Comparative analysis of commercial assays for the detection and quantification of Human Immunodeficiency Virus Type 1 (HIV-1) RNA in plasma from patients infected with HIV-1 subtype C.

The commercial assays commonly used to quantify plasma human immunodeficiency virus type 1 (HIV-1) RNA in clinical settings were designed to assess HIV-1 subtype B. We compared the performance of 4 commercial assays (Amplicor versions 1.0 and 1.5 [Roche]; Quantiplex [Chiron]; and NASBA HIV-1 RNA QT [Organon Teknika]) in detecting and quantifying HIV-1 RNA in plasma from HIV-infected persons from Zambia, an area where HIV-1 subtype C is predominant. Each assay detected plasma HIV-1 RNA, but they do not all measure statistically similar quantities of plasma HIV-1 RNA.

HIV-1 subtypes and the HIV epidemics in four cities in sub-Saharan Africa.

OBJECTIVE: To describe the distribution of HIV-1 subtypes in two cities with high HIV prevalence (Kisumu, Kenya and Ndola, Zambia) and two with relatively low prevalence (Cotonou, Benin and Yaoundé, Cameroon), and to examine whether the differences in prevalence of HIV infection could be due to the predominance within the infected populations of subtypes with differing efficiency of heterosexual transmission. METHODS: For around 100 randomly selected HIV-positive sera from the general population and 60 from sex workers in each city, the HIV-1 subtype was determined in the envfragment. For between 19 and 52 of the sera from the general population and 20-32 sera from sex workers, the subtype was also determined in the gag fragment. RESULTS: Over 70% of infections in Cotonou, Yaoundé and Kisumu were with subtype A (by env). However, around one-half of subtype A infections in Cotonou and Yaoundé were found to be the circulating recombinant form CRF02_AG when the gag fragment was also examined. A large number of different HIV strains were found in Yaoundé, including some belonging to group O. Over 20% of infections in Kisumu and around 10% in Yaoundé were with isolated intersubtype recombinant forms. All but a few infections in Ndola were with subtype C and no recombinants were found. CONCLUSIONS: The pattern of distribution of subtypes that we found does not suggest that differences in circulating subtypes play a major role in explaining the differences in prevalence of HIV-1 infection between the four cities. The emergence and spread of recombinants requires close surveillance to adapt testing strategies if needed, to inform vaccine development and to ascertain their role in the future spread of HIV.

Ecological and individual level analysis of risk factors for HIV infection in four urban populations in sub-Saharan Africa with different levels of HIV infection.

OBJECTIVE: To identify factors that could explain differences in rate of spread of HIV between different regions in sub-Saharan Africa. DESIGN: Cross-sectional study. METHODS: The study took place in two cities with a relatively low HIV prevalence (Cotonou, Benin and Yaoundé, Cameroon), and two cities with a high HIV prevalence (Kisumu, Kenya and Ndola, Zambia). In each of these cities, a representative sample was taken of about 1000 men and 1000 women aged 15-49 years. Consenting men and women were interviewed about their socio-demographic background and sexual behaviour; and were tested for HIV, herpes simplex virus type 2 (HSV-2), syphilis, Chlamydia trachomatis and Neisseria gonorrhoea infection, and (women only) Trichomonas vaginalis. Analysis of risk factors for HIV infection was carried out for each city and each sex separately. Adjusted odds ratios (aOR) were obtained by multivariate logistic regression. RESULTS: The prevalence of HIV infection in sexually active men was 3.9% in Cotonou, 4.4% in Yaoundé, 21.1% in Kisumu, and 25.4% in Ndola. For women, the corresponding figures were 4.0, 8.4, 31.6 and 35.1%. High-risk sexual behaviour was not more common in the high HIV prevalence cities than in the low HIV prevalence cities, but HSV-2 infection and lack of circumcision were consistently more prevalent in the high HIV prevalence cities than in the low HIV prevalence cities. In multivariate analysis, the association between HIV infection and sexual behavioural factors was variable across the four cities. Syphilis was associated with HIV infection in Ndola in men [aOR = 2.7, 95% confidence interval (CI) = 1.5-4.91 and in women (aOR = 1.7, 95% CI = 1.1-2.6). HSV-2 infection was strongly associated with HIV infection in all four cities and in both sexes (aOR ranging between 4.4 and 8.0). Circumcision had a strong protective effect against the acquisition of HIV by men in Kisumu (aOR = 0.25, 95% CI = 0.12-0.52). In Ndola, no association was found between circumcision and HIV infection but sample sizes were too small to fully adjust for confounding. CONCLUSION: The strong association between HIV and HSV-2 and male circumcision, and the distribution of the risk factors, led us to conclude that differences in efficiency of HIV transmission as mediated by biological factors outweigh differences in sexual behaviour in explaining the variation in rate of spread of HIV between the four cities.

Male circumcision and HIV infection in four cities in sub-Saharan Africa.

OBJECTIVES: To explore the role of male circumcision in the spread of HIV infection in four urban populations in sub-Saharan Africa. DESIGN AND METHODS: A cross-sectional population based study was conducted in four cities in sub-Saharan Africa with different levels of HIV infection. HIV prevalence among adults was relatively low in Cotonou (Benin) and in Yaoundé (Cameroon), and exceeded 25% in Kisumu (Kenya) and in Ndola (Zambia). In each city, a random sample was taken of men and women aged 15-49 years from the general population. Consenting study participants were interviewed about their sociodemographic characteristics and their sexual behaviour, and were tested for HIV, herpes simplex virus type 2, syphilis, gonorrhoea and chlamydial infection. Men underwent a genital examination. RESULTS: In Cotonou and in Yaoundé, the two low HIV prevalence cities, 99% of men were circumcised. In Kisumu 27.5% of men were circumcised, and in Ndola this proportion was 9%. In Kisumu, the prevalence of HIV infection was 9.9% among circumcised men and 26.6% among uncircumcised men. After controlling for socio-demographic characteristics, sexual behaviour and other sexually transmitted infections, the protective effect of male circumcision remained with an adjusted odds ratio of 0.26 (95% confidence interval = 0.12-0.56). In Ndola, the prevalence of HIV infection was 25.0% in circumcised men and 26.0% in uncircumcised men. The power was insufficient to adjust for any differences in sexual behaviour. CONCLUSIONS: The differences in epidemic spread of HIV are likely to be due to differences in the probability of transmission of HIV during sexual exposure as well as differences in sexual behaviour. Male circumcision is one of the factors influencing the transmission of HIV during sexual intercourse, and this study confirms the population level association between HIV and lack of male circumcision, as well as a strong individual level association in Kisumu, the only city with sufficient power to analyze this association.

Why do young women have a much higher prevalence of HIV than young men? A study in Kisumu, Kenya and Ndola, Zambia.

OBJECTIVE: To examine the factors responsible for the disparity in HIV prevalence between young men and women in two urban populations in Africa with high HIV prevalence. DESIGN: Cross-sectional survey, aiming to include 1000 men and 1000 women aged 15-49 years in Kisumu, Kenya and Ndola, Zambia. METHODS: Participants were interviewed and tested for HIV and other sexually transmitted infections. Analyses compared the marital and non-marital partnership patterns in young men and women, and estimated the likelihood of having an HIV-infected partner. RESULTS: Overall, 26% of individuals in Kisumu and 28% in Ndola were HIV-positive. In both sites, HIV prevalence in women was six times that in men among sexually active 1 5-19 year olds, three times that in men among 20-24 year olds, and equal to that in men among 25-49 year olds. Age at sexual debut was similar in men and women, and men had more partners than women. Women married younger than men and marriage was a risk factor for HIV, but the disparity in HIV prevalence was present in both married and unmarried individuals. Women often had older partners, and men rarely had partners much older than themselves. Nevertheless, the estimated prevalence of HIV in the partners of unmarried men aged under 20 was as high as that for unmarried women. HIV prevalence was very high even among women reporting one lifetime partner and few episodes of sexual intercourse. CONCLUSIONS: Behavioural factors could not fully explain the discrepancy in HIV prevalence between men and women. Despite the tendency for women to have older partners, young men were at least as likely to encounter an HIV-infected partner as young women. It is likely that the greater susceptibility of women to HIV infection is an important factor both in explaining the male-female discrepancy in HIV prevalence and in driving the epidemic. Herpes simplex virus type 2 infection, which is more prevalent in young women than in young men, is probably one of the factors that increases women's susceptibility to HIV infection.

Multicentre study on factors determining differences in rate of spread of HIV in sub-Saharan Africa: methods and prevalence of HIV infection.

OBJECTIVE: The objective of this study was to explore whether the differences in rate of spread of HIV in different regions in sub-Saharan Africa could be explained by differences in sexual behaviour and/or factors influencing the probability of HIV transmission during sexual intercourse. METHODS: A cross-sectional, population-based study was conducted in two cities with a high HIV prevalence (Kisumu in Kenya and Ndola in Zambia) and two cities with a relatively low HIV prevalence (Cotonou in Benin and Yaoundé in Cameroon). In each of these cities, approximately 1000 men and 1000 women, aged 15-49 years, were randomly selected from the general population. Consenting men and women were interviewed and were tested for HIV, syphilis, herpes simplex virus type 2 (HSV-2), gonorrhoea, chlamydial infection and trichomoniasis (the latter for women only). In addition, a survey was conducted on a random sample of 300 sex workers in each city. The research instruments, including the questionnaires and the laboratory procedures, were standardized to permit comparison of results. RESULTS: The numbers of men interviewed were 1021 in Cotonou, 973 in Yaoundé, 829 in Kisumu, and 720 in Ndola. The corresponding figures for women were 1095, 1116, 1060 and 1130. In Yaoundé, Kisumu and Ndola, the response rates for men were lower than for women due to failure to make contact with eligible men. The proportion of eligible women who were interviewed was 86% in Yaoundé, and 89% in Kisumu and Ndola. In Yaoundé, 76% of eligible men were interviewed, along with 82% in Kisumu and 75% in Ndola. The prevalence of HIV infection in men was 3.3% in Cotonou, 4.1% in Yaoundé, 19.8% in Kisumu and 23.2% in Ndola. For women, the respective figures were 3.4, 7.8, 30.1 and 31.9%. The prevalence of HIV infection among women aged 15-19 years was 23.0% in Kisumu and 15.4% in Ndola. Among women in Kisumu who had their sexual debut 5 years before the interview, the prevalence of HIV infection was 46%; in Ndola, it was 59%. Among sex workers, the prevalence of HIV infection was 57.5% in Cotonou, 34.4% in Yaoundé, 74.7% in Kisumu and 68.7% in Ndola. CONCLUSIONS: The HIV prevalence rates in the general population confirmed our preliminary assessment of the level of HIV infection in the four cities, which was based on estimates of HIV prevalence from sentinel surveillance among pregnant women. The very high prevalence of HIV infection among young women in Kisumu and Ndola calls for urgent intervention.

The epidemiology of gonorrhoea, chlamydial infection and syphilis in four African cities.

OBJECTIVES: To compare the epidemiology of gonorrhoea, chlamydial infection and syphilis in four cities in sub-Saharan Africa; two with a high prevalence of HIV infection (Kisumu, Kenya and Ndola, Zambia), and two with a relatively low HIV prevalence (Cotonou, Benin and Yaoundé, Cameroon). DESIGN: Cross-sectional study, using standardized methods, including a standardized questionnaire and standardized laboratory tests, in four cities in sub-Saharan Africa. METHODS: In each city, a random sample of about 2000 adults aged 15-49 years was taken. Consenting men and women were interviewed about their socio-demographic characteristics and their sexual behaviour, and were tested for HIV, syphilis, herpes simplex virus type 2 (HSV-2), gonorrhoea, chlamydial infection, and (women only) Trichomonas vaginalis infection. Risk factor analyses were carried out for chlamydial infection and syphilis seroreactivity. RESULTS: The prevalence of gonorrhoea ranged between 0% in men in Kisumu and 2.7% in women in Yaoundé. Men and women in Yaoundé had the highest prevalence of chlamydial infection (5.9 and 9.4%, respectively). In the other cities, the prevalence of chlamydial infection ranged between 1.3% in women in Cotonou and 4.5% in women in Kisumu. In Ndola, the prevalence of syphilis seroreactivity was over 10% in both men and women; it was around 6% in Yaoundé, 3-4% in Kisumu, and 1-2% in Cotonou. Chlamydial infection was associated with rate of partner change for both men and women, and with young age for women. At the population level, the prevalence of chlamydial infection correlated well with reported rates of partner change. Positive syphilis serology was associated with rate of partner change and with HSV-2 infection. The latter association could be due to biological interaction between syphilis and HSV-2 or to residual confounding by sexual behaviour. At the population level, there was no correlation between prevalence of syphilis seroreactivity and reported rates of partner change. CONCLUSION: Differences in prevalence of chlamydial infection could be explained by differences in reported sexual behaviour, but the variations in prevalence of syphilis seroreactivity remained unexplained. More research is needed to better understand the epidemiology of sexually transmitted infections in Africa.

The epidemiology of trichomoniasis in women in four African cities.

OBJECTIVES: To describe the epidemiology of Trichomonas vaginalis infection and its association with HIV infection, in women in four African cities with different levels of HIV infection. DESIGN: Cross-sectional study, using standardized methods, including a standardized questionnaire and standardized laboratory tests, in four cities in sub-Saharan Africa: two with a high prevalence of HIV infection (Kisumu, Kenya and Ndola, Zambia), and two with a relatively low prevalence of HIV (Cotonou, Benin and Yaoundé, Cameroon). METHODS: In each city, a random sample of about 2000 adults aged 15-49 years was taken. Consenting men and women were interviewed about their socio-demographic characteristics and their sexual behaviour, and were tested for HIV, syphilis, herpes simplex virus type 2 (HSV-2), gonorrhoea, chlamydial infection, and (women only) T. vaginalis infection. Risk factor analyses were carried out for trichomoniasis for each city separately. Multivariate analysis, however, was only possible for Yaoundé, Kisumu and Ndola. RESULTS: The prevalence of trichomoniasis was significantly higher in the high HIV prevalence cities (29.3% in Kisumu and 34.3% in Ndola) than in Cotonou (3.2%) and Yaoundé (17.6%). Risk of trichomoniasis was increased in women who reported more lifetime sex partners. HIV infection was an independent risk factor for trichomonas infection in Yaoundé [adjusted odds ratio (OR) = 1.8, 95% confidence interval (CI) = 0.9-3.7] and Kisumu (adjusted OR = 1.7, 95% CI = 1.1-2.7), but not in Ndola. A striking finding was the high prevalence (40%) of trichomonas infection in women in Ndola who denied that they had ever had sex. CONCLUSION: Trichomoniasis may have played a role in the spread of HIV in sub-Saharan Africa and may be one of the factors explaining the differences in levels of HIV infection between different regions in Africa. The differences in prevalence of trichomoniasis between the four cities remain unexplained, but we lack data on the epidemiology of trichomoniasis in men. More research is required on the interaction between trichomoniasis and HIV infection, the epidemiology of trichomoniasis in men, and trichomonas infections in women who deny sexual activity.

The epidemiology of HSV-2 infection and its association with HIV infection in four urban African populations.

OBJECTIVES: To estimate age- and sex-specific herpes simplex virus type-2 (HSV-2) prevalence in urban African adult populations and to identify factors associated with infection. DESIGN AND METHODS: Cross-sectional, population-based samples of about 2000 adults interviewed in each of the following cities: Cotonou, Benin; Yaoundé, Cameroon; Kisumu, Kenya and Ndola, Zambia. Consenting study participants were tested for HIV, HSV-2 and other sexually transmitted infections. RESULTS: HSV-2 prevalence was over 50% among women and over 25% among men in Yaoundé, Kisumu and Ndola, with notably high rates of infection among young women in Kisumu and Ndola (39% and 23%, respectively, among women aged 15-19 years). The prevalence in Cotonou was lower (30% in women and 12% in men). Multivariate analysis showed that HSV-2 prevalence was significantly associated with older age, ever being married, and number of lifetime sexual partners, in almost all cities and both sexes. There was also a strong, consistent association with HIV infection. Among women, the adjusted odds ratios for the association between HSV-2 and HIV infections ranged from 4.0 [95% confidence interval (CI) = 2.0-8.0] in Kisumu to 5.5 (95% CI = 1.7-18) in Yaoundé, and those among men ranged from 4.6 (95% CI = 2.7-7.7) in Ndola to 7.9 (95% CI = 4.1-15) in Kisumu. CONCLUSIONS: HSV-2 infection is highly prevalent in these populations, even at young ages, and is strongly associated with HIV at an individual level. At a population level, HSV-2 prevalence was highest in Kisumu and Ndola, the cities with the highest HIV rates, although rates were also high among women in Yaoundé, where there are high rates of partner change but relatively little HIV infection. The high prevalence of both infections among young people underlines the need for education and counselling among adolescents.

Factors influencing the difference in HIV prevalence between antenatal clinic and general population in sub-Saharan Africa.

OBJECTIVE: To compare HIV prevalence in antenatal clinics (ANC) and the general population, and to identify factors determining the differences that were found. DESIGN: Cross-sectional surveys in the general population and in ANC in three cities. METHODS: HIV prevalence measured in adults in the community was compared with that measured by sentinel surveillance in ANC in Yaoundé, Cameroon, Kisumu, Kenya, and Ndola, Zambia. RESULTS: In Yaoundé and Ndola, the HIV prevalence in ANC attenders was lower than that in women in the population overall, and for age groups over 20 years. In Kisumu, the HIV prevalence in ANC attenders was similar to that in women in the population at all ages. The only factors identified that influenced the results were age, marital status, parity, schooling, and contraceptive use. The HIV prevalence in women in ANC was similar to that in the combined male and female population aged 15-40 years in Yaoundé and Ndola, but overestimated it in Kisumu. In Yaoundé and Ndola, the overall HIV prevalence in men was approximated by using the age of the father of the child reported by ANC attenders, but this method overestimated the HIV prevalence in Kisumu, and did not give good age-specific estimates. CONCLUSION: Few factors influenced the difference in HIV prevalence between ANC and the population, which could aid the development of adjustment procedures to estimate population HIV prevalence. However, the differences between cities were considerable, making standard adjustments difficult. The method of estimating male HIV prevalence should be tested in other sites.

'Behind walls': a study of HIV risk behaviours and seroprevalence in prisons in Zambia.

Inmate populations include a large number of individuals at risk of HIV infection. However, there is insufficient data about HIV/AIDS epidemiology in prisons. Our study, conducted in Zambia, a sub-Saharan African nation with an estimated HIV prevalence of 19% in adults, was designed to address this shortfall.

Educational level is associated with condom use within non-spousal partnerships in four cities of sub-Saharan Africa.

BACKGROUND: Rates of condom use in sub-Saharan Africa have remained too low to curb HIV/sexually transmitted disease (STD) epidemics. A better understanding of the main determinants of condom use would aid promotion. METHODS: Cross-sectional population surveys were conducted in four cities in sub-Saharan Africa: Yaoundé, Cameroon; Cotonou, Benin; Ndola, Zambia; and Kisumu, Kenya. In each city, the aim was to interview a random sample of 1000 men and 1000 women aged 15--49 years, including questions on characteristics of non-spousal partnerships in the past 12 months. RESULTS: Data on condom use were available for 4624 non-spousal partnerships. In the four cities, the proportion of partnerships in which condoms were used always or most of the time ranged from 23.8 to 33.5% when reported by men and from 10.7 to 25.9% when reported by women. Based on the reports from men, condom use was associated with higher educational level of the male partner in Yaoundé [adjusted odds ratio (aOR) = 1.76] and Ndola (aOR = 2.94) and with higher educational level of the female partner in Cotonou (aOR = 2.36) and Kisumu (aOR = 2.76). Based on the reports from women, condom use was associated with higher educational level of the female partner in Kisumu (aOR = 2.60) and Ndola (aOR = 4.50) and with higher educational level of the male partner in Yaoundé (aOR = 3.32). Associations with other determinants varied across cities and for men and women. CONCLUSIONS: Education was found to be a key determinant of condom use in all four cities. This suggests that educational level increases response to condom promotion and highlights the need for special efforts to reach men and women with low educational attainment.

Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa.

More than 80% of the world's HIV-infected adults live in sub-Saharan Africa, where heterosexual transmission is the predominant mode of spread. The virologic and immunologic correlates of female-to-male (FTM) and male-to-female (MTF) transmission are not well understood. A total of 1022 heterosexual couples with discordant HIV-1 serology results (one partner HIV infected, the other HIV uninfected) were enrolled in a prospective study in Lusaka, Zambia and monitored at 3-month intervals. A nested case-control design was used to compare 109 transmitters and 208 nontransmitting controls with respect to plasma HIV-1 RNA (viral load, VL), virus isolation, and CD4(+) cell levels. Median plasma VL was significantly higher in transmitters than nontransmitters (123,507 vs. 51,310 copies/ml, p < 0.001). In stratified multivariate Cox regression analyses, the risk ratio (RR) for FTM transmission was 7.6 (95% CI: 2.3, 25.5) for VL > or = 100,000 copies/ml and 4.1 (95% CI: 1.2, 14.1) for VL between 10,000 and 100,000 copies/ml compared with the reference group of <10,000 copies/ml. Corresponding RRs for MTF transmission were 2.1 and 1.2, respectively, with 95% CI both bounding 1. Only 3 of 41 (7%) female transmitters had VL < 10,000 copies/ml compared with 32 of 93 (34%) of female nontransmitters (p < 0.001). The transmission rate within couples was 7.7/100 person-years and did not differ from FTM (61/862 person-years) and MTF (81/978 person-years) transmission. We conclude that the association between increasing plasma viral load was strong for female to male transmission, but was only weakly predictive of male to female transmission in Zambian heterosexual couples. FTM and MTF transmission rates were similar. These data suggest gender-specific differences in the biology of heterosexual transmission.

Declining HIV prevalence and risk behaviours in Zambia: evidence from surveillance and population-based surveys.

OBJECTIVE: To examine trends in HIV prevalence and behaviours in Zambia during the 1990s. METHODS: The core Zambian system for epidemiological surveillance and research has two major components: (i) HIV sentinel surveillance at selected antenatal clinics (ANC) in all provinces; and (ii) population-based HIV surveys in selected sentinel populations (1996 and 1999). The former was refined in 1994 to improve the monitoring of prevalence trends, whereas the latter was designed to validate ANC-based data, to study change in prevalence and behaviour concomitantly and to assess demographic impacts. RESULTS: The ANC-based data showed a dominant trend of significant declines in HIV prevalence in the 15--19 years age-group, and for urban sites also in age-group 20--24 years and overall when rates were adjusted for over-representation of women with low education. In the general population prevalence declined significantly in urban women aged 15--29 years whereas it showed a tendency to decline among rural women aged 15-24 years. Prominent decline in prevalence was associated with higher education, stable or rising prevalence with low education. There was evidence in urban populations of increased condom use, decline in multiple sexual partners and, among younger women, delayed age at first birth. CONCLUSIONS: The results suggested a dominant declining trend in HIV prevalence that corresponds to declines in incidence since the early 1990s attributable to behavioural changes. Efforts to sustain the ongoing process of change in the well-educated segments of the population should not be undervalued, but the modest change in behaviour identified among the most deprived groups represents the major preventive challenge.

Genotyping TAP2 variants in North American Caucasians, Brazilians, and Africans.

The protein forms of transporter associated with antigen processing, subunit 2 (TAP2), differ either by amino acid substitutions (Thr374Ala, Ile379Val, Ile467Val, Thr565Ala, Val577Met, Cys651Arg, and Ala665Thr) or by a truncation (Gln687Stop) of 17 amino acid residues at the C-terminus. Nonsynonymous single nucleotide polymorphisms (N-SNPs) causing these amino acid variations except 577Val were detected in genomic DNA samples from North American Caucasians (n = 76), Brazilians (n = 148), Rwandans (n = 285), and Zambians (n = 117). Exclusive (100%) and nearly exclusive (>95%) linkage disequilibrium was seen with a number of N-SNPs. The average heterozygosity at any given dimorphic site ranged from 7.3% to 44.6%, and at least four N-SNPs showed clear population specificity. N-SNP combinations alone led to the identification of 16 relatively common alleles, which appeared to form at least three lineages. Further analyses of 101 cDNA samples from Brazilians detected nine expressed TAP2 alleles, four of which matched the official assignments. Genetic complexity at the TAP2 locus was further enhanced by two out of five synonymous SNPs (S-SNPs), especially the GGT386GGG (Gly) that had similar heterozygosity rates in Caucasians (28.9%), Rwandans (33.3%), and Zambians (33.3%). Overall, distribution of both synonymous and nonsynonymous SNPs in the various ethnic groups examined here conformed well to the Hardy-Weinberg equilibrium, and between 57.9% and 77.0% of subjects in each ethnic group were heterozygous with two TAP2 alleles predicted to differ by at least one amino acid residue. Such complexity of TAP2 polymorphisms, in the form of SNPs as well as alleles, is likely to complicate the analyses of disease associations and haplotype structures in the HLA class II region.

TAPI polymorphisms in several human ethnic groups: characteristics, evolution, and genotyping strategies.

Genetic variations in the locus encoding the transporter associated with antigen processing, subunit 1 (TAP1), were systematically studied using samples from Caucasians, Africans, Brazilians, and compared with data from chimpanzees. PCR-amplified genomic sequences corresponding to the 11 exons were analyzed by single-strand conformation polymorphism (SSCP) and sequencing. Six nonsynonymous and 2 synonymous single nucleotide polymorphisms (SNPs) were found to be common in one ethnic group or another, and they involved codons 254 (Gly-GGC/Gly-GGT) in exon 3, 333 (Ile-ATC/Val-GTC) in exon 4, 370 (Ala-GCT/Val-GTT) in exon 5, 458 (Val-GTG/Leu-TTG) in exon 6, 518 (Val-GTC/Ile-ATC) in exon 7, 637 (Asp-GAC/Gly-GGC), 648 (Arg-CGA/Gln-CAA) and 661 (Pro-CCG/Pro-CCA) in exon 10. At each SNP site the sequence listed first was predominant in all ethnic groups. Several SNPs segregated on the same chromosome regardless of populations and species. Together, the SNPs produced 5 major human TAP1 alleles, 4 of which matched the officially recognized alleles *0101, *02011, *0301, and *0401; the 5th allele differed from each of those by at least 4 SNPs. Overall, TAP1*0101 was the predominant allele in all ethnic groups, with frequencies ranging from 0.667 in Zambians to 0.808 in US Caucasians. The TAP1*0401 frequency showed the greatest difference between Africans (0.221-0.254) and Caucasians (0.033), with Brazilians (0.058) fitting in the middle. Consistent with earlier work based on Caucasians and gorillas, *0101 appeared to be the newest human TAP1 allele, suggesting a dramatic spread of *0101 into all human populations examined. Characterization of TAP1 polymorphisms allowed the design of a PCR-based genotyping scheme that targeted 7 SNP sites and required 2 separate genotyping techniques.

Novel alleles at the lymphotoxin alpha (LTalpha) locus mark extended HLA haplotypes in native Africans.

Genetic variations at the closely related tumor necrosis factor alpha (TNFalpha or TNF) and lymphotoxin alpha (LTalpha, formerly TNFbeta) loci have been well documented in various human populations, and several haplotypes spanning the MHC class I and class II loci are known to carry specific TNF alleles. Genotyping of the TNFc microsatellite within the first intron of LTalpha in 285 Rwandans and 319 Zambians revealed two predominant alleles, c1 at frequencies of 0.598 and 0.683 and c2 at 0.384 and 0.307, respectively. Overall, the distribution of TNFc genotypes containing the major alleles conformed well to the Hardy-Weinberg equilibrium in both cohorts. Two previously unrecognized minor TNFc alleles were also detected: the first, designated c0, was found in 10 native Africans and was the only allele present in 10 chimpanzees; the second, designated c3, was seen in 6 other African patients. Further genotyping at loci for HLA class I, class II, and for transporters associated with antigen processing, subunit 1 (TAP1) in those 16 individuals suggested a tight, stable extended haplotype involving c0 and 26Asn (LTalpha)-TNF3 (TNF promoter -238A and -308G)-DRB1*1503-DQB1*0602-TAP1.2 (333Val)-TAP1.4 (637Gly). The c3 allele was observed on another extended haplotype with 26Thr (LTalpha)-TNF1 (TNF promoter -238G and -308G)-DQB1*0102-DQB1*0501-TAP1*0101 (333Ile and 637Asp). The c3-tagged haplotype further extended to Cw*15 at the HLA class I C locus, but no specific A or B alleles could be unambiguously assigned. Positive associations between c2 homozygosity and HIV-1 seronegative status in both Rwandans and Zambians (odds ratio = 2.03 and 2.00, p = 0.04 and 0.07, respectively) had little effect on the haplotype assignments. These findings suggest a preferential expansion of the human TNFc dinucleotide (CT/AG) repeat sequence and further imply the existence of two extended MHC lineages that have not been disrupted by recombinations.

Decreased fertility among HIV-1-infected women attending antenatal clinics in three African cities.

Population HIV prevalence estimates rely heavily on sentinel surveillance in antenatal clinics (ANCs), but because HIV reduces fertility, these estimates are biased. To aid interpretation of such data, we estimated HIV-associated fertility reduction among pregnant women in ANCs in Yaoundé (Cameroon), Kisumu (Kenya), and Ndola (Zambia). Data collection followed existing HIV sentinel surveillance procedures as far as possible. HIV prevalence among the women was 5.5% in Yaoundé, 30.6% in Kisumu, and 27.3% in Ndola. The birth interval was prolonged in HIV-positive multiparous women compared with HIV-negative multiparous women in all three sites: adjusted hazard ratios of pregnancy were 0.84 (95% confidence interval [CI]: 0.62-1.1) in Yaoundé, 0.82 (95% CI: 0.70-0.96) in Kisumu, and 0.74 (95% CI: 0.61-0.90) in Ndola, implying estimated reductions in the risk of pregnancy in HIV-positive women of between 16% and 26%. For primiparous women, the interval between sexual debut and birth was longer in HIV-positive women than in HIV-negative women in all sites, although the association was lost in Ndola after adjusting for age and other factors. Consistent results in different study sites help in the development of standard methods for improving ANC-based surveillance estimates of HIV prevalence. These may be easier to devise for multiparous women than for primiparous women.