid change specific for the GGC sequences. In the phylogenetic and principal coordinate analyses, the GGC sequences from heterosexually infected individuals clustered separately from the non-GGC sequences and together with the IDU consensus sequence. Both the nonsynonymous and particularly the synonymous distances amongst the GGC sequences were significantly lower than amongst the non-GGC sequences.

CONCLUSIONS

Our data provide evidence for a common origin of the viruses in Dutch IDU and the GGC viruses in heterosexuals. We suggest that a considerable proportion of the viruses in heterosexually infected individuals in The Netherlands may have originated from Dutch IDU.

Introduction of HIV-1 subtypes C, E and A into Austria

BACKGROUND

Different subtypes of HIV-1 are prevalent in various geographical regions. Knowledge of their distribution is of importance with respect to possible differences in biological properties (such as reported for subtype E) as well as to diagnostic problems that may arise when specific subtypes are not recognized by standard serological assays.

OBJECTIVES

The objectives of this study were to investigate the presence of the five major subtypes of HIV-1 (A-E) in the Austrian population and to estimate the prevalence of the individual subtypes in different risk groups.

STUDY DESIGN

Serum samples from 88 HIV-1 positive patients were tested for the presence of subtype-specific antibodies using a peptide ELISA.

RESULTS

The majority of the patients were shown to be infected with HIV-1 subtype B, but infections with subtypes A, C, and E were also detected in the Austrian population, primarily in the heterosexual transmission group. While subtypes A and C were probably imported from different African countries, subtype E appears to have been introduced by sex tourists returning from Thailand.

CONCLUSION

Introduction of HIV subtypes other than B from Africa and Asia into Austria has already occurred and will certainly increase within the next few years.

Increasing diversity of HIV-1M serotypes in French blood donors over a 10-year period (1985-1995). Retrovirus Study Group of the French Society of Blood Transfusion

OBJECTIVE

Phylogenetic analysis of gene sequences of HIV-1 has led to the classification of isolates into a major group (M) of viruses, itself divided into subtypes (A to I), and a minor group (O) of rare isolates. Subtype B viruses are the most prevalent in Western countries but little is known about the dynamics of diffusion of the other subtypes in these regions. The prevalence of B subtypes and non-B subtypes in French blood donors between 1985 and 1995 was evaluated.

METHODS

A retrospective study was conducted in 490 blood donors, identified as positive for antibody to HIV-1, by twelve French blood banks between 1985 and 1995. Serological subtyping was performed with a subtype-specific enzyme immunoassay, the reliability for genotyping of which has been demonstrated previously.

RESULTS

Of 450 typable samples, 48 (10.7%) were non-B subtypes. Non-B reactive samples were found in all of the regions. An increasing prevalence of individuals infected by non-B viruses was observed, from approximately 4% in the early period to more than 20% in 1994-1995 (P = 0.0004). Non-B viruses did not appear to be restricted to patients with direct or indirect epidemiological links to non-European populations.

CONCLUSION

We observed an increasing diversity of HIV-1 strains in the population of blood donors residing in France. This stresses the necessity to broaden the surveillance of HIV-1 diversity in order to improve measures to prevent HIV-1 infections.

The impact of exposure group on the progression rate to acquired immunodeficiency syndrome. A comparison between intravenous drug users, homosexual men and heterosexually infected subjects

The objective was to study the impact of exposure group on the progression rate to the acquired immunodeficiency syndrome (AIDS). 289 subjects in Oslo, Norway, infected with the human immunodeficiency syndrome (HIV) and without major clinical signs of HIV infection (102 intravenous drug users, 151 homosexual men and 36 heterosexually infected subjects) were recruited to the Oslo HIV Cohort Study from 1989 and followed until 1 January 1995. 15 (14.7%) of the intravenous drug users, 56 (37.1%) of the homosexual men and 5 (12.5%) of the heterosexually infected subjects developed AIDS during a mean time of 47 months (p < 0.001, log rank test). When controlling for possible confounding variables (age, number of CD4+ lymphocytes, antiviral therapy at study entry, gender and year of HIV diagnosis), the relative risk of AIDS progression was 2.2 [1.1-4.5, 95% confidence interval (CI)] for homosexual men and 0.5 (0.2-1.3, 95% CI) for heterosexually infected subjects as compared to intravenous drug users. In a subgroup with known time of seroconversion (n = 60), 47% (18/38) of the homosexual men, 20% (3/15) of the intravenous users and none (0/7) of the heterosexually infected subjects developed AIDS (p = 0.04, log rank test). The results suggest that homosexual men have more rapid progression to AIDS than intravenous drug users and heterosexually infected subjects.