Presence of human immunodeficiency virus (HIV) type 1 subtype A infection in a New York community with high HIV prevalence: a sentinel site for monitoring HIV genetic diversity in North America. Centers for Disease Control and Prevention-Bronx Lebanon HIV Serosurvey Team

Epidemiology of HIV-1 subtypes in an urban area of northern Italy

The distribution of the different subtypes of HIV varies from one region of the world to another. Subtype B is predominant in Europe and the USA, but there has been a gradual increase in non-B subtypes as a result of migration from regions where they are endemic, and this may have important implications for the control of HIV-1. The aim of this study was to assess the prevalence of HIV-1 subtypes in an urban area of northern Italy in the period 1997-2008. Forty-nine (12.2%; 95% CI, 9.00-15.40) of 401 patients investigated carried a non-B subtype, the prevalence of which was 7.7% (95% CI, 4.96-10.44) among native Italians and 55.3% (95% CI, 39.49-71.11) among non-Italians, 1.6% (95% CI, 0.00-3.81) among ex-intravenous drug addicts, 7.6% (95% CI, 1.21-13.99) among homosexual/bisexual men and 20.5% (95% CI, 14.83-26.17) among heterosexuals, 6.8% (95% CI, 3.37-10.23) among Italians infected as a result of sexual contacts in Italy, and 55.0% (95% CI, 33.20-76.80) among Italians infected abroad or by foreign partners. Overall prevalence increased from 2.9% (95% CI, 0.00-6.11) before 1993 to 23.0% (95% CI, 16.31-29.69) in the period 2001-2008. The results demonstrate that there has been an increase in non-B subtypes (especially sexually transmitted infections), particularly among patients infected abroad or by foreign partners.

HIV infection among U.S. Army and Air Force military personnel: sociodemographic and genotyping analysis

Since 1985, the U.S. Department of Defense has periodically screened all military personnel for HIV allowing for the monitoring of the infection in this dynamic cohort population. A nested case-control study was performed to study sociodemographics, overseas assignment, and molecular analysis of HIV. Cases were newly identified HIV infections among U.S. Army and Air Force military personnel from 2000 to 2004. Controls were frequency matched to cases by gender and date of case first positive HIV screening test. Genotyping analysis was performed using high-throughput screening assays and partial genome sequencing. HIV was significantly associated with black race [odds ratio (OR) = 6.65], single marital status (OR = 4.45), and age (OR per year = 1.07). Ninety-seven percent were subtype B and 3% were non-B subtypes (A3, CRF01_AE, A/C recombinant, G, CRF02_AG). Among cases, overseas assignment in the period at risk prior to their first HIV-positive test was associated with non-B HIV subtype infection (OR = 8.44). Black and single military personnel remain disproportionately affected by HIV infection. Most non-B HIV subtypes were associated with overseas assignment. Given the increased frequency and length of assignments, and the expanding HIV genetic diversity observed in this population, there is a need for active HIV genotyping surveillance and a need to reinforce primary HIV prevention efforts.

Human immunodeficiency virus (HIV) antigens and RNA in HIV-seronegative women with cervical intraepithelial neoplasia

While investigating whether proteins retrieved by cervicovaginal lavages (CVL) from women with cervical intraepithelial neoplasia (CIN) might correlate with risk of progression to invasive cervical cancer, we unexpectedly identified HIV gag and env glycoprotein in CVL from women with HIV-negative serology. HIV antigens were consistently identified by mass spectrometry (MS) in CVL from 4 women but were absent in CVL from the remaining 16 women. HIV serologies of all 20 patients were negative for both HIV-1 and HIV-2 antibodies. To validate the unexpected MS findings we performed Western blot (WB) and immunoaffinity chromatography (IC) analysis of CVL for HIV proteins, viral load assays of paired CVL and blood samples, and immunohistochemical HIV p24 expression in cervical biopsy specimens. WB analysis of CVL for prostate-specific antigen (PSA) was performed to exclude semen contamination as the source of HIV proteins. WB and IC results demonstrated the presence of HIV-1 gp41 and p24 antigens in four CVL that were identified by MS to have the HIV proteins. Despite negative serology, HIV RNA in CVL and HIV p24 in cervix biopsies were detected in patients with HIV antigen-positive CVL. HIV p24-positive CVL were PSA negative. All 20 subjects remained HIV seronegative throughout the study. Women with HIV proteins and RNA were comparatively older. Our findings suggest that CVL HIV proteins in women with CIN could be markers for unrecognized HIV exposure or subclinical infection. Proteomic screening of cervical secretions may be useful in identifying seronegative women exposed to HIV and/or at risk for AIDS.

An HIV-preventive intervention for youth living with HIV

As the number of youth infected with HIV rises, secondary prevention programs are needed to help youth living with HIV meet three goals: (a) increase self-care behaviors, medical adherence, and health-related interactions; (b) reduce transmission acts; and (c) enhance their quality of life. This article describes an intervention program for youth living with HIV. Youth engage in small-group activities with other infected peers to modify their behavioral patterns. The intervention aims to (a) reduce substance use and sexual behaviors that may transmit or enhance transmission of the HIV virus; (b) reduce negative impacts of substance use on seeking and utilizing health care, assertiveness, and adherence to health regimens; and (c) enhance the quality of life to maintain behavior changes over time. Interventions that target youth living with HIV are warranted. A variety of delivery strategies are discussed for secondary interventions.

Genetic characterization of diverse HIV-1 strains in an immigrant population living in New York City

New York City (NYC) is one of the original foci of the HIV-1 epidemic and has a greater number of AIDS cases than any other city in the United States. NYC also hosts the highest number of immigrants among the nation's cities: more than 2 million among a total population of 8 million. Such a high rate of immigration could act as a potential source for introducing and disseminating novel HIV-1 strains into the United States. Our current study focuses on the genetic characterization of HIV-1 strains circulating in an immigrant population in NYC. Of the 505 HIV-1-positive specimens obtained, 196 were available for viral sequencing from the C2 to V3 region of env. Phylogenetic analysis using maximum-likelihood and neighbor-joining methods demonstrated that non-B subtypes and circulating recombinant forms (CRFs) accounted for 43.4% (85 of 196 cases), whereas the remaining 56.6% (111 of 196) cases had viral variants similar to the typical North American subtype B virus. Of those non-B subtypes and CRFs, subtype A and CRF02 dominated (63.5% combined); other subtypes, including C, D, F1, G, CRF01_AE, and CRF06_cpx, were also detected. Two HIV-1 sequences do not cluster with any known subtypes or CRFs. Furthermore, the distribution of non-B subtypes and CRFs was consistent with the countries of origin, suggesting that many of the study subjects were likely infected in their home country before they entered the United States. Subtype B viruses identified in the immigrant population showed no significant differences from the typical North American B subtype, however, indicating that a significant proportion of the immigrants must have been infected after they came to the United States. Public health officials and physicians should be aware of the growing genetic diversity of HIV-1 in this country, particularly in areas with sizable immigrant populations.

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.

HIV-1 subtypes and circulating recombinant forms (CRFs) from HIV-infected patients residing in two regions of central and southern Italy

A total of 347 pol gene sequences from 88 Tuscan and 259 Apulian subjects (including 52 non-Italians and 9 children) were analyzed phylogenetically. Forty-four (12.6%) non-B subtypes were found, including 3.4% C, 1.4% F1, 0.8% G, and 0.3% each for J and A pure subtypes, and 3.7% CRF02_AG, 1.4% CRF01_AE, 0.6% BF, and 0.3% CRF06-cpx recombinant forms. An additional sample close-matched the pol gene of an unique recombinant form (URF AGK 99GR303). The non-B subtypes were from 40 adults and 4 children; 12 of these 44 patients were epidemiologically linked. Thirty-three of the 44 non-B viruses pertained to non-Italian immigrants and 11 to Italians, signifying that 63.4% immigrants and 3.7% Italians harbored non-B subtypes. The overall frequency of non-B subtypes was higher in Tuscany than in Apulia (18.1% vs. 10.8%). Moreover, 6.1% and 3.0% non-B subtypes were found among Italians from Florence and Apulia, respectively, while 52.1% and 72.4% of immigrants living in Tuscany and Apulia harbored non-B subtypes. Women infected by means of sexual contact prevailed among non-Italian adults; the majority of Italians were males and admitted high-risk sexual behavior. Four Italians had a history of extensive travel in countries of high endemicity. Social and epidemiological changes are responsible for an increasing circulation of non-B subtypes in Italy. Although non-B subtypes principally infect non-Italian patients, in Italy they can no longer be considered exclusively restricted to subjects from endemic areas.

Prevention for substance-using HIV-positive young people: telephone and in-person delivery

SUMMARY

HIV risky behaviors and health practices were examined among young people living with HIV (YPLH) in Los Angeles, San Francisco, and New York over 15 months in response to receiving a preventive intervention. YPLH aged 16 to 29 years (n = 175; 26% black and 42% Latino; 69% gay men) were randomly assigned to a 3-module intervention totaling 18 sessions delivered by telephone, in person, or a delayed-intervention condition. Intention-to-treat analyses found that the in-person intervention resulted in a significantly higher proportion of sexual acts protected by condoms overall and with HIV-seronegative partners. Pre- and postanalyses of YPLH in the delayed-intervention condition alone found that YPLH tended to have fewer sexual partners, used fewer drugs, reported less emotional distress, and decreased their use of antiretroviral therapies. Prevention programs can be delivered in alternative formats while retaining efficacy. When YPLH are using hard drugs, drug treatment may be needed before delivery of preventive interventions.

HIV-1 subtype distribution and the problem of drug resistance

Genetic diversity is a hallmark of HIV-1 infection with regard to the expansion of distinct viral subtypes (clades A, B, C, D, E, F, G, K, and O) in different geographical regions. Here, we discuss the issues of HIV-1 sensitivity to antiretroviral drugs and drug resistance in the context of HIV-1 subtype diversity. Virtually all available evidence suggests that all subtypes of HIV display similar sensitivity to antiviral drugs, but viruses from some subtypes or geographical regions may occasionally have a greater propensity to develop resistance against certain drugs than other viral variants. In some situations, the types of mutations associated with resistance may vary, as a result of subtle differences among subtypes with regard to the genetic code. This consideration notwithstanding, drug resistance is unlikely to become a more serious issue in developing than developed countries, and there is an urgency to make anti-HIV drugs available to all who are in need.

Drug resistance in non-subtype B HIV-1

Treatment of HIV-1 with antiretroviral therapy may select mutations in the pol gene associated with resistance to reverse transcriptase inhibitors and protease inhibitors. To provide durable clinical benefit, emergence of drug resistance is countered by prescription of alternative drug regimens. Data on sequential treatments that are effective after virologic failure and the selection of drug resistance is largely confined to HIV-1 subtype B, the clade that has circulated in North America and Europe. However, HIV-1 subtype B currently accounts for only 12% of the estimated 40 million HIV infected individuals worldwide. The global HIV-1 epidemic includes infection with nine identified HIV-1 group M subtypes (A-K), as well as distinct sub-subtypes and numerous chimerical or recombinant forms. Increasing access to treatment of HIV-1 in the developing world and increasing non-subtype B infection through travel and migration pose new questions about the susceptibility and response of these diverse HIV-1 viruses to antiretroviral drugs. Here we review HIV diversity and the published literature on drug resistance, comparing the known resistance mutations in individuals infected with subtype B to the growing experience in the treatment of non-subtype B HIV-1 worldwide.

Antiretroviral Drug Resistance in Non-Subtype B HIV-1, HIV-2 and Siv

Patients infected with HIV-1 of subtype other than B (‘non-subtype B’) or with HIV-2 are being treated with antiretroviral drugs in increasing numbers. In addition, healthcare providers and laboratory workers working with clinical specimens or animals infected with HIV, SIV or SHIV are at risk of being exposed to the virus and might require post-exposure prophylactic treatment. Thus, it is important to understand the inherent antiviral susceptibility of non-subtype B HIV-1, HIV-2 and SIV to currently available antiretroviral drugs, which have been developed with subtype B HIV-1-infected patients as the primary target population. In addition, knowledge about the consequences of treatment failure in non-subtype B HIV-1- and HIV-2-infected patients, with respect to the development of drug resistance, is crucial for designing optimal treatment strategies. This review summarizes the current state of knowledge in these areas. Non-subtype B group M HIV-1 appears to be susceptible to available agents, but follows several unique pathways to resistance to some drugs that have important clinical implications. Group O HIV-1 is naturally resistant to the non-nucleoside reverse transcriptase inhibitors (NNRTIs). HIV-2 and SIVsm are also naturally resistant to the NNRTIs as well as the protease inhibitor amprenavir. More research into the clinical responses to existing drugs and interpretation of genotypic information is needed, as well as development of diagnostic assays specific for non-subtype B HIV-1 and HIV-2.

Two percent of HIV-positive U.S. blood donors are infected with non-subtype B strains

To estimate the prevalence of HIV strains other than the predominant HIV-1B subtype in the U.S. blood donor population we genetically and serologically characterized HIV in infected blood donations collected throughout he United States from 1997 to mid-2000. Using a combination of DNA heteroduplex mobility and DNA sequence analyses of the env and gag regions of HIV-1 we determined that 285 of 312 infections were caused by HIV-1B and six by non-subtype B HIV-1 (four HIV-1C, one HIV-1AE, one HIV-1A). Genetic distances of greater than 14% in the envelope V3-V5 region of the four HIV-1C strains indicated that they did not share a recent common origin. HIV-1 group M, N, and O, and HIV-2 specific peptide serological testing of the 20 PCR-negative samples determined that one infection was caused by HIV-2 and none by HIV-1 group N and O. The major risk factor for infection with a non-HIV-1B strain was sex with an HIV-infected person from Africa although three of seven non-HIV-1B-infected subjects did not fit that category. For four of seven non-HIV-1B-infected subjects the subtype detected was consistent with the African country of origin of the infected person or of their sexual partner. The frequency of genetically confirmed non-subtype-B HIV infection in a geographically dispersed group of infected U.S. blood donors in 1977-2000 was therefore 2.0% (6/312).

U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains

Human immunodeficiency virus (HIV) type 1 subtype B sequences (whole envelope and the p17 region of gag) were obtained from peripheral blood mononuclear cell samples collected in 1981 from seven HIV-infected U.S. individuals and in 1982 from one infected Canadian resident. Phylogenetic and nucleotide distance analyses were performed by using database sequences representing North American strains collected from 1978 to 1995. The estimated phylogeny was starlike, with early strains represented on different lineages. When sequences were grouped by years of collection, nucleotide distance comparisons demonstrated an increase in diversity over time and indicated that contemporary strains are more closely related to early epidemic strains than to each other. Using a recently developed likelihood ratio reduction procedure, the date of origin of the U.S. epidemic was estimated to be 1968 +/- 1.4 years. A coalescent approach was also used to estimate the population history of the U.S. subtype B epidemic. Our analyses provide new information that implies an exponential growth rate from the beginning of the U.S. HIV epidemic. The dating results suggest a U.S. introduction date (or date of divergence from the most recent common ancestor) that precedes the date of the earliest known AIDS cases in the late 1970s. Furthermore, the estimated epidemic growth curve shows a period of exponential growth that preceded most of the early documented cases and also indicates a leveling of prevalence rates in the recent past.

Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B

Given the diversity of human immunodeficiency virus type 1 (HIV-1) subtypes and the emergence of subtypes other than HIV-1 subtype B in the United States, genotypic assays must be capable of delivering sequence data on diverse HIV-1 subtypes. We evaluated the performance of Visible Genetics TRUGENE HIV-1 genotyping kit and Applied Biosystems ViroSeq HIV-1 genotyping system on a panel of 34 well-characterized HIV-1 viral stocks (subtypes A through H). Both assays perform well on diverse HIV-1 subtypes despite being designed for HIV-1 subtype B. The TRUGENE assay produced sequence data for 31 isolates but not for one C and two G isolates. The TRUGENE assay using prototype 1.5 RT-PCR primers and the ViroSeq assay were both successful for all variants tested, although five isolates lacked double-strand sequence coverage in the ViroSeq assay. The availability of standardized HIV-1 genotyping kits that perform reliably with all HIV subtypes will facilitate broad implementation of HIV-1 resistance testing.

HIV-1 subtypes in Luxembourg, 1983-2000

OBJECTIVES

To study the prevalence of HIV-1 subtypes in Luxembourg between 1983 and 2000. To compare the drug susceptibility of non-B and B clade viruses and the prevalence of resistance-associated mutations and polymorphisms before antiretroviral treatment.

DESIGN

A retrospective study on plasma samples of HIV-infected patients registered at the National Service of Infectious Diseases, Luxembourg, between 1983 and 2000.

METHODS

Genotyping was performed by sequencing of the reverse transcriptase (RT) and protease coding region of the pol gene. Drug susceptibility was assessed in a recombinant virus assay.

RESULTS

A total of 20.1% of the HIV-positive patients were infected with non-B subtypes, and since 1990 the proportion of non-B viruses has increased ninefold. Eleven out of 14 F1 subtypes occurred in patients native to Luxembourg. Major resistance mutations related to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) occurred in less than 3% of treatment-naive viruses; however, 87% of the viruses had at least one PI-associated mutation. Natural polymorphism of the protease and RT coding region was observed more frequently among non-B than B viruses. Significantly more B viruses displayed resistance to the tested PI, NRTI and NNRTI (P = 0.044).

CONCLUSION

The proportion of non-B viruses has increased dramatically since 1990. Non-B subtypes showed no decreased susceptibility to antiretroviral drugs, but displayed minor mutations and polymorphisms at higher frequency in their protease and RT coding region. In contrast, a significantly higher proportion of B viruses showed resistance to a range of antiretroviral drugs.

Sequence variability of the integrase protein from a diverse collection of HIV type 1 isolates representing several subtypes

HIV-1 recombinants between viruses from different subtypes appear to be surprisingly common in several regions of the world. To detect such intersubtype recombinants that contain mosaic genomes, we have analyzed sequences from the integrase (IN)-coding region of the polymerase (pol) gene from 23 viruses of known envelope (env) subtype from South America and Africa. As defined by env sequences, these viral genomes included nine subtype A, four subtype B, three subtype C, and four subtype D viruses from group M, and three viruses from group O HIV-1. Mosaic genomes were common, with 7 mosaic genomes among the 20 group M isolates analyzed. Two of these isolates had mosaic IN-coding regions that were distinct, but that had recombination breakpoints at the same location, in the highly conserved polypurine track. Mosaic genomes were particularly common in the viruses from Kenya (five of nine), consistent with our previous prediction that there was a high frequency of intersubtype recombinants circulating in this country. The IN amino acid sequence was highly conserved among the several represented subtypes, including group O. Group M IN sequences shared 94% or greater amino acid sequence identity within a subtype and 91% or greater identity between subtypes. The most divergent M and O variant amino acid sequences differed by only 19%, and the known functional domains were conserved among all of the isolates. The high degree of genetic homogeneity among the virus isolates representing several subtypes indicates that a single drug targeted against IN might be effective for all HIV-1 infections.

Development of multiplexed nucleic acid testing for human immunodeficiency virus type 1 and hepatitis C virus

BACKGROUND AND OBJECTIVES

In most Western countries, blood donations are routinely screened for hepatitis C virus (HCV) RNA by polymerase chain reaction (PCR) or other nucleic acid tests. We describe the development of a multiplexed assay for human immunodeficiency virus type 1 (HIV-1) and HCV in an internally controlled PCR suitable for large-scale blood donor screening.

MATERIALS AND METHODS

The HIV/HCV multiplexed PCR used primers from highly conserved regions in the long terminal repeat region. The National Institute for Biological Standards and Controls (NIBSC) International HIV-1 RNA standard, run control and HIV-1 subtype panel were used for assay evaluation.

RESULTS

The HIV-1 PCR showed a sensitivity of 24 IU/ml for HIV-1 RNA (a dilution where 95% of replicate reactions were positive), which was at least five times more sensitive than the Roche Monitor version 1.5 (using the ultrasensitive extraction protocol) and Organon NASBA assays. The assay was capable of detecting all subtypes of HIV-1 (A to H), as well as the more divergent group N and O variants. The sensitivity of the PCR was unaffected by multiplexing with HCV primers and by the presence of a bovine viral diarrhoea virus (BVDV) internal control.

CONCLUSION

We have developed a highly sensitive multiplexed PCR for HIV-1 and HCV RNA screening that can be introduced into current PCR-based blood donor screening at minimal cost and without significant operational changes.

Health and risk behaviors over time among youth living with HIV

Health practices and transmission behaviors were examined over time among 25 disabled youth living with HIV (YLH) living in a comprehensive residential care program. YLH were aged 19-24 years (M=23.4 years); 89 per cent of males were gay, bisexual, or transgendered (60% Caucasian); all had physical and mental health problems, as well as substance abuse disorders. YLH were assessed at least four times at 3-month intervals and reported high lifetime rates of sexual and substance-use risk acts. Over four assessments, YLH improved their nutrition and hygiene and decreased their worry about their health status. YLH evidenced no decrease in the frequency of substance use and sexual risk. Depression, self-esteem, and health status also were stable over time. YLH who have a lifetime history of multiple problem behaviors are likely to change slowly over time, even when receiving comprehensive residential care.

Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda

The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non-subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97%) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 (88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.

Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population

Phylogenetic analysis of the reverse transcriptase (RT) and protease of 117 published complete human immunodeficiency virus (HIV) type 1 genome sequences demonstrated that these genes cluster into distinct subtypes. There was a slightly higher proportion of informative sites in the RT (40.4%) than in the protease (34.8%; P= .03). Although most variation between subtypes was due to synonymous nucleotide substitutions, several subtype-specific amino acid patterns were observed. In the protease, the subtype-specific variants included 7 positions associated with drug resistance. Variants at positions 10, 20, 36, and 82 were more common in non-B isolates, whereas variants at positions 63, 77, and 93 were more common in subtype B isolates. In the RT, the subtype-specific mutations did not include positions associated with anti-retroviral drug resistance. RT and protease sequences from 2246 HIV-infected persons in northern California were also examined: 99.4% of the sequences clustered with subtype B, whereas 0.6% clustered with subtype A, C, or D.

Determination of human immunodeficiency virus type 1 subtypes by a rapid method useful for the routine diagnostic laboratory

The existence of human immunodeficiency virus type 1 (HIV-1) subtypes has many important implications for the global evolution of HIV and for the evaluation of pathogenicity, transmissibility, and candidate HIV vaccines. The aim of this study was to establish a rapid method for determination of HIV-1 subtypes useful for a routine diagnostic laboratory and to investigate the distribution of HIV-1 subtypes in Austrian patients. Samples were tested by a subtyping method based on a 1.3-kb sequence of the polymerase gene generated by a commercially available drug resistance assay. The generated sequence was subtyped by means of an HIV sequence database. Results of 74 routine samples revealed subtype B (71.6%) as the predominant subtype, followed by subtype A (13.5%) and subtype C (6.8%). Subtypes E, F, G, and AE (CM240) were also detected. This subtyping method was found to be very easy to handle, rapid, and inexpensive and has proved suitable for high-throughput routine diagnostic laboratories. The specific polymerase gene sequence, however, must be existent.

National surveillance of HIV-1 subtypes for England and Wales: design, methods, and initial findings

The HIV-1 infections detected in an ongoing national unlinked anonymous HIV surveillance program were subtyped and analyzed according to demographic and risk characteristics. Of the 893 anti--HIV-1--positive specimens allocated to an exposure group, 70% could be subtyped. Almost 25% of infections subtyped were non-B, mostly subtypes A, C, and D. Non-B infections were rare in homosexual and bisexual men and in drug injectors. Forty percent of infections in heterosexual men attending genitourinary medicine clinics were non-B subtypes; of these, 25% were subtype A infections and 59% were subtype C infections. For female clinic attendees, 61% were non-B subtype infections, of which 48% were subtype A infections and 42% were subtype C infections. Of the clinic attendees born in the United Kingdom and Europe, 14% of the men and 35% of the women were infected with non-B subtypes. In contrast, 78% of infections in antenatal patients were non-B subtypes, of which 61% were subtype A and 29% were subtype C. Extrapolation to the estimated 29,700 prevalent adult infections in the United Kingdom indicates that approximately 8,100 (27%) such infections are non-B subtypes and that these are found almost entirely in heterosexuals. The findings suggest spread of infection of non-B subtypes to heterosexuals born in the United Kingdom from individuals infected in regions of high prevalence.

Efficacy of a preventive intervention for youths living with HIV

OBJECTIVES

HIV transmission behaviors and health practices of HIV-infected youths were examined over a period of 15 months after they received a preventive intervention.

METHODS

HIV-infected youths aged 13 to 24 years (n = 310; 27% African American, 37% Latino) were assigned by small cohort to (1) a 2-module ("Stay Healthy" and "Act Safe") intervention totaling 23 sessions or (2) a control condition. Among those in the intervention condition, 73% attended at least 1 session.

RESULTS

Subsequent to the "Stay Healthy" module, number of positive lifestyle changes and active coping styles increased more often among females who attended the intervention condition than among those in the control condition. Social support coping also increased significantly among males and females attending the intervention condition compared with those attending the control condition. Following the "Act Safe" module, youths who attended the intervention condition reported 82% fewer unprotected sexual acts, 45% fewer sexual partners, 50% fewer HIV-negative sexual partners, and 31% less substance use, on a weighted index, than those in the control condition.

CONCLUSIONS

Prevention programs can effectively reduce risk acts among HIV-infected youths. Alternative formats need to be identified for delivering interventions (e.g., telephone groups, individual sessions).

Variation in health and risk behavior among youth living with HIV

Lifetime and current health practices and risk behaviors were examined among 350 youth living with HIV (YLH) aged 14-23 years from four AIDS epicenters (72.6% male; 26.2% African American, 36.9% Latino). YLH were relatively healthy (M CD4 cells = 499), had used substantial health care and were satisfied with the care. YLH's sexual and substance-use histories indicated substantial HIV related risk acts: the median number of lifetime partners was 25 with only 8% using condoms consistently; 14.9% had injected drugs, and 61.2% had used hard drugs. Compared with females, males had more lifetime and recent sexual partners and had used more drugs. Youth who were recently sexually active (81.3%) had multiple partners. Most of the sexually active YLH used condoms consistently (81.6%). YLH who were symptomatic or had an AIDS diagnosis were likely to have recently had more seropositive sexual partners than the asymptomatic youth. Youth disclosed their serostatus to about half of their sexual partners (53.9%). YLH with AIDS used fewer hard drugs than those without an AIDS diagnosis. Health and risk behaviors of the YLH varied significantly based on their disease stage, gender, and ethnicity, suggesting the need for tailoring interventions for subgroups of YLH.

Surveillance of HIV-1 genetic subtypesand diversity in the US blood supply

BACKGROUND

Recent reports of variant (non-subtype B) HIV infections in US populations have raised concerns about the sensitivity of subtype B virus-based donor screening and diagnostic assays. This study was designed to determine the prevalence and genetic diversity of HIV subtypes in US blood donors over the last two decades.

STUDY DESIGN AND METHODS

Three groups were studied: hemophiliacs infected by clotting factor concentrates in the early 1980s (n = 49), blood donors retrospectively identified as being seropositive in 1985 (n = 97), and blood donors identified as seropositive between 1993 and 1996 (n = 405). Subtype assignment was based primarily on heteroduplex mobility analysis (HMA) of HIV-1 env, with DNA sequence confirmation of selected specimens. HIV peptide-based EIA serotyping was used to rule out HIV-2 and group O infections and to serotype HMA-refractory specimens.

RESULTS

Of 551 specimens, 535 (97%) were assigned subtypes; 532 (99%) of these were subtype B. Three postscreening donations (1%) were assigned non-B subtypes (2 A, 1 C). Two of these three donors were born in Africa; the third was born in the United States and reported no risk factors other than heterosexual activity. HMA distribution plots showed an increase in env diversity among HIV-1 group B strains over time.

CONCLUSION

The results support the need for continued surveillance of HIV subtype diversity and ongoing validation of the sensitivity of HIV diagnostic assays to non-B subtype infections.

Apparent founder effect during the early years of the San Francisco HIV type 1 epidemic (1978-1979)

HIV-1 envelope sequence variants were RT-PCR amplified from serum samples cryopreserved in San Francisco in 1978-1979. The HIV-1 subtype B env V3-V5 sequences from four homosexual men clustered phylogenetically, with a median nucleotide distance of 2.8%, reflecting a recent common origin. These early U.S. HIV-1 env variants mapped close to the phylogenetic root of the subtype B tree while env variants collected in the United States throughout the 1980s and 1990s showed, on average, increasing genetic diversity and divergence from the subtype B consensus sequence. These results indicate that the majority of HIV-1 currently circulating in the United States may be descended from an initial introduction and rapid spread during the mid- to late 1970s of subtype B viruses with limited variability (i.e., a founder effect). As expected from the starburst-shaped phylogeny of HIV-1 subtype B, contemporary U.S. strains were, on average, more closely related at the nucleic acid and amino acid levels to the earlier 1978-1979 env variants than to each other. The growing levels of HIV-1 genetic diversity, one of multiple obstacles in designing a protective vaccine, may therefore be mitigated by using epidemic founding variants as antigenic strains for protection against contemporary strains.

The Changing Epidemic of HIV

Now in its third decade, the epidemiology of human immunodeficiency virus (HIV) transmission in the United States has changed considerably since the epidemic began. Our increased understanding of the virus has fueled development of new treatments to prolong life, and research into a viable vaccine offers hope to those at risk in developed and less developed countries alike. In this review, we provide information about the current trends in HIV and Acquired Immune Deficiency Syndrome (AIDS) among those in the United States who are hardest hit by the epidemic. We also offer insights into and explanations of these changes; update the epidemiology of HIV subtypes and antiretroviral resistance; and describe current strategies for HIV surveillance.

Clinical implications of identifying non-B subtypes of human immunodeficiency virus type 1 infection

Although human immunodeficiency virus type 1 (HIV-1) infection in the United States has predominantly involved subtype B, increasing global travel is leading to wider dissemination of genetically heterogeneous subtypes. While physicians depend on HIV-1 viral load measurements to guide antiretroviral therapy, commonly used molecular assays may underestimate the viral load of patients with non-B subtypes. Nine patients with non-B subtypes of HIV-1 were identified by physicians who suspected a non-B subtype on the basis of a low or undetectable HIV-1 viral load, by the Amplicor HIV-1 Monitor test, version 1.0, in conjunction with either a declining CD4 cell count or history of travel outside the United States. Use of version 1.5 of the Amplicor HIV-1 Monitor test detected a median HIV-1 viral load that was 2.0 log(10) RNA copies/mL higher than was determined with version 1.0. Clinical management was altered in all cases after diagnosis of a non-B-subtype infection. These cases demonstrate that it is critical for physicians to suspect and diagnose non-B subtypes of HIV-1 so that an assay with reliable subtype performance can be used to guide antiretroviral therapy.

Evaluation of performance of the Gen-Probe human immunodeficiency virus type 1 viral load assay using primary subtype A, C, and D isolates from Kenya

Accurate and sensitive quantification of human immunodeficiency virus type 1 (HIV-1) RNA has been invaluable as a marker for disease prognosis and for clinical monitoring of HIV-1 disease. The first generation of commercially available HIV-1 RNA tests were optimized to detect the predominant HIV-1 subtype found in North America and Europe, subtype B. However, these tests are frequently suboptimal in detecting HIV-1 genetic forms or subtypes found in other parts of the world. The goal of the present study was to evaluate the performance of a new viral load assay with non-subtype B viruses. A transcription-mediated amplification method for detection and quantitation of diverse HIV-1 subtypes, called the Gen-Probe HIV-1 viral load assay, is under development. In this study we examined the performance of the Gen-Probe HIV-1 viral load assay relative to that of the commonly used commercial HIV-1 RNA assays using a panel of primary isolates from Kenya. For comparison, we included several subtype B cloned viruses, and we quantified each virus using an in-house quantitative-competitive reverse transcriptase PCR (QC-RT-PCR) method and gag(p24) antigen capture. The Gen-Probe HIV-1 viral load assay and a version of the Roche AMPLICOR HIV-1 MONITOR test (version 1.5) that was designed to detect a broader range of subtypes were both sensitive for the quantification of Kenyan primary isolates, which represented subtype A, C, and D viruses. The Gen-Probe HIV-1 viral load assay was more sensitive for the majority of viruses than the Roche AMPLICOR HIV-1 MONITOR test version 1.0, the Bayer Quantiplex HIV RNA 3.0 assay, or a QC-RT-PCR method in use in our laboratory, suggesting that it provides a useful method for quantifying HIV-1 RNAs from diverse parts of the world, including Africa.

Evidence of a high frequency of HIV-1 subtype F infections in a heterosexual population in Buenos Aires, Argentina

We analyzed HIV-1 genetic variability, phylogenetic relationships, and association with transmission modes among 58 HIV-1-infected patients from Buenos Aires City, Argentina. The 58 strains were classified as env(gp41) HIV-1 group M subtype B (n = 34) and subgroup F1 of subtype F (n = 24). Potential recombinants combining parts of viral regions from different subtypes, B(prot)/F(env) and F(prot)/B(env), were found in two patients, and a dual infection with HIV-1 prot subtypes B and F was identified in one individual. Epidemiologic analysis of behavioral risks revealed that the frequency of infection with subtype F viruses was significantly higher (p < 0.0001) among heterosexual patients (71%) compared with homosexual patients (11%). The spread of non-B subtypes into heterosexual populations may be more common than previously thought. Our findings provide important information for monitoring the transmission of HIV-1 strains among different risk groups in Argentina as well as for vaccine development.

Analysis of HIV type 1 protease and reverse transcriptase in antiretroviral drug-naive Ugandan adults

We analyzed plasma HIV-1 from 27 antiretroviral drug-naive Ugandan adults. Previous subtype analysis of env and gag sequences from these samples identified subtypes A, C, D, and recombinant HIV-1. Sequences of HIV-1 protease and reverse transcriptase (RT) were obtained with a commercial HIV-1 genotyping system. Subtypes based on protease sequences differed from gag subtypes for 5 of 27 samples, demonstrating a high rate of recombination between the gag and pol regions. Protease and RT sequences were analyzed for the presence of amino acid polymorphisms at positions that are sites of previously characterized drug resistance mutations. At those sites, frequent polymorphisms were detected at positions 36 and 69 in protease and positions 179, 211, and 214 in RT. Subtype-specific amino acid motifs were identified in protease. Most of the subtype A sequences had the amino acids DKKM at positions 35, 57, 69, and 89, whereas most subtype D sequences had the amino acids ERHL at those positions. Detection of those polymorphisms may provide a useful approach for rapid identification of subtype A and D isolates in Uganda. This analysis significantly increases the number of Ugandan protease and RT sequences characterized to date and demonstrates successful use of a commercial HIV-1 genotyping system for analysis of diverse non-B HIV-1 subtypes.

Genetic heterogeneity of HIV-1 in Greece

The aim of this study was to detect and determine the genetic variation of HIV-1 in Greece and to analyze the phylogenetic relationships and transmission dynamics of identified variants. Eighty-six blood samples from HIV-1 seroconverted patients of different risk groups were collected from the AIDS clinic, AHEPA Hospital, Thessaloniki, Greece. Retroviral DNA was extracted from uncultured peripheral blood mononuclear cells. HIV-1 DNA sequences encoding a 500-bp fragment of the gp120 C2-C3 region were amplified from each study subject, and they were genetically subtyped by heteroduplex mobility assay and DNA sequencing. Genetic distances and phylogenetic relationships of DNA sequences were estimated using PHYLIP software. Our results revealed that 82 out of 86 (95.3%) subjects carried subtype B sequences, while four (4.7%) carried subtype A sequences. Subtype A in Greek individuals not having traveled abroad was documented. An average of intrasubtype B genetic divergence of 15% was noted. Our findings demonstrate the presence of at least two genetic subtypes of HIV-1 in northern Greece--subtype B and subtype A. The predominant subtype is subtype B, which was transmitted into Greece by multiple sources. Our observations lend support to the argument that the distribution of HIV-1 subtypes is determined by founder effects or other processes rather than any tropism for particular cell types or mode of transmission.

Human immunodeficiency virus infection, Part I

Initially recognized in 1982, acquired immunodeficiency syndrome (AIDS) has been the leading cause of death among young adults in the United States for much of this decade, and it has had a devastating impact on people in the developing world. It is estimated that 42 million people worldwide have been infected with human immunodeficiency virus (HIV), the virus that causes AIDS, and that almost 12 million people have died from AIDS-related diseases through 1997. Among these 12 million are 3 million children. Two thirds of the more than 30 million people with HIV or AIDS reside in sub-Saharan Africa. In the United States, 641,086 patients have been diagnosed with AIDS through 1997, and at least 385,000 have died. However, for the first time, new highly active antiretroviral therapies that include multiple drugs that attack the virus at several sites have slowed the progression from HIV to AIDS and from AIDS to death for those infected with HIV. The cumulative effect of these changes has been a reduction in both AIDS incident cases and AIDS deaths. Recent epidemiologic trends indicate that the proportion of AIDS incident cases and new HIV infections are increasing among women, African-Americans, and Hispanics, and the infections are more likely to be acquired through heterosexual transmission. The clinical management of HIV infection and AIDS has become increasingly complex in recent years. In addition to complete medical and social histories and physical examinations, hematologic, biochemical, serologic, and immunologic laboratory tests are required to predict the likelihood that patients will develop opportunistic infections and other complications related to HIV infection. Among the most important laboratory tests are measurements of HIV in plasma (viral load) in conjunction with peripheral blood CD4+ helper T lymphocyte counts. These tests are potent predictors of disease progression and their results have become markers for clinical response to therapy. The development of highly active antiretroviral therapy has had a profound impact on the epidemiology of AIDS and on the lives of individual patients. Through combinations of antiretroviral drugs, especially protease inhibitors, viral suppression can be achieved. However, adherence to these complex medical regimens and drug interactions have been problems for many patients. In addition, numerous questions remain unanswered, most importantly those regarding the timing of the initiation of treatment, the durability of viral suppression and clinical response, and the optimal "salvage" regimens for patients failing therapy either clinically or virologically.

Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants

Multiple genetic subtypes and intersubtype recombinant strains have been identified among isolates of HIV-1. The greatest diversity of strains has been recovered from Central Africa, where mixtures of subtypes and recombinant forms have been recovered. However, many of the HIV-1 subtypes and recombinants have been characterized by partial rather than full-length genome sequencing. Here we report the first two virtually full-length genome sequences from HIV-1 subtype G, isolated in Sweden and Finland but originating in Congo and Kenya, and from two Djibouti isolates sharing the A/G recombinant structure of Nigerian isolate, IbNG. By comparison with reference sequences of other subtypes, it appears that the subtype G strains are largely nonrecombinant, while the Djibouti strains show alternating segments from subtypes A and G. In the cytoplasmic domain of the gp41 protein of the Djibouti viruses the E, G, and IbNG strains form a single cluster, separate from subtype A, clouding the subtype origin of these particular segments. Within the resolution of current technology, the structure of the Djibouti strains is identical to that of IbNG, establishing for the first time the geographic spread of this recombinant in Africa. The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name "IbNG subtype" is proposed.

A human monoclonal antibody specific for the V3 loop of HIV type 1 clade E cross-reacts with other HIV type 1 clades

To ascertain the antigenic relationship between HIV-1 viruses belonging to various genetically defined subgroups (clades), shared epitopes need to be defined. Human monoclonal antibodies (MAbs) are particularly useful for this purpose because they can detect complex regions of viral proteins that may be missed by sequence analysis and because, by definition, they react with epitopes that stimulate the human immune system. Monoclonal antibodies derived from the cells of HIV-1 clade B-infected subjects have been used extensively for this purpose. Here we describe the first human MAb derived from a clade E-infected individual; the MAb is specific for the V3 loop, recognizing a core epitope represented by the amino acids TRTSVR on the N-terminal side of the crown of the V3 loop. The IgG1(kappa) MAb, designated 1324E, binds to the clade E consensus V3 loop, to rgp120 proteins from clade E and to peripheral blood mononuclear cells infected in vitro with the virus that infected the subject from whose cells the MAb-producing heterohybridoma was derived. Strong cross-reactivity of the MAb to the V3 peptides, rgp120 proteins, and native monomeric gp120s representing clades A and C, as well as to cells infected with a clade C primary isolate, revealed a shared V3 epitope between these clades. When tested for its neutralizing ability, MAb 1324E neutralized a clade E isolate that had been adapted for growth in H9 cells but failed to neutralize five clade E primary isolates.