Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.

Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded ß-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.

Systematic review and meta-analysis: prevalence of alcohol use among young people in eastern Africa.

OBJECTIVE: Systematic review and meta-analysis of published studies of alcohol use among young people (age 15-24 years) in eastern Africa to estimate prevalence of alcohol use and determine the extent of use of standardised screening questionnaires in alcohol studies. METHODS: Five databases (MEDLINE, EMBASE, Global Health, Africa-wide, and PsycINFO) were searched for publications until 30th June 2013. Results were summarised using the guidelines on preferred reporting items for systematic reviews and meta-analyses (PRISMA) and on quality assessment using the modified quality assessment tool for systematic reviews of observational studies (QATSO). Heterogeneity was assessed using the I(2) statistic (DerSimonian-Laird). RESULTS: We identified 2785 potentially relevant studies, of which 56 were eligible for inclusion. Only two studies (4%) used the standardised Alcohol Use Disorder Identification Test (AUDIT) questionnaire, and six studies (13%) used the Cut down, Annoyed, Guilt, Eye opener (CAGE) questionnaire. The reported median prevalence of alcohol use was ever-use 52% [interquartile range (IQR): 20-58%], use in the last month 28% (IQR: 17-37%), use in the last year 26% (IQR: 22-32%), and problem drinking as defined by CAGE or AUDIT 15% (IQR: 3-36%). We observed high heterogeneity between studies, with the highest prevalence of ever use of alcohol among university students (82%; 95%CI: 79-85%) and female sex workers (66%; 95%CI: 58-74%). Current use was most prevalent among male sex workers (69%; 95%CI: 63-75%). CONCLUSIONS: Reported alcohol use and problem drinking were common among diverse groups of young people in eastern Africa, indicating the urgent need for alcohol-focused interventions in this population. Few studies have used standardised alcohol screening questionnaires. Epidemiological research to investigate alcohol-focused interventions in young people should aim to apply such questionnaires that should be validated for use in this population.

Association of Bacterial vaginosis and other Sexually Transmitted Infections with HIV among pregnant women in Nigeria.

OBJECTIVES: To determine the association of Bacterial vaginosis (BV) and other sexually transmissible infections (STIs) with HIV prevalence among pregnant women in Jos, Nigeria. METHODS: This was a cross- sectional study of pregnant women who participated in the Prevention of Mother-to-Child Transmission of HIV program of the AIDS Prevention Initiative in Nigeria, between April 2002 and July 2004, at the Jos University Teaching Hospital in Jos, Nigeria. Blood, high vaginal and endocervical samples were obtained for diagnosis of HIV, BV and other STIs. Data were analyzed for prevalence of HIV, BV and other STIs. Univariate and multivariate logistic regression models generated unadjusted and adjusted odds ratios (OR) as well as 95% confidence intervals (CI) of the association of BV and other STIs with HIV prevalence. P value <0.05 was considered statistically significant. RESULTS: A total of 4,046 pregnant women were studied and 97.6% (3,950/4,046) had complete laboratory records for analysis. The prevalence of HIV was 8.2% (CI: 7.4-9.1); BV 11.9% (CI: 10.9-12.9); Candida 10.7% (CI: 9.7-11.7); mixed infection of BV and Candida 2.8% (CI: 2.3-3.4); Trichomonads 0.6% (CI: 0.3-0.8) and syphilis 0.35% (0.16-0.54). BV, Candida, mixed BV and Candida; and Trichomonads were independently associated with HIV infection [adjusted OR (95% CI), 2.9 (CI: 2.2-3.9); 2.0 (CI: 1.5-2.9); 3.4 (CI: 2.0-5.6), and 3.3 (CI: 1.1-9.7) respectively]. CONCLUSION: HIV prevalence is higher among pregnant women who have BV, Candida and Trichomonads vaginal infections compared with women who have no evidence of infection. The practice of routine screening for BV and other STIs among pregnant women as a strategy for identifying women at risk for prevalent HIV infection should be sustained/ encouraged and the syndromic management of STIs should be integrated into all antenatal care management protocols in antenatal clinics in order to curb the epidemic of heterosexual HIV transmission.

Two distinct broadly neutralizing antibody specificities of different clonal lineages in a single HIV-1-infected donor: implications for vaccine design.

Plasma from a small subset of subjects chronically infected with HIV-1 shows remarkable magnitude and breadth of neutralizing activity. From one of these individuals (CH0219), we isolated two broadly neutralizing antibodies (bnAbs), CH01 and VRC-CH31, from two clonal lineages of memory B cells with distinct specificities (variable loop 1 and 2 [V1V2] conformational specificity and CD4-binding site specificity, respectively) that recapitulate 95% of CH0219 serum neutralization breadth. These data provide proof of concept for an HIV-1 vaccine that aims to elicit bnAbs of multiple specificities.

Hypertension among adolescents in sub-Saharan Africa: a systematic review.

Introduction: Hypertension (HTN) among adolescents is common in high-income countries, and leads to increased premature cardiovascular diseases (CVD). In sub-Saharan Africa (SSA), the prevalence of HTN among adolescents, associated risk factors and CVD complications are not well-described. Such data is needed for planning public health programs to prevent premature CVD in SSA. Methods: We systematically searched 5 databases (MEDLINE, Embase, Google Scholar, Web of Science, and African Index Medicus) from their establishment to December 2021. Key search terms were: adolescent, arterial hypertension, and names of the 48 countries in SSA. We used Covidence® to manage the search results. The review was registered in the Open Science Framework (OSF) https://osf.io/p5sbt/. Results: We identified 4,008 articles out of which we screened 3,088 abstracts, and reviewed 583 full-text articles. We finally included 92 articles that were published between 1968 to December 2021. The majority were cross-sectional studies (80%) and conducted in school settings (78%). The risk of bias was low for 59 studies (64.1%), moderate for 29 studies (31.5%), and high for 4 studies (4.3%). Overall, the prevalence of HTN varied widely from 0.18% to 34.0% with a median (IQR) of 5.5% (3.1%, 11.1%). It was relatively higher in studies using automated blood pressure (BP) devices, and in studies defining HTN using thresholds based on percentile BP distribution for one's height, age, and sex. In addition, the prevalence of HTN was significantly higher in studies from Southern Africa region of SSA and positively correlated with the year of publication. Across studies, traditional risk factors such as age, sex, body mass index, and physical inactivity, were commonly found to be associated with HTN. In contrast, non-traditional risk factors related to poverty and tropical diseases were rarely assessed. Only three studies investigated the CVD complications related to HTN in the study population. Conclusion: The prevalence of HTN among adolescents in SSA is high indicating that this is a major health problem. Data on non-traditional risk factors and complications are scarce. Longitudinal studies are needed to clearly define the rates, causes, and complications of HTN. Systematic Review Registration: https://osf.io/p5sbt/, identifier (10.17605/OSF.IO/P5SBT).

Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors.

V2/V3 conformational epitope antibodies that broadly neutralize HIV-1 (PG9 and PG16) have been recently described. Since an elicitation of previously known broadly neutralizing antibodies has proven elusive, the induction of antibodies with such specificity is an important goal for HIV-1 vaccine development. A critical question is which immunogens and vaccine formulations might be used to trigger and drive the development of memory B cell precursors with V2/V3 conformational epitope specificity. In this paper we identified a clonal lineage of four V2/V3 conformational epitope broadly neutralizing antibodies (CH01 to CH04) from an African HIV-1-infected broad neutralizer and inferred their common reverted unmutated ancestor (RUA) antibodies. While conformational epitope antibodies rarely bind recombinant Env monomers, a screen of 32 recombinant envelopes for binding to the CH01 to CH04 antibodies showed monoclonal antibody (MAb) binding to the E.A244 gp120 Env and to chronic Env AE.CM243; MAbs CH01 and CH02 also bound to transmitted/founder Env B.9021. CH01 to CH04 neutralized 38% to 49% of a panel of 91 HIV-1 tier 2 pseudoviruses, while the RUAs neutralized only 16% of HIV-1 isolates. Although the reverted unmutated ancestors showed restricted neutralizing activity, they retained the ability to bind to the E.A244 gp120 HIV-1 envelope with an affinity predicted to trigger B cell development. Thus, E.A244, B.9021, and AE.CM243 Envs are three potential immunogen candidates for studies aimed at defining strategies to induce V2/V3 conformational epitope-specific antibodies.

Alcohol use before sex and HIV risk: situational characteristics of protected and unprotected encounters among high-risk African women.

OBJECTIVES: To compare the situational characteristics of protected and unprotected sexual encounters that involved alcohol use 2 hours prior with ones that did not. METHODS: Data were collected between December 2002 and December 2005 as part of enrollment in a prospective cohort study designed to identify HIV seroconversion risk factors among women bar and hotel workers in Northern Tanzania. A total of 608 (37.3%) of the women who were inconsistent condom users were asked a set-matched questions concerning situational characteristics surrounding their last protected and unprotected sexual encounter including whether they had been drinking within 2 hours of sex. The associations between drinking 2 hours before sex (yes/no), condom use (protected/unprotected), and their interaction with the situational descriptors were examined with a 2 x 2 model for paired categorical data after controlling for time since the last type of encounter. RESULTS: Condom failure was 5 times more likely if someone (woman, man, or both partners) had been drinking in advance of the encounter (OR, 5.19; 95% CI, 2.05-15.46) and was especially likely to occur if only the woman had been drinking before sex (OR, 14.05; 95% CI, 4.03-50.41). Alcohol use before sex was associated with sexual contacts where the woman was having sex with her partner for the first time, their relationship was casual or transitory or sex was transactional, the location was unfamiliar and less under her control, and the partner had been drinking or using drugs before having sex. Condom use was more frequent in precisely the same types of encounters. Interestingly, there were no significant interactions between alcohol use before sex and condom use, suggesting that drinking before sex and use of condom are distinct and not contingent risk factors. CONCLUSIONS: Alcohol use before sex is associated with an increased likelihood of condom failures and with high-risk sexual encounters, ones that have consistent situational characteristics regardless of whether condoms are used or not.

Modern contraceptive use among sexually active women aged 15-19 years in North-Western Tanzania: results from the Adolescent 360 (A360) baseline survey.

OBJECTIVES: To describe differences in modern contraceptive use among adolescent women aged 15-19 years according to their marital status and to determine factors associated with modern contraceptive use among sexually active women in this population. DESIGN: Cross-sectional analysis of Adolescent 360 evaluation baseline survey. SETTING: The 15 urban and semiurban wards of Ilemela district, Mwanza region, North-Western Tanzania. PARTICIPANTS: Adolescent women aged 15-19 years who were living in the study site from August 2017 to February 2018 and who provided informed consent. Women were classified as married if they had a husband or were living as married. Unmarried women were classified as sexually active if they reported having sexual intercourse in the last 12 months. OUTCOME MEASURE: Prevalence of modern contraceptive among adolescent women aged 15-19 years. RESULTS: Data were available for 3511 women aged 15-19 years, of which 201 (5.7%) were married and 744 (22.5%) were unmarried-sexually active. We found strong evidence of differences in use of modern contraceptive methods according to marital status of adolescent women. Determinants of modern contraception use among unmarried-sexually active women were increasing age, increasing level of education, being in education, hearing of modern contraception from interpersonal sources or in the media in the last 12 months, perceiving partner and/or friends support for contraceptive use, as well as higher knowledge and self efficacy for contraception. CONCLUSIONS: Sexual and reproductive health programmes aiming to increase uptake of modern contraceptives in this population of adolescent women should consider the importance of girl's education and social support for contraceptive use particularly among unmarried-sexually active women.

Vitamin A serostatus and heterosexual transmission of HIV: case-control study in Tanzania and review of the evidence.

Results from a randomized clinical trial suggested that vitamin A/beta-carotene supplementation to HIV-1-infected women during pregnancy and lactation may increase the risk of vertical transmission. Limited information is available on the potential role of vitamin A on heterosexual HIV transmission. This is a relevant question in many resource-limited settings where both vitamin A deficiency and HIV infection are highly prevalent. We conducted a case-control study (34 cases and 38 controls) nested within a cohort of HIV-negative women attending family planning clinics in Tanzania, to examine whether low serum concentrations at baseline were associated with the risk of seroconversion. There was not a significant association (OR = 2.14, 95% C I = 0.54, 8.45). In light of these and previous results, we conclude that there is not enough evidence yet to suggest a causal association between vitamin A and heterosexual transmission.

Transmission of HIV-1 infection in sub-Saharan Africa and effect of elimination of unsafe injections.

During the past year, a group has argued that unsafe injections are a major if not the main mode of HIV-1 transmission in sub-Saharan Africa. We review the main arguments used to question the epidemiological interpretations on the lead role of unsafe sex in HIV-1 transmission, and conclude there is no compelling evidence that unsafe injections are a predominant mode of HIV-1 transmission in sub-Saharan Africa. Conversely, though there is a clear need to eliminate all unsafe injections, epidemiological evidence indicates that sexual transmission continues to be by far the major mode of spread of HIV-1 in the region. Increased efforts are needed to reduce sexual transmission of HIV-1.

Validation of the MINI (DSM IV) Tool for the Assessment of Alcohol Dependence among Young People in Northern Tanzania Using the Alcohol Biomarker Phosphatidylethanol (PEth).

The alcohol dependence section of the Mini International Neuropsychiatric Interview questionnaire (MINI) has not been evaluated in young Africans. We applied the MINI in a cross-sectional study of 202 alcohol users from northern-Tanzania, aged 18-24 years (103 male casual workers and 99 students), and validated it against phophatidylethanol (PEth) at a cut-off suggesting heavy chronic alcohol use (≥0.30 µmol/L). Blood was assayed for PEth (16:0/18:1-subform) by liquid chromatography-tandem mass spectrometry. The MINI dependence criteria (≥3 positive responses) were met by 39% participants although their PEth levels were low. Contrary, many young people with high PEth levels were not classified as dependent. The sensitivity of the MINI ranged from 0% to 69% (female students and male workers, respectively) and specificity from 52% to 85% (workers and female students, respectively). The highest AUROC (0.68) occurred with a cut-off of ≥4 positive responses. A modified MINI with three affirmative responses to five questions increased specificity to 92%-97%; however, sensitivity remained low. The performance of the MINI in detecting dependence among young people from northern-Tanzania is unsatisfactory. Specificity was improved using a modified version but sensitivity remained low. An accurate tool for the diagnosis of alcohol dependence is needed for epidemiological and clinical purposes.

The Epidemiology of Alcohol Use and Alcohol Use Disorders among Young People in Northern Tanzania.

INTRODUCTION: Alcohol use is a global public health problem, including as a risk factor for HIV infection, but few data are available on the epidemiology of alcohol use and alcohol use disorders (AUD) among young people in sub-Saharan Africa. METHODS: We conducted a cross-sectional survey among 4 groups of young people aged 15-24 years old (secondary school students, college/university students, employees of local industries and casual labourers) in two regions (Kilimanjaro and Mwanza) of northern Tanzania. Using a multistage stratified random sampling strategy, we collected information on demographics, alcohol use, and behavioural factors. We screened severity of alcohol use using the Alcohol Use Disorder Identification Test (AUDIT) and estimated the quantity and frequency of alcohol consumption using the timeline-follow-back-calendar (TLFB) method. RESULTS: A total of 1954 young people were surveyed. The prevalence of reported alcohol use was higher among males (47-70% ever users and 20-45% current users) than females (24-54% ever users and 12-47% current users). Prevalence of use was substantially higher in Kilimanjaro than Mwanza region. In both regions, participants reported high exposure to alcohol advertisements, and wide alcohol availability. College students reported the highest prevalence of current alcohol use (45% among males; 26% among females) and of heavy episodic drinking (71% among males; 27% among females) followed by casual labourers. Males were more likely to have AUD (an AUDIT score ≥8) than females, with 11-28% of males screening positive for AUD. Alcohol use was associated with male gender, being in a relationship, greater disposable income, non-Muslim religion and a higher number of sexual partners. CONCLUSIONS: Alcohol use is a significant problem among young people in northern Tanzania. There is an urgent need to develop, pilot and deliver interventions to help young people delay initiation and reduce levels of harmful drinking, particularly among college students and casual labourers.

Comparison of self-reported alcohol use with the alcohol biomarker phosphatidylethanol among young people in northern Tanzania.

BACKGROUND: The one-month Time Line Follow Back calendar (TLFB) and the Alcohol Use Disorders Identification Test (AUDIT) are used to collect self-reported alcohol intake data. We compared these instruments with the alcohol biomarker phosphatidylethanol (PEth) among young-people in northern Tanzania. METHODS: AUDIT and TLFB were applied in a cross-sectional study of 202 young people (18-24 years), who reported using alcohol during the past year (103 male casual labourers; 99 college students). We assayed whole blood for PEth 16:0/18:1, using liquid chromatography-tandem mass spectrometry. RESULTS: For both self-report methods, alcohol consumption was high, particularly among men (e.g. a median of 54 drinks per month in labourers), and about half of male students (48%) reported hazardous or harmful levels of drinking (AUDIT ≥8). Almost half (49%) of participants were PEth-positive (median concentration 0.03µmol/L). There were significant positive correlations between reported total alcohol intake and PEth concentration in males (Spearman's correlation rs=0.65 in college students and rs=0.57 in casual labourers; p<0.001). Self-reported use in the past month was a sensitive marker of having a positive PEth result (≥0.01µmol/L) with 89% of those with a PEth positive result reporting alcohol use, and this was similar in all groups. The proportion of those with AUDIT scores ≥8 and AUDIT-C scores ≥6 among those with a high cut-off positive PEth result (≥0.30µmol/L) ranged between 94 and 100%. CONCLUSION: TLFB and AUDIT are sensitive measures to detect heavy alcohol use among young-people in northern Tanzania. They can be used to identify young people who may benefit from alcohol-focused interventions.

HIV-1 pol diversity among female bar and hotel workers in Northern Tanzania.

A national ART program was launched in Tanzania in October 2004. Due to the existence of multiple HIV-1 subtypes and recombinant viruses co-circulating in Tanzania, it is important to monitor rates of drug resistance. The present study determined the prevalence of HIV-1 drug resistance mutations among ART-naive female bar and hotel workers, a high-risk population for HIV-1 infection in Moshi, Tanzania. A partial HIV-1 pol gene was analyzed by single-genome amplification and sequencing in 45 subjects (622 pol sequences total; median number of sequences per subject, 13; IQR 5-20) in samples collected in 2005. The prevalence of HIV-1 subtypes A1, C, and D, and inter-subtype recombinant viruses, was 36%, 29%, 9% and 27%, respectively. Thirteen different recombination patterns included D/A1/D, C/A1, A1/C/A1, A1/U/A1, C/U/A1, C/A1, U/D/U, D/A1/D, A1/C, A1/C, A2/C/A2, CRF10_CD/C/CRF10_CD and CRF35_AD/A1/CRF35_AD. CRF35_AD was identified in Tanzania for the first time. All recombinant viruses in this study were unique, suggesting ongoing recombination processes among circulating HIV-1 variants. The prevalence of multiple infections in this population was 16% (n = 7). Primary HIV-1 drug resistance mutations to RT inhibitors were identified in three (7%) subjects (K65R plus Y181C; N60D; and V106M). In some subjects, polymorphisms were observed at the RT positions 41, 69, 75, 98, 101, 179, 190, and 215. Secondary mutations associated with NNRTIs were observed at the RT positions 90 (7%) and 138 (6%). In the protease gene, three subjects (7%) had M46I/L mutations. All subjects in this study had HIV-1 subtype-specific natural polymorphisms at positions 36, 69, 89 and 93 that are associated with drug resistance in HIV-1 subtype B. These results suggested that HIV-1 drug resistance mutations and natural polymorphisms existed in this population before the initiation of the national ART program. With increasing use of ARV, these results highlight the importance of drug resistance monitoring in Tanzania.

Frequent intra-subtype recombination among HIV-1 circulating in Tanzania.

The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR) of 38 (28-50) sequences per subject). Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84%) subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60%) subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69%) to 36 (82%) over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.

The epidemiology of HIV and HSV-2 infections among women participating in microbicide and vaccine feasibility studies in Northern Tanzania.

OBJECTIVES: To prepare for future HIV prevention trials, we conducted prospective cohort studies among women working in food and recreational facilities in northern Tanzania. We examined the prevalence and incidence of HIV and HSV-2, and associated risk factors. METHODS: Women aged 18-44 years working in food and recreational facilities were screened to determine their eligibility for the studies. Between 2008-2010, HIV-negative women were enrolled and followed for 12 months. At enrolment and 3-monthly, we collected socio-demographic and behavioural data, and performed clinical examinations for collection of biological specimens that were tested for reproductive tract infections. Risk factors for HIV and HSV-2 incidence were investigated using Poisson regression models. RESULTS: We screened 2,229 and enrolled 1,378 women. The median age was 27 years (interquartile range, IQR 22, 33), and median duration working at current facility was 2 years. The prevalences of HIV at screening and HSV-2 at enrolment were 16% and 67%, respectively. Attendance at the 12-month visit was 86%. HIV and HSV-2 incidence rates were 3.7 (95% confidence interval, CI: 2.8,5.1) and 28.6 (95% CI: 23.5,35.0)/100 person-years, respectively. Women who were separated, divorced, or widowed were at increased risk of HIV (adjusted incidence rate ratio, aRR = 6.63; 95% CI: 1.97,22.2) and HSV-2 (aRR = 2.00; 95% CI: 1.15,3.47) compared with married women. Women reporting ≥3 partners in the past 3 months were at higher HIV risk compared with women with 0-1 partner (aRR = 4.75; 95% CI: 2.10,10.8), while those who had reached secondary education or above were at lower risk of HSV-2 compared with women with incomplete primary education (aRR = 0.42; 95% CI: 0.22,0.82). CONCLUSIONS: HIV and HSV-2 rates remain substantially higher in this cohort than in the general population, indicating urgent need for effective interventions. These studies demonstrate the feasibility of conducting trials to test new interventions in this highly-mobile population.

Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania.

BACKGROUND: Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort). METHODS: The polymerase encompassing partial reverse transcriptase was sequenced and phylogenetic analysis performed and subtype determined. Questionnaires documented demographic data. We examined factors associated with subtype using multinomial logistic regression, adjusted for study, age, and sex. RESULTS: Among 140 individuals (125 women and 15 men), subtype A1 predominated (54, 39%), followed by C (46, 33%), D (25, 18%) and unique recombinant forms (URFs) (15, 11%). There was weak evidence to suggest different subtype frequencies by study (for example, 18% URFs in the Kisesa cohort versus 5-9% in the hospitality facility-worker cohorts; adjusted relative-risk ratio (aRR) = 2.35 [95% CI 0.59,9.32]; global p = 0.09). Compared to men, women were less likely to have subtype D versus A (aRR = 0.12 [95% CI 0.02,0.76]; global p = 0.05). There was a trend to suggest lower relative risk of subtype D compared to A with older age (aRR = 0.44 [95% CI 0.23,0.85] per 10 years; global p = 0.05). CONCLUSIONS: We observed multiple subtypes, confirming the complex genetic diversity of HIV-1 strains circulating in northern Tanzania, and found some differences between cohorts and by age and sex. This has important implications for vaccine design and development, providing opportunity to determine vaccine efficacy in diverse HIV-1 strains.

HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies.

This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28-50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.

Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing.

Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.