Evaluation of an HIV nucleic acid testing program with automated Internet and voicemail systems to deliver results

Association between where men who have sex with men (MSM) meet sexual partners and chlamydia/gonorrhoea infection before and during the COVID-19 pandemic in San Diego, California

BACKGROUND

Meeting sex partners online is associated with increased risk of acquiring sexually transmitted infections. We examined whether different venues where men who have sex with men (MSM) meet sex partners was associated with prevalent Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection, and whether prevalence increased during (vs before) the COVID-19 pandemic.

METHODS

We conducted a cross-sectional analysis of data from San Diego's 'Good To Go' sexual health clinic from two enrolment periods: (1) March-September 2019 (pre-COVID-19) and (2) March-September 2021 (during COVID-19). Participants completed self-administered intake assessments. This analysis included males aged ≥18 years self-reporting sex with males within 3 months before enrolment. Participants were categorised as (1) meeting new sex partners in-person only (eg, bars, clubs), (2) meeting new sex partners online (eg, applications, websites) or (3) having sex only with existing partners. We used multivariable logistic regression, adjusting for year, age, race, ethnicity, number of sex partners, pre-exposure prophylaxis use and drug use to examine whether venue or enrolment period were associated with CT/NG infection (either vs none).

RESULTS

Among 2546 participants, mean age was 35.5 (range: 18-79) years, 27.9% were non-white and 37.0% were Hispanic. Overall, CT/NG prevalence was 14.8% and was higher during COVID-19 vs pre-COVID-19 (17.0% vs 13.3%). Participants met sex partners online (56.9%), in-person (16.9%) or only had existing partners (26.2%) in the past 3 months. Compared with having only existing sex partners, meeting partners online was associated with higher CT/NG prevalence (adjusted OR (aOR) 2.32; 95% CI 1.51 to 3.65), while meeting partners in-person was not associated with CT/NG prevalence (aOR 1.59; 95% CI 0.87 to 2.89). Enrolment during COVID-19 was associated with higher CT/NG prevalence compared with pre-COVID-19 (aOR 1.42; 95% CI 1.13 to 1.79).

CONCLUSIONS

CT/NG prevalence appeared to increase among MSM during COVID-19, and meeting sex partners online was associated with higher prevalence.

Assessing the reliability of the CD4 depletion model in the presence of Ending the HIV Epidemic initiatives

BACKGROUND

Accurate estimates of HIV incidence are necessary to monitor progress towards Ending the HIV Epidemic (EHE) initiative targets (90% decline by 2030). U.S. incidence estimates are derived from a CD4 depletion model (CD4 model). We performed simulation-based analyses to investigate the ability of this model to estimate HIV incidence when implementing EHE interventions that have the potential to shorten the duration between HIV infection and diagnosis (diagnosis delay).

METHODS

Our simulation study evaluates the impact of three parameters on the accuracy of incidence estimates derived from the CD4 model: rate of HIV incidence decline, length of diagnosis delay, and sensitivity of using CD4 + cell counts to identify new infections (recency error). We model HIV incidence and diagnoses after the implementation of a theoretical prevention intervention and compare HIV incidence estimates derived from the CD4 model to simulated incidence.

RESULTS

Theoretical interventions that shortened the diagnosis delay (10-50%) result in overestimation of HIV incidence by the CD4 model (10-92%) in the first year and by more than 10% for the first 6 years after implementation of the intervention. Changes in the rate of HIV incidence decline and the presence of recency error had minimal impact on the accuracy of incidence estimates derived from the CD4 model.

CONCLUSION

In the setting of EHE interventions to identify persons with HIV earlier during infection, the CD4 model overestimates HIV incidence. Alternative methods to estimate incidence based on objective measures of incidence are needed to assess and monitor EHE interventions.

Brief Report: Comparative Analysis of Pre-existing HIV Drug Resistance Mutations in Proviral DNA Using Next-Generation Sequencing and Routine HIV RNA Genotyping

BACKGROUND

We investigated whether deep sequencing of archived HIV DNA of antiretroviral-naive persons with acute/early HIV infection could identify transmitted drug resistance mutations (DRM), per the IAS drug resistance algorithm, which are not detected by routine bulk (consensus) sequencing.

METHODS

Deep sequencing of HIV DNA from peripheral blood mononuclear cells and consensus sequencing from concurrent blood plasma (BP) was performed from antiretroviral (ART)-naive adults with recent infection. We compared the prevalence of low-frequency (2%-20%) and high-frequency (>20%) nonnucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), and protease inhibitor (PI) DRM.

RESULTS

Overall, 190 individuals were included, 72 (37.9%) with acute, 20 (10.5%) with very early, and 98 (51.6%) with recent HIV infection. Although all DRM detected in plasma appeared in archived proviral DNA, 9 high-frequency mutations were only detected in HIV DNA. These included 3 NRTI mutations, 4 NNRTI mutations, 1 PI mutation, and 1 H221Y (associated rilpivirine resistance) mutation. When considering DRM <20%, 11 NNRTI, 7 NRTI, 6 PI, and 3 F227L (associated doravirine resistance) mutations were found exclusively in HIV DNA. Interestingly, although 2 high-frequency M184V appeared in both DNA and RNA, low-frequency M184I were exclusive to HIV DNA (n = 6). No participants experienced virologic failure after initiating ART during the median 25.39 ± 3.13 months of follow-up on treatment.

CONCLUSION

Although most high-frequency DRMs were consistently detected in HIV RNA and HIV DNA, the presence of low-frequency DRM in proviral DNA may be relevant for clinicians because these mutations could become dominant under drug selection pressure.

Predictors of Human Immunodeficiency Virus Pre-Exposure Prophylaxis (PrEP) Uptake in a Sexual Health Clinic With Rapid PrEP Initiation

Background

Improved pre-exposure prophylaxis (PrEP) uptake is essential for human immunodeficiency virus (HIV) prevention initiatives. Offering PrEP at the time of HIV and sexually transmitted infection (STI) testing can improve uptake. We offered rapid PrEP initiation in a sexual health clinic and assessed predictors of PrEP interest, initiation, linkage, and retention.

Methods

Between November 2018 and February 2020, PrEP-eligible individuals who presented to a sexual health clinic were offered a free 30-day supply of PrEP plus linkage to continued PrEP care. Univariable and multivariable analyses of demographic and HIV risk data were conducted to determine predictors of PrEP uptake.

Results

Of 1259 adults who were eligible for PrEP (99.7% male, 42.7% White, 36.2% Hispanic), 456 were interested in PrEP, 249 initiated PrEP, 209 were linked, and 67 were retained in care. Predictors of PrEP interest included younger age (P < .01), lower monthly income (P = .01), recreational drug use (P = .02), and a greater number of sexual partners (P < .01). Negative predictors of PrEP initiation included lower monthly income (P = .04), testing positive for chlamydia (P = .04), and exchanging money for sex (P = .01). Negative predictors of linkage included self-identifying as Black (P = .03) and testing positive for an STI (P < .01). Having health insurance positively predicted both linkage (P < .01) and retention (P < .03).

Conclusions

A minority of PrEP-eligible HIV and STI testers initiated PrEP when offered, suggesting that easy PrEP access in sexual health clinics alone may not improve uptake. Predictors of uptake included established HIV risk factors and markers of higher socioeconomic status, suggesting that those aware of their risk and with the means to utilize health services engaged best with this model.

Direct Access for Patients to Diagnostic Testing and Results Using eHealth: Systematic Review on eHealth and Diagnostics

BACKGROUND

The number of people with chronic diseases and the subsequent pressure on health care is increasing. eHealth technology for diagnostic testing can contribute to more efficient health care and lower workload.

OBJECTIVE

This systematic review examines the available methods for direct web-based access for patients to diagnostic testing and results in the absence of a health care professional in primary care.

METHODS

We searched the PubMed, Embase, Web of Sciences, Cochrane Library, Emcare, and Academic Search Premier databases in August 2019 and updated in July 2021. The included studies focused on direct patient access to web-based triage leading to diagnostic testing, self-sampling or testing, or web-based communication of test results. A total of 45 studies were included. The quality was assessed using the Mixed Methods Appraisal Tool.

RESULTS

Most studies had a quantitative descriptive design and discussed a combination of services. Diagnostic test services mainly focused on sexually transmitted infections. Overall, the use was high for web-based triage (3046/5000, >50%, who used a triage booked a test), for self-sampling or self-testing kits (83%), and the result service (85%). The acceptability of the test services was high, with 81% preferring home-based testing over clinic-based testing. There was a high rate of follow-up testing or treatment after a positive test (93%).

CONCLUSIONS

The results show that direct access to testing and result services had high use rates, was positively evaluated, and led to high rates of follow-up treatment. More research on cost-effectiveness is needed to determine the potential for other diseases. Direct access to diagnostic testing can lower the threshold for testing in users, potentially increase efficiency, and lower the workload in primary care.

Rapid Antiretroviral Therapy Among Individuals With Acute and Early HIV

HIV transmission is increased during acute and early HIV (AEH). Rapid antiretroviral therapy may shorten the duration of infectivity. We show rapid antiretroviral therapy in AEH is acceptable and effective, with 69.0% of participants starting ART within 7 days of HIV diagnosis disclosure, and 88.1% achieving suppression by 48 weeks.

Effective HIV Molecular Surveillance Requires Identification of Incident Cases of Infection

BACKGROUND

Ending the HIV epidemic requires knowledge of key drivers of spread of HIV infection.

METHODS

Between 1996 and 2018, 1119 newly and previously diagnosed, therapy-naïve persons with HIV (PWH) from San Diego were followed. A genetic distance-based network was inferred using pol sequences, and genetic clusters grew over time through linkage of sequences from newly observed infections. Cox proportional hazards models were used to identify factors associated with the rate of growth. These results were used to predict the impact of a hypothetical intervention targeting PWH with incident infection. Comparison was made to the CDC EHE molecular surveillance strategy, which prioritizes clusters recently linked to all new HIV diagnoses and does not incorporate data on incident infections.

RESULTS

Overall, 219 genetic linkages to incident infections were identified over a median follow-up of 8.8 years. Incident cluster growth was strongly associated with proportion of PWH in the cluster who themselves had incident infection. (HR 44.09; 95% CI: 17.09, 113.78). The CDC EHE molecular surveillance strategy identified 11 linkages to incident infections a genetic distance threshold of 0.5%, and 24 linkages at 1.5%.

CONCLUSIONS

Over the past two decades, incident infections drove incident HIV cluster growth in San Diego. The current CDC EHE molecular detection and response strategy would not have identified most transmission events arising from those with incident infection in San Diego. Molecular surveillance that includes detection of incident cases will provide a more effective strategy for EHE.

Online self-sampling kits to screen multipartner MSM for HIV and other STIs: participant characteristics and factors associated with kit use in the first 3 months of the MemoDepistages programme, France, 2018

OBJECTIVES

In 2017, to reduce the proportion of men who have sex with men (MSM) in the undiagnosed HIV population in France (38%), HIV screening is advised each 3 months and STI screening is advised each year in multipartner MSM. Despite the range of testing solutions, over 40% of MSM were not tested for HIV and over 50% for STIs in the past year. Based on international experiments that offer screening solutions via online advertising, the French National Health Agency launched a programme (MemoDepistages) to provide a free self-sampling kit (SSK) for HIV and STIs. This article analyses the sociodemographic and behavioural characteristics of MSM in terms of kit acceptance and sample return.

METHODS

Participants were registered for the programme online after ordering an SSK. The study included men aged over 18 years, living in one of the four selected French regions, and willing to disclose their postal and email address; they had health insurance, acknowledged more than one male partner in the past year, indicated a seronegative or unknown HIV status and were not taking medically prescribed pre-exposure prophylaxis drugs. Samples were collected by users and posted directly to the laboratory. Characteristics associated with kit acceptance and sample return were analysed using logistic regression.

RESULTS

Overall, 7158 eligible MSM were offered to participate in the programme, with 3428 ordering the kit (47.9%) and 1948 returning their sample, leading to a return rate of 56.8% and an overall participation rate of 27.2%. Acceptance and return rates were strongly associated with sociodemographic characteristics, mainly education level but not with behavioural characteristics. Non-college graduates had lower acceptance (44.2%) and return rates (47.7%).

CONCLUSION

The programme rapidly recruited a large number of MSM. It removed geographical inequalities related to screening access.

Genetic Network Analysis to Assess the Risk of Human Immunodeficiency Virus Transmission Among Men Who Have Sex With Men Seeking Partners on the Internet

BACKGROUND

Online partner seeking (OPS) among men who have sex with men (MSM) is associated with increased risk behavior including frequency of unprotected anal intercourse, number of partners, and incidence of sexually transmitted infections (STIs). However, the impact on transmission of human immunodeficiency virus (HIV) is uncertain.

METHODS

MSM diagnosed with acute and early HIV infection were recruited from the Primary Infection Resource Consortium. HIV transmission events in the year following infection were inferred using estimated date of infection combined with genetic network analysis with linked sequences defined as ≤0.015 sequences/site difference in the HIV type 1 (HIV-1) pol coding region. Participants completed a detailed baseline questionnaire including reported methods of meeting sexual partners, including OPS, in the prior 3 months, and regression was performed with inferred transmission as the outcome.

RESULTS

From 147 MSM who completed the questionnaire, there were an associated 20 inferred HIV transmissions. No association with OPS was found (odds ratio, 0.64 [95% confidence interval, .24-1.69]; P = .37), though individuals who reported OPS were more likely to have reported a greater number of partners (P = .003) and prior STIs (P = .002). Geospatial analysis did not indicate that OPS was associated with increased geographical reach of the user (P = .68).

CONCLUSIONS

Individuals reporting OPS did not have increased odds of inferred HIV-1 transmission in the year following infection using genetic linkage analysis despite apparently increased risk behavior. OPS also did not increase the geographic distance between genetically clustered HIV infections, suggesting that individuals mainly use the internet to meet partners in their local region.

Optimizing Screening for HIV

BACKGROUND

The HIV epidemic is unevenly distributed throughout the United States, even within neighborhoods. This study evaluated how effectively current testing approaches reached persons at risk for HIV infection across San Diego (SD) County, California.

METHODS

HIV case and testing data, sexually transmitted infection (STI) data, and sociodemographic data for SD County were collected from the SD Health and Human Services Agency and the "Early Test" community-based HIV screening program between 1998 and 2016. Relationships between HIV diagnoses, HIV prevalence, and STI diagnoses with screening at the ZIP code level were evaluated.

RESULTS

Overall, 379 074 HIV tests were performed. The numbers of HIV tests performed on persons residing in a ZIP code or region overall strongly correlated with prevalent HIV cases (R 2 = .714), new HIV diagnoses (R 2 = .798), and STI diagnoses (R 2 = .768 [chlamydia], .836 [gonorrhea], .655 [syphilis]) in those regions. ZIP codes with the highest HIV prevalence had the highest number of tests per resident and fewest number of tests per diagnosis. Even though most screening tests occurred at fixed venues located in high-prevalence areas, screening of residents from lower-prevalence areas was mostly proportional to the prevalence of HIV and rates of new HIV and STI diagnoses in those locales.

CONCLUSIONS

This study supported the ability of a small number of standalone testing centers to reach at-risk populations dispersed across SD County. These methods can also be used to highlight geographic areas or demographic segments that may benefit from more intensive screening.

The use of technology to find sexual health information online among men who have sex with men in Hanoi, Vietnam, 2016

In an era where mobile phones and computers are ubiquitous, technology-based interventions to reduce HIV and other sexually transmitted infections (STIs) have great potential to reach high-risk groups, including men who have sex with men (MSM). This study aimed to examine technology usage to find sexual health information online among MSM in Hanoi, Vietnam. A cross-sectional study of 205 MSM in Hanoi was conducted from February to May 2016. Overall, 50.7% of participants reported having used a smartphone, computer, or tablet to find HIV/STI testing locations in the past year, and 75.1% reported having used such devices to find other HIV/STI information online. Unemployment (adjusted prevalence ratio [aPR]: 1.13, 95%CI: 1.00-1.28) and having been tested for HIV (aPR: 1.27, 95%CI: 1.07-1.51) were significantly associated with using technology to find online sexual health information. MSM who had ever exchanged sex for money or drugs (aPR: 0.80; 95%CI: 0.68-0.94) were less likely to use technology to find sexual health information online. Technology is a promising platform for HIV/STI prevention programs among MSM, with the potential to reach different subgroups. Further efforts to develop technology-based interventions tailored to the needs of the MSM communities in Hanoi and to encourage MSM who were not currently seeking sexual health information and testing services online to do so are necessary.

Observational study of factors associated with return of home sampling kits for sexually transmitted infections requested online in the UK

OBJECTIVES

To investigate factors associated with the return of home sampling kits for sexually transmitted infections (STIs).

SETTING

Online STI testing service offered to the residents of Birmingham and Solihull.

PARTICIPANTS

All patients requesting STI home sampling kits via the Umbrella sexual health service website between 15 July 2016 and 14 December 2016.

INTERVENTIONS

Associations between data collected at online registration and the rate of return of STI home sampling kits within 30 days of request was assessed.

RESULTS

A total of 5310 kits were requested, of which 3099 (58.4%) were returned to the medical microbiology laboratory. On multivariable analysis, women and men who have sex with men were similarly likely to return their sampling kits (adjusted OR (OR_adj) 1.06, 95% CI 0.86 to 1.30), while heterosexual men were significantly less likely to return their sampling kits (OR_adj 0.63, 95% CI 0.55 to 0.72, p<0.001 vs women). Patients reporting symptoms were also less likely to return kits (OR_adj 0.77, 95% CI 0.67 to 0.89, p=0.001 vs asymptomatic patients). Kits that were delivered to the patient's home, rather than to a clinic or pharmacy (p<0.001), and those requested from less economically deprived neighbourhoods (p=0.029) were significantly more likely to be returned.

CONCLUSION

STI self-sampling testing kits delivered to patients' homes are most likely to be returned. Heterosexual men and those from more economically deprived areas are the less likely groups to return the kits. Further research on the barriers to return self-sampling STI testing kits of these subgroups of patients is warranted.

TRIAL REGISTRATION NUMBER

Registered with R&D department at University Hospitals Birmingham; CARMS-13551.

No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men

During primary HIV infection, the presence of minority drug resistance mutations (DRM) may be a consequence of sexual transmission, de novo mutations, or technical errors in identification. Baseline blood samples were collected from 24 HIV-infected antiretroviral-naive, genetically and epidemiologically linked source and recipient partners shortly after the recipient's estimated date of infection. An additional 32 longitudinal samples were available from 11 recipients. Deep sequencing of HIV reverse transcriptase (RT) was performed (Roche/454), and the sequences were screened for nucleoside and nonnucleoside RT inhibitor DRM. The likelihood of sexual transmission and persistence of DRM was assessed using Bayesian-based statistical modeling. While the majority of DRM (>20%) were consistently transmitted from source to recipient, the probability of detecting a minority DRM in the recipient was not increased when the same minority DRM was detected in the source (Bayes factor [BF] = 6.37). Longitudinal analyses revealed an exponential decay of DRM (BF = 0.05) while genetic diversity increased. Our analysis revealed no substantial evidence for sexual transmission of minority DRM (BF = 0.02). The presence of minority DRM during early infection, followed by a rapid decay, is consistent with the "mutation-selection balance" hypothesis, in which deleterious mutations are more efficiently purged later during HIV infection when the larger effective population size allows more efficient selection. Future studies using more recent sequencing technologies that are less prone to single-base errors should confirm these results by applying a similar Bayesian framework in other clinical settings.IMPORTANCE The advent of sensitive sequencing platforms has led to an increased identification of minority drug resistance mutations (DRM), including among antiretroviral therapy-naive HIV-infected individuals. While transmission of DRM may impact future therapy options for newly infected individuals, the clinical significance of the detection of minority DRM remains controversial. In the present study, we applied deep-sequencing techniques within a Bayesian hierarchical framework to a cohort of 24 transmission pairs to investigate whether minority DRM detected shortly after transmission were the consequence of (i) sexual transmission from the source, (ii) de novo emergence shortly after infection followed by viral selection and evolution, or (iii) technical errors/limitations of deep-sequencing methods. We found no clear evidence to support the sexual transmission of minority resistant variants, and our results suggested that minor resistant variants may emerge de novo shortly after transmission, when the small effective population size limits efficient purge by natural selection.

Sexual Partner Concurrency Among Partners Reported by MSM with Recent HIV Infection

We examined concurrency among sexual partners reported by men who have sex with men (MSM) with recent (acute or early) HIV infection in San Diego, California (2002-2015). Partners overlapping in time in the past 3 months were considered concurrent. Logistic generalized linear mixed models were used to identify factors associated with concurrency at the partner-level. 56% (388/699) of partners were concurrent to ≥1 other partner. The odds of concurrency were higher among partners >10 years younger than the participant (vs. within 10 years of age) [adjusted odds ratio (AOR) = 2.22, 95% confidence interval (CI) 1.09-4.52], longer term partners (AOR per month = 1.02, 95% CI 1.01-1.03), and partners met online (AOR = 1.56, 95% CI 0.98-2.48). Concurrency is common among partners of recently HIV-infected MSM. Tailored HIV prevention strategies for MSM with older partners, longer term partners, and partners met online may help minimize the potential impact of concurrency on HIV transmission.

Intrasubtype B HIV-1 Superinfection Correlates with Delayed Neutralizing Antibody Response

Understanding whether the neutralizing antibody (NAb) response impacts HIV-1 superinfection and how superinfection subsequently modulates the NAb response can help clarify correlates of protection from HIV exposures and better delineate pathways of NAb development. We examined associations between the development of NAb and the occurrence of superinfection in a well-characterized, antiretroviral therapy (ART)-naive, primary infection cohort of men who have sex with men. Deep sequencing was applied to blood plasma samples from the cohort to detect cases of superinfection. We compared the NAb activity against autologous and heterologous viruses between 10 participants with intrasubtype B superinfection and 19 monoinfected controls, matched to duration of infection and risk behavior. Three to 6 months after primary infection, individuals who would later become superinfected had significantly weaker NAb activity against tier 1 subtype B viruses (P = 0.003 for SF-162 and P = 0.017 for NL4-3) and marginally against autologous virus (P = 0.054). Lower presuperinfection NAb responses correlated with weaker gp120 binding and lower plasma total IgG titers. Soon after superinfection, the NAb response remained lower, but between 2 and 3 years after primary infection, NAb levels strengthened and reached those of controls. Superinfecting viruses were typically not susceptible to neutralization by presuperinfection plasma. These observations suggest that recently infected individuals with a delayed NAb response against primary infecting and tier 1 subtype B viruses are more susceptible to superinfection.IMPORTANCE Our findings suggest that within the first year after HIV infection, a relatively weak neutralizing antibody response against primary and subtype-specific neutralization-sensitive viruses increases susceptibility to superinfection in the face of repeated exposures. As natural infection progresses, the immune response strengthens significantly in some superinfected individuals. These findings will inform HIV vaccine design by providing testable correlates of protection from initial HIV infection.

Increased HIV-1 superinfection risk in carriers of specific human leukocyte antigen alleles

OBJECTIVE

The aim of this study was to characterize the demographic, behavioural, clinical and immunogenetic determinants of HIV-1 superinfection in a high-risk cohort of MSM.

DESIGN

A retrospective cohort study of prospectively followed MSM.

METHODS

Ninety-eight MSM with acute or early HIV-1 monoinfection were followed for a median of 15.6 months. Demographic and human leukocyte antigen (HLA) genotype data were collected at enrolment. Sexual behaviour, clinical and the infection status (monoinfection or superinfection) data were recorded at each visit (at enrolment and thereafter at a median of 4.2-month intervals). HIV-1 superinfection risk was determined by Cox regression and Kaplan-Meier survival analysis.

RESULTS

Ten individuals (10.2%) had superinfection during follow-up. Cox regression did not show significantly increased superinfection risk for individuals with an increased amount of condomless anal intercourse, lower CD4 T-cell count or higher viral load, but higher number of sexual contacts demonstrated a trend towards significance [hazard ratio, 4.74; 95% confidence interval (95% CI), 0.87-25.97; P = 0.073]. HLA-A*29 (hazard ratio, 4.10; 95% CI, 0.88-14.76; P = 0.069), HLA-B*35 (hazard ratio, 4.64; 95% CI, 1.33-18.17; P = 0.017), HLA-C*04 (hazard ratio, 5.30; 95% CI, 1.51-20.77; P = 0.010), HLA-C*16 (hazard ratio, 4.05; 95% CI, 0.87-14.62; P = 0.071), HLA-DRB1*07 (hazard ratio, 3.29; 95% CI, 0.94-12.90; P = 0.062) and HLA-DRB1*08 (hazard ratio, 15.37; 95% CI, 2.11-79.80; P = 0.011) were associated with an increased risk of superinfection at α = 0.10, whereas HLA-DRB1*11 was associated with decreased superinfection risk (hazard ratio, 0.13; 95% CI, 0.00-1.03; P = 0.054).

CONCLUSION

HLA genes may, in part, elucidate the genetic basis of differential superinfection risk, and provide important information for the development of efficient prevention and treatment strategies of HIV-1 superinfection.

Risk profile and HIV testing outcomes of women undergoing community-based testing in San Diego 2008-2014

Women comprised 19% of new HIV diagnoses in the United States in 2014, with significant racial and ethnic disparities in infection rates. This cross-sectional analysis of women enrolled in a cohort study compares demographics, risk behaviour, and sexually transmitted infections (STI) in those undergoing HIV testing in San Diego County. Data from the most recent screening visit of women undergoing voluntary HIV screening April 2008 -July 2014 was used. HIV diagnosis, risk behaviour and self-reported STIs were compared among women aged ≤24, 25-49, and ≥50, as well as between HIV-infected and uninfected women and between Hispanic and non-Hispanic women. Among the 2535 women included, Hispanic women were less likely than other women to report unprotected vaginal intercourse (p = 0.026) or stimulant drug use (p = 0.026), and more likely to report one or fewer partners (p < 0.0001), but also more likely to report sex with an HIV-infected individual (p = 0.027). New HIV infection was significantly more prevalent among Hispanic women (1.6% vs. 0.2%; p < 0.001). Hispanic women were more likely than other women to be diagnosed with HIV despite significantly lower rates of risk behaviour. Culturally specific risk reduction interventions for Hispanic women should focus on awareness of partner risk and appropriate testing.

Partner services in adults with acute and early HIV infection

BACKGROUND

To examine the yield of HIV partner services provided to persons newly diagnosed with acute and early HIV infection (AEH) in San Diego, United States.

DESIGN

Observational cohort study.

METHODS

The study investigated the yield (i.e. number of new HIV and AEH diagnoses, genetically linked partnerships and high-risk uninfected partners) of partner services (confidential contact tracing) for individuals with AEH enrolled in the San Diego Primary Infection Resource Consortium 1996-2014.

RESULTS

A total of 107 of 574 persons with AEH (19%; i.e. index cases) provided sufficient information to recruit 119 sex partners. Fifty-seven percent of the 119 recruited partners were HIV infected, and 33% of the 119 were newly HIV diagnosed. Among those newly HIV diagnosed, 36% were diagnosed during AEH. There were no significant demographic or behavioral risk differences between HIV-infected and HIV-uninfected recruited partners. Genetic sequences were available for both index cases and partners in 62 partnerships, of which 61% were genetically linked. Partnerships in which both index case and partner enrolled within 30 days were more likely to yield a new HIV diagnosis (P = 0.01) and to be genetically linked (P < 0.01).

CONCLUSION

Partner services for persons with AEH within 30 days of diagnosis represents an effective tool to find HIV-unaware persons, including those with AEH who are at greatest risk of HIV transmission.

Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations

Even when antiretroviral therapy (ART) is started early after infection, HIV DNA might persist in the central nervous system (CNS), possibly contributing to inflammation, brain damage and neurocognitive impairment. Paired blood and cerebrospinal fluid (CSF) were collected from 16 HIV-infected individuals on suppressive ART: 9 participants started ART <4 months of the estimated date of infection (EDI) ("early ART"), and 7 participants started ART >14 months after EDI ("late ART"). For each participant, neurocognitive functioning was measured by Global Deficit Score (GDS). HIV DNA levels were measured in peripheral blood mononuclear cells (PBMCs) and CSF cell pellets by droplet digital (dd)PCR. Soluble markers of inflammation (sCD163, IL-6, MCP-1, TNF-α) and neuronal damage (neurofilament light [NFL]) were measured in blood and CSF supernatant by immunoassays. HIV-1 partial C2V3 env deep sequencing data (Roche 454) were obtained for 8 paired PBMC and CSF specimens and used for phylogenetic and compartmentalization analysis. Median exposure to ART at the time of sampling was 2.6 years (IQR: 2.2-3.7) and did not differ between groups. We observed that early ART was significantly associated with lower molecular diversity of HIV DNA in CSF (p<0.05), and lower IL-6 levels in CSF (p = 0.02), but no difference for GDS, NFL, or HIV DNA detectability compared to late ART. Compartmentalization of HIV DNA populations between CSF and blood was detected in 6 out of 8 participants with available paired HIV DNA sequences (2 from early and 4 from late ART group). Phylogenetic analysis confirmed the presence of monophyletic HIV DNA populations within the CSF in 7 participants, and the same population was repeatedly sampled over a 5 months period in one participant with longitudinal sampling. Such compartmentalized provirus in the CNS needs to be considered for the design of future eradication strategies and might contribute to the neuropathogenesis of HIV.

Concurrency and HIV transmission network characteristics among MSM with recent HIV infection

OBJECTIVE

Sexual partner concurrency is common among MSM and may increase the probability of HIV transmission during recent (acute or early) infection. We examined the relationship between concurrency and HIV transmission network characteristics (proxies for HIV transmission) among MSM with recent HIV infection.

DESIGN

Observational study integrating behavioral, clinical, and molecular epidemiology.

METHODS

We inferred a partial HIV transmission network using 986 HIV-1 pol sequences obtained from HIV-infected individuals in San Diego, California (1996-2015). We further analyzed data from 285 recently HIV-infected MSM in the network who provided information on up to three sexual partners in the past 3 months, including the timing of intercourse with each partner. Concurrency was defined as sexual partners overlapping in time. Logistic and negative binomial regressions were used to investigate the link between concurrency and HIV transmission network characteristics (i.e. clustering and degree or number of connections to others in the network) among these MSM.

RESULTS

Of recently HIV-infected MSM (n = 285), 54% reported concurrent partnerships and 54% were connected by at least one putative transmission link to others (i.e. clustered) in the network (median degree = 1.0; interquartile range: 0.0-3.0). Concurrency was positively associated with HIV transmission network clustering (adjusted odds ratio = 1.83, 95% confidence interval: 1.08, 3.10) and degree (adjusted incidence rate ratio = 1.48, 95% confidence interval: 1.02, 2.15).

CONCLUSION

Our findings provide empirical evidence consistent with the hypothesis that concurrency facilitates HIV transmission during recent infection. Interventions to mitigate the impact of concurrency on HIV transmission may help curb the HIV epidemic among MSM.

Clear Links Between Starting Methamphetamine and Increasing Sexual Risk Behavior: A Cohort Study Among Men Who Have Sex With Men

BACKGROUND

It remains unclear if methamphetamine is merely associated with high-risk behavior or if methamphetamine use causes high-risk behavior. Determining this would require a randomized controlled trial, which is clearly not ethical. A possible surrogate would be to investigate individuals before and after starting the use of methamphetamine.

METHODS

We performed a cohort study to analyze recent self-reported methamphetamine use and sexual risk behavior among 8905 men who have sex with men (MSM) receiving the "Early Test," a community-based HIV screening program in San Diego, CA, between April 2008 and July 2014 (total 17,272 testing encounters). Sexual risk behavior was evaluated using a previously published risk behavior score [San Diego Early Test (SDET) score] that predicts risk of HIV acquisition.

RESULTS

Methamphetamine use during the last 12 months (hereafter, recent-meth) was reported by 754/8905 unique MSM (8.5%). SDET scores were significantly higher in the 754 MSM with recent-meth use compared with the 5922 MSM who reported that they have never used methamphetamine (P < 0.001). Eighty-two repeat testers initiated methamphetamine between testing encounter, with significantly higher SDET scores after starting methamphetamine [median 5 (interquartile range, 2-7) at recent-meth versus median 3 (interquartile range, 0-5) at never-meth; P < 0.001, respectively].

CONCLUSIONS

Given the ethical impossibility of conducting a randomized controlled trial, the results presented here provide the strongest evidence yet that initiation of methamphetamine use increases sexual risk behavior among HIV-uninfected MSM. Until more effective prevention or treatment interventions are available for methamphetamine users, HIV-uninfected MSM who use methamphetamine may represent ideal candidates for alternative effective prevention interventions (ie, preexposure prophylaxis).

Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples

The ability to study rapidly evolving viral populations has been constrained by the read length of next-generation sequencing approaches and the sampling depth of single-genome amplification methods. Here, we develop and characterize a method using Pacific Biosciences' Single Molecule, Real-Time (SMRT®) sequencing technology to sequence multiple, intact full-length human immunodeficiency virus-1 env genes amplified from viral RNA populations circulating in blood, and provide computational tools for analyzing and visualizing these data.

A practical online tool to estimate antiretroviral coverage for HIV infected and susceptible populations needed to reduce local HIV epidemics

It remains unclear what proportions of HIV-infected and uninfected people should receive effective antiretroviral therapy (ART) to control local HIV epidemics. We developed a flexible model to evaluate the impact of treatment as prevention (TasP) and pre-exposure prophylaxis (PrEP) on HIV incidence in local communities. We evaluated this tool for determining what TasP and PrEP targets are needed to substantially reduce the HIV epidemic in San Diego, which is predominately comprised of men who have sex with men. By increasing the proportion of HIV-infected individuals on ART from 30% to 50%, 686 new infections would be prevented over five years in San Diego. By providing PrEP to 30% of MSM to the age group that account for 90% of local HIV incident cases (21-52 years), we could prevent 433 infections over five years. When combining these initiatives, a PrEP coverage rate of 40% and TasP coverage rate of 34% would be expected to decrease the number of new infections by over half in one year. This online tool is designed to help local public health planners and policy makers to estimate program outcomes and costs that may lead to better control of their local HIV epidemics.

Prevalence of Transmitted HIV Drug Resistance Among Recently Infected Persons in San Diego, CA 1996-2013

BACKGROUND

Transmitted drug resistance (TDR) remains an important concern when initiating antiretroviral therapy (ART). Here, we describe the prevalence and phylogenetic relationships of TDR among ART-naive, HIV-infected individuals in San Diego from 1996 to 2013.

METHODS

Data were analyzed from 496 participants of the San Diego Primary Infection Cohort who underwent genotypic resistance testing before initiating therapy. Mutations associated with drug resistance were identified according to the WHO-2009 surveillance list. Network and phylogenetic analyses of the HIV-1 pol sequences were used to evaluate the relationships of TDR within the context of the entire cohort.

RESULTS

The overall prevalence of TDR was 13.5% (67/496), with an increasing trend over the study period (P = 0.005). TDR was predominantly toward nonnucleoside reverse transcriptase inhibitors (NNRTIs) [8.5% (42/496)], also increasing over the study period (P = 0.005). By contrast, TDR to protease inhibitors and nucleos(t)ide reverse transcriptase inhibitors were 4.4% (22/496) and 3.8% (19/496), respectively, and did not vary with time. TDR prevalence did not differ by age, gender, race/ethnicity, or risk factors. Using phylogenetic analysis, we identified 52 transmission clusters, including 8 with at least 2 individuals sharing the same mutation, accounting for 23.8% (16/67) of the individuals with TDR.

CONCLUSIONS

Between 1996 and 2013, the prevalence of TDR significantly increased among recently infected ART-naive individuals in San Diego. Around one-fourth of TDR occurred within clusters of recently infected individuals. These findings highlight the importance of baseline resistance testing to guide selection of ART and for public health monitoring.

HIV Infection Rates and Risk Behavior among Young Men undergoing community-based Testing in San Diego

Approximately 80% of new HIV infections in the United States occur in men. Four out of five men diagnosed with HIV infection are men who have sex with men (MSM), with an increasing proportion of young MSM (i.e. ≤24 years of age). We performed a retrospective analysis 11,873 cisgender men participating in a community based HIV screening program in San Diego between 2008 and 2014 to characterize the HIV prevalence and sexual risk behaviors among young men. In young heterosexual men HIV prevalence was lower compared to heterosexual men between 25 and 49 years of age (0.3% vs. 1.4%, p = 0.043). Among young MSM, HIV prevalence was 5.5%, per test positivity rate 3.6%, and HIV incidence 3.4 per 100 person years (95% CI 2.2–5.4). Per test positivity rate (p = 0.008) and incidence (p < 0.001) were significantly higher among young MSM than among MSM above 24-years of age. Young MSM diagnosed with HIV infection reported significantly more serodiscordant condomless anal intercourse, bacterial sexually transmitted infections, and higher rates of methamphetamine and gamma hydroxybutyrate use when compared to young MSM who tested negative. In conclusion, young MSM are particularly vulnerable to HIV infection and may represent ideal candidates for targeted prevention interventions that increase testing uptake and/or decrease the risk of acquiring HIV infection.

Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California

BACKGROUND

Because recently infected individuals disproportionately contribute to the spread of human immunodeficiency virus (HIV), we evaluated the impact of a primary HIV screening program (the Early Test) implemented in San Diego.

METHODS

The Early Test program used combined nucleic acid and serology testing to screen for primary infection targeting local high-risk individuals. Epidemiologic, HIV sequence, and geographic data were obtained from the San Diego County Department of Public Health and the Early Test program. Poisson regression analysis was performed to determine whether the Early Test program was temporally and geographically associated with changes in incident HIV diagnoses. Transmission chains were inferred by phylogenetic analysis of sequence data.

RESULTS

Over time, a decrease in incident HIV diagnoses was observed proportional to the number primary HIV infections diagnosed in each San Diego region (P < .001). Molecular network analyses also showed that transmission chains were more likely to terminate in regions where the program was marketed (P = .002). Although, individuals in these zip codes had infection diagnosed earlier (P = .08), they were not treated earlier (P = .83).

CONCLUSIONS

These findings suggests that early HIV diagnoses by this primary infection screening program probably contributed to the observed decrease in new HIV diagnoses in San Diego, and they support the expansion and evaluation of similar programs.

HIV Transmission Networks in the San Diego-Tijuana Border Region

BACKGROUND

HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego-Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sides of the border.

METHODS

We gathered sociodemographic, geographic, clinical, and viral sequence data from HIV infected individuals participating in ten studies in the San Diego-Tijuana border region. Phylogenetic and network analysis was performed to infer putative relationships between HIV sequences. Correlates of identified clusters were evaluated and spatiotemporal relationships were explored using Bayesian phylogeographic analysis.

FINDINGS

After quality filtering, 843 HIV sequences with associated demographic data and 263 background sequences from the region were analyzed, and 138 clusters were inferred (2-23 individuals). Overall, the rate of clustering did not differ by ethnicity, residence, or sex, but bisexuals were less likely to cluster than heterosexuals or men who have sex with men (p = 0.043), and individuals identifying as white (p ≤ 0.01) were more likely to cluster than other races. Clustering individuals were also 3.5 years younger than non-clustering individuals (p < 0.001). Although the sampled San Diego and Tijuana epidemics were phylogenetically compartmentalized, five clusters contained individuals residing on both sides of the border.

INTERPRETATION

This study sampled ~ 7% of HIV infected individuals in the border region, and although the sampled networks on each side of the border were largely separate, there was evidence of persistent bidirectional cross-border transmissions that linked risk groups, thus highlighting the importance of the border region as a "melting pot" of risk groups.

FUNDING

NIH, VA, and Pendleton Foundation.

Risk Behavior and Sexually Transmitted Infections Among Transgender Women and Men Undergoing Community-Based Screening for Acute and Early HIV Infection in San Diego

The transgender community represents an understudied population in the literature. The objective of this study was to compare risk behavior, and HIV and sexually transmitted infection (STI) rates between transgender women and transgender men undergoing community-based HIV testing.With this retrospective analysis of a cohort study, we characterize HIV infection rates as well as reported risk behaviors and reported STI in 151 individual transgender women and 30 individual transgender men undergoing community based, voluntary screening for acute and early HIV infection (AEH) in San Diego, California between April 2008 and July 2014.HIV positivity rate was low for both, transgender women and transgender men undergoing AEH screening (2% and 3%, respectively), and the self-reported STI rate for the prior 12 months was 13% for both. Although transgender women appeared to engage in higher rates of risk behavior overall, with 69% engaged in condomless receptive anal intercourse (CRAI) and 11% engaged in sex work, it is important to note that 91% of transgender women reported recent sexual intercourse, 73% had more than 1 sexual partner, 63% reported intercourse with males, 37% intercourse with males and females, and 30% had CRAI.Our results indicate that in some settings rates of HIV infection, as well as rates of reported STIs and sexual risk behavior in transgender men may resemble those found in transgender women. Our findings support the need for comprehensive HIV prevention in both, transgender women and men.

Repeat HIV-testing is associated with an increase in behavioral risk among men who have sex with men: a cohort study

BACKGROUND

The Center for Disease Control and Prevention recommends that high-risk groups, like sexually active men who have sex with men (MSM), receive HIV testing and counseling at least annually. The objective of this study was to investigate the relationship between voluntary repeat HIV testing and sexual risk behavior in MSM receiving rapid serologic and nucleic acid amplification testing.

METHODS

We performed a cohort study to analyze reported risk behavior among MSM receiving the "Early Test", a community-based, confidential acute and early HIV infection screening program in San Diego, California, between April 2008 and July 2014. The study included 8,935 MSM receiving 17,333 "Early Tests". A previously published risk behavior score for HIV acquisition in MSM (i.e. Menza score) was chosen as an outcome to assess associations between risk behaviors and number of repeated tests.

RESULTS

At baseline, repeat-testers (n = 3,202) reported more male partners and more condomless receptive anal intercourse (CRAI) when compared to single-testers (n = 5,405, all P <0.001). In 2,457 repeat testers there was a strong association observed between repeated HIV tests obtained and increased risk behavior, with number of male partners, CRAI with high risk persons, non-injection stimulant drug use, and sexually transmitted infections all increasing between the first and last test. There was also a linear increase of risk (i.e. high Menza scores) with number of tests up to the 17th test. In the multivariable mixed effects model, more HIV tests (OR = 1.18 for each doubling of the number of tests, P <0.001) and younger age (OR = 0.95 per 5-year increase, P = 0.006) had significant associations with high Menza scores.

CONCLUSIONS

This study found that the highest risk individuals for acquiring HIV (e.g. candidates for antiretroviral pre-exposure prophylaxis) can be identified by their testing patterns. Future studies should delineate causation versus association to improve prevention messages delivered to repeat testers during HIV testing and counseling sessions.

Seminal Shedding of CMV and HIV Transmission among Men Who Have Sex with Men

As in many urban areas in the United States, the largest burden of the HIV epidemic in San Diego is borne by men who have sex with men (MSM). Using data from well-characterized HIV transmitting and non-transmitting partner pairs of MSM in San Diego, we calculated the population attributable risk (PAR) of HIV transmissions for different co-infections common among MSM in this area. We found that over a third of HIV transmissions could be potentially attributed to genital shedding of cytomegalovirus (CMV) (111 transmission events), compared to 21% potentially attributed to bacterial sexually transmitted infections (STI) (62 events) and 17% to herpes simplex virus type-2 (HSV-2) (51 events). Although our study cannot infer causality between the described associations and is limited in sample size, these results suggest that interventions aimed at reducing CMV shedding might be an attractive HIV prevention strategy in populations with high prevalence of CMV co-infection.

Risk Factors for Acute and Early HIV Infection Among Men Who Have Sex With Men (MSM) in San Diego, 2008 to 2014: A Cohort Study

The objectives of this study were to identify risk factors associated with acute and early HIV infection (AEH) among men who have sex with men (MSM) undergoing community HIV testing and to compare demographics in those diagnosed with AEH with those diagnosed at chronic stage of HIV infection.In this retrospective cohort study, we analyzed risk factors associated with AEH among 8925 unique MSM (including 200 with AEH [2.2%] and 219 [2.5%] with newly diagnosed chronic HIV infection) undergoing community-based, confidential AEH screening in San Diego, California.The combination of condomless receptive anal intercourse (CRAI) plus ≥5 male partners, CRAI with an HIV-positive male, CRAI with a person who injects drugs, and prior syphilis diagnosis were significant predictors of AEH in the multivariable Cox regression model. Individuals reporting ≥1 of these 4 risk factors had a hazard ratio of 4.6 for AEH. MSM diagnosed with AEH differed in race (P = 0.005; more reported white race [P = 0.001], less black race [P = 0.030], trend toward less Native American race [P = 0.061]), when compared to those diagnosed with chronic HIV infection, while there was no difference observed regarding age.We established a multivariate model for the predicting risk of AEH infection in a cohort of MSM undergoing community HIV screening, which could be potentially used to discern those in need of further HIV nucleic acid amplification testing for community screening programs that do not test routinely for AEH. In addition, we found that race differed between those diagnosed with AEH and those diagnosed at chronic stage of HIV infection underlining the need for interventions that reduce stigma and promote the uptake of HIV testing for black MSM.

Development and validation of the San Diego Early Test Score to predict acute and early HIV infection risk in men who have sex with men

BACKGROUND

Although men who have sex with men (MSM) represent a dominant risk group for human immunodeficiency virus (HIV), the risk of HIV infection within this population is not uniform. The objective of this study was to develop and validate a score to estimate incident HIV infection risk.

METHODS

Adult MSM who were tested for acute and early HIV (AEH) between 2008 and 2014 were retrospectively randomized 2:1 to a derivation and validation dataset, respectively. Using the derivation dataset, each predictor associated with an AEH outcome in the multivariate prediction model was assigned a point value that corresponded to its odds ratio. The score was validated on the validation dataset using C-statistics.

RESULTS

Data collected at a single HIV testing encounter from 8326 unique MSM were analyzed, including 200 with AEH (2.4%). Four risk behavior variables were significantly associated with an AEH diagnosis (ie, incident infection) in multivariable analysis and were used to derive the San Diego Early Test (SDET) score: condomless receptive anal intercourse (CRAI) with an HIV-positive MSM (3 points), the combination of CRAI plus ≥5 male partners (3 points), ≥10 male partners (2 points), and diagnosis of bacterial sexually transmitted infection (2 points)-all as reported for the prior 12 months. The C-statistic for this risk score was >0.7 in both data sets.

CONCLUSIONS

The SDET risk score may help to prioritize resources and target interventions, such as preexposure prophylaxis, to MSM at greatest risk of acquiring HIV infection. The SDET risk score is deployed as a freely available tool at http://sdet.ucsd.edu.

Independent assessment of candidate HIV incidence assays on specimens in the CEPHIA repository

Objective:

Cross-sectional HIV incidence surveillance, using assays that distinguish ‘recent’ from ‘nonrecent’ infections, has been hampered by inadequate performance and characterization of incidence assays. In this study, the Consortium for the Evaluation and Performance of HIV Incidence Assays presents results of the first independent evaluation of five incidence assays (BED, Limiting Antigen Avidity, Less-sensitive Vitros, Vitros Avidity and BioRad Avidity).

Design:

A large repository of diverse specimens from HIV-positive patients was established, multiple assays were run on 2500 selected specimens, and data were analyzed to estimate assay characteristics relevant for incidence surveillance.

Methods:

The mean duration of recent infection (MDRI, average time ‘recent’ while infected for less than some time cut-off T) was estimated from longitudinal data on seroconverters by regression. The false-recent rate (FRR, probability of testing ‘recent’ when infected for longer than T) was explored by measuring the proportions of ‘recent’ results in various subsets of patients.

Results:

Assays continue to fail to attain the simultaneously large MDRI and small FRR demanded by existing performance guidelines. All assays produce high FRRs amongst virally suppressed patients (>40%), including elite controllers and treated patients.

Conclusions:

Results from this first independent evaluation provide valuable information about the current performance of assays, and suggest the need for further optimization. Variation of ‘recent’/‘nonrecent’ thresholds and the use of multiple antibody-maturation assays, as well as other biomarkers, can now be explored, using the rich data generated by the Consortium for the Evaluation and Performance of HIV Incidence Assays. Consistently high FRRs amongst those virally suppressed suggest that viral load will be a particularly valuable supplementary marker.

Video abstract:

Using HIV networks to inform real time prevention interventions

Objective

To reconstruct the local HIV-1 transmission network from 1996 to 2011 and use network data to evaluate and guide efforts to interrupt transmission.

Design

HIV-1 pol sequence data were analyzed to infer the local transmission network.

Methods

We analyzed HIV-1 pol sequence data to infer a partial local transmission network among 478 recently HIV-1 infected persons and 170 of their sexual and social contacts in San Diego, California. A transmission network score (TNS) was developed to estimate the risk of HIV transmission from a newly diagnosed individual to a new partner and target prevention interventions.

Results

HIV-1 pol sequences from 339 individuals (52.3%) were highly similar to sequences from at least one other participant (i.e., clustered). A high TNS (top 25%) was significantly correlated with baseline risk behaviors (number of unique sexual partners and insertive unprotected anal intercourse (p = 0.014 and p = 0.0455, respectively) and predicted risk of transmission (p<0.0001). Retrospective analysis of antiretroviral therapy (ART) use, and simulations of ART targeted to individuals with the highest TNS, showed significantly reduced network level HIV transmission (p<0.05).

Conclusions

Sequence data from an HIV-1 screening program focused on recently infected persons and their social and sexual contacts enabled the characterization of a highly connected transmission network. The network-based risk score (TNS) was highly correlated with transmission risk behaviors and outcomes, and can be used identify and target effective prevention interventions, like ART, to those at a greater risk for HIV-1 transmission.

Dual-mixed HIV-1 coreceptor tropism and HIV-associated neurocognitive deficits

HIV coreceptor usage of CXCR4 (X4) is associated with decreased CD4+ T-cell counts and accelerated disease progression, but the role of X4 tropism in HIV-associated neurocognitive disorders (HAND) has not previously been described. This longitudinal study evaluated data on 197 visits from 72 recently HIV-infected persons who had undergone up to four sequential neurocognitive assessments over a median of 160 days (IQR, 138–192). Phenotypic tropism testing (Trofile ES, Monogram, Biosciences) was performed on stored blood samples. Multivariable mixed model repeated measures regression was used to determine the association between HAND and dual-mixed (DM) viral tropism, estimated duration of infection (EDI), HIV RNA, CD4 count, and problematic methamphetamine use. Six subjects (8.3 %) had DM at their first neurocognitive assessment and four converted to DM in subsequent sampling (for total of 10 DM) at a median EDI of 10.1 months (IQR, 7.2–12.2). There were 44 (61.1 %) subjects who demonstrated HAND on at least one study visit. HAND was associated with DM tropism (odds ratio, 4.4; 95 % CI, 0.9–20.5) and shorter EDI (odds ratio 1.1 per month earlier; 95 % CI, 1.0–1.2). This study found that recency of HIV-1 infection and the development of DM tropism may be associated with HAND in the relatively early stage of infection. Together, these data suggest that viral interaction with cellular receptors may play an important role in the early manifestation of HAND.

Activities of transmitted/founder and chronic clade B HIV-1 Vpu and a C-terminal polymorphism specifically affecting virion release

Acute HIV-1 infection is characterized by a type I interferon response, resulting in the induction of host restriction factors. HIV-1 has evolved to counteract these factors, and one such adaptation, the ability of Vpu to counteract BST2/tetherin, is associated with the evolution of simian immunodeficiency virus (SIVcpz) into pandemic group M human immunodeficiency virus type 1 (HIV-1). During transmission between individuals, very few viruses or even a single virus, the "transmitted/founder" (T/F) virus, gives rise to the new infection, but in the new host the selective pressure of the immune response yields the diverse "quasispecies" of chronic infection. Here we examine the functional characteristics of Vpu proteins encoded by T/F viruses compared to acute and chronic viruses from longitudinally sampled subjects. The studied T/F Vpu proteins showed a trend toward optimized CD4 downregulation compared to chronic Vpu proteins but did not differ substantially in their ability to downregulate BST2 or enhance virion release, although individual clones from each group were impaired in these activities. Analysis of the functionally impaired clones identified a C-terminal residue, W76, as important specifically for Vpu enhancement of virion release. Primary Vpu clones encoding a W76G polymorphism, or site-directed mutants encoding a W76G substitution, were impaired in their ability to enhance virion release, but they were not defective for BST2 surface downregulation. Conversely, the virion release function of impaired primary clones was restored by creating a G76W substitution. The identification of W76 as important for virion release enhancement that is independent of BST2 surface downregulation supports the potential to mechanistically separate these functions of Vpu.

IMPORTANCE

To establish infection in a host, HIV-1 must evade the host's immune response, including the production of antiviral factors. HIV-1 encodes proteins that antagonize these defenses, including Vpu. Vpu counteracts the host protein BST2, which blocks the release of progeny viruses from the host cell. To determine the importance of Vpu activity to HIV-1 transmission, this study assessed the functionality of Vpu from viruses isolated soon after transmission ("transmitted/founder" viruses) compared to isolates from chronic infection. Although the anti-BST2 activity of Vpu proteins from the tested transmitted/founder viruses did not differ from the activity of the chronic Vpu proteins, the transmitted/founder Vpu proteins trended toward having superior activity against another host protein, CD4. Further, this study identified an amino acid near the C terminus of Vpu that is specifically important for Vpu's ability to enhance the release of progeny virus from the host cell, supporting the notion of a new mechanism for this function of Vpu.

Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) dual infection (DI) has been associated with decreased CD4 T-cell counts and increased viral loads; however, the frequency of intrasubtype DI is poorly understood. We used ultradeep sequencing (UDS) to estimate the frequency of DI in a primary infection cohort of predominantly men who have sex with men (MSM).

METHODS

 HIV-1 genomes from longitudinal blood samples of recently infected, therapy-naive participants were interrogated with UDS. DI was confirmed when maximum sequence divergence was excessive and supported by phylogenetic analysis. Coinfection was defined as DI at baseline; superinfection was monoinfection at baseline and DI at a later time point.

RESULTS

 Of 118 participants, 7 were coinfected and 10 acquired superinfection. Superinfection incidence rate was 4.96 per 100 person-years (95% confidence interval [CI], 2.67-9.22); 6 occurred in the first year and 4 in the second. Overall cumulative prevalence of intrasubtype B DI was 14.4% (95% CI, 8.6%-22.1%). Primary HIV-1 incidence was 4.37 per 100 person-years (95% CI, 3.56-5.36).

CONCLUSIONS

 Intrasubtype DI was frequent and comparable to primary infection rates among MSM in San Diego; however, superinfection rates declined over time. DI is likely an important component of the HIV epidemic dynamics, and development of stronger immune responses to the initial infection may protect from superinfection.

Factors associated with intention to use internet-based testing for sexually transmitted infections among men who have sex with men

BACKGROUND

Internet-based testing programs are being increasingly used to reduce testing barriers for individuals at higher risk of infection, yet the population impact and potential for exacerbation of existing health inequities of these programs are not well understood.

OBJECTIVE

We used a large online sample of men who have sex with men (MSM) in Canada to measure acceptability of Internet-based testing and perceived advantages and disadvantages of this testing approach.

METHODS

We asked participants of the 2011/2012 Sex Now Survey (a serial online survey of gay and bisexual men in Canada) whether they intended to use Internet-based testing and their perceived benefits and disadvantages of use. We examined whether intention to use was associated with explanatory variables spanning (A) sociodemographics, (B) Internet and technology usage, (C) sexually transmitted infections (STI)/ human immunodeficiency virus (HIV) and risk, and (D) health care access and testing, using multivariable logistic regression (variable selection using Bayesian information criterion).

RESULTS

Overall, intention to use was high (5678/7938, 71.53%) among participants with little variation by participant characteristics. In our final model, we retained the variables related to (B) Internet and technology usage: use of Internet to cruise for sex partners (adjusted odds ratio [AOR] 1.46, 95% CI 1.25-1.70), use of Internet to search for sexual health information (AOR 1.36, 95% CI 1.23-1.51), and mobile phone usage (AOR 1.19, 95% 1.13-1.24). We also retained the variables for (D) health care access and testing: not "out" to primary care provider (AOR 1.24, 95% CI 1.10-1.41), delayed/avoided testing due to privacy concerns (AOR 1.77, 95% CI 1.49-2.11), and delayed/avoided testing due to access issues (AOR 1.65, 95% CI 1.40-1.95). Finally, we retained the variable being HIV positive (AOR 0.56, 95% CI 0.46-0.68) or HIV status unknown (AOR 0.89, 95% CI 0.77-1.01), age <30 years (AOR 1.41, 95% CI 1.22-1.62), and identifying as bisexual (AOR 1.18, 95% CI 1.04-1.34) or straight/other (AOR 0.67, 95% CI 0.50-0.90). The greatest perceived benefits of Internet-based testing were privacy (2249/8388, 26.81%), general convenience (1701/8388, 20.28%), and being able to test at any time (1048/8388, 12.49%). The greatest perceived drawbacks were the inability to see a doctor or nurse (1507/8388, 17.97%), wanting to talk to someone about results (1430/8388, 17.97%), not wanting online results (1084/8388, 12.92%), and low trust (973/8388, 11.60%).

CONCLUSIONS

The high and wide-ranging intention to use that we observed suggests Internet-based testing has the potential to reach into all subgroups of MSM and may be particularly appealing to those facing current barriers to accessing STI/HIV testing and who are more comfortable with technology. These findings will be used to inform the promotion and further evaluation of an Internet-based testing program currently under development in British Columbia, Canada.

Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment

Standard methods used to estimate HIV-1 population diversity are often resource intensive (e.g., single genome amplification, clonal amplification and pyrosequencing) and not well suited for large study cohorts. Additional approaches are needed to address the relationships between intraindividual HIV-1 genetic diversity and 2 disease. With a small cohort of individuals, we validated three methods for measuring diversity: Shannon entropy and average pairwise distance (APD) using single genome sequences, and counts of mixed bases (i.e. ambiguous nucleotides) from population based sequences. In a large cohort, we then used the mixed base approach to determine associations between measure HIV-1 diversity and HIV associated disease. Normalized counts of mixed bases correlated with Shannon Entropy at both the nucleotide (rho=0.72, p=0.002) and amino acid level (rho=0.59, p=0.015), and APD (rho=0.75, p=0.001). Among participants who underwent neuropsychological and clinical assessments (n=187), increased HIV-1 population diversity was associated with both a diagnosis of AIDS and neuropsychological impairment.

Diagnosing acute HIV infection

Individuals with acute HIV infection (AHI) pose a greater transmission risk than most chronically HIV-infected patients and prevention efforts targeting these individuals are important for reducing the spread of HIV infection. Rapid and accurate diagnosis of AHI is crucial. Since symptoms of AHI are nonspecific, its diagnosis requires a high index of suspicion and appropriate HIV laboratory tests. However, even 30 years after the start of the HIV epidemic, laboratory tools remain imperfect and only a few individuals with AHI are identified. We review the clinical presentation of the acute retroviral syndrome, the laboratory markers and their detection methods, and propose an algorithm for the laboratory diagnosis of AHI.

Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California

BACKGROUND

Specific sequence changes of human immunodeficiency virus type 1 (HIV-1) in the presence of specific HLA molecules may alter the composition and processing of viral peptides, leading to immune escape. Persistence of these mutations after transmission may leave the genetic fingerprint of the transmitter's HLA profile. Here, we evaluated the associations between HLA profiles and the phylogenetic relationships of HIV sequences sampled from a cohort of recently infected individuals in San Diego, California.

METHODS

We identified transmission clusters within the study cohort, using phylogenetic analysis of sampled HIV pol genotypes at a genetic distance of <1.5%. We then evaluated the association of specific HLA alleles, HLA homozygosity, HLA concordance, race and ethnicity, and mutational patterns within the clustering and nonclustering groups.

RESULTS

From 350 cohort participants, we identified 162 clustering individuals and 188 nonclustering individuals. We identified trends for enrichment of particular alleles within individual clusters and evidence of viral escape within those clusters. We also found that discordance of HLA alleles was significantly associated with clustering individuals.

CONCLUSIONS

Some transmission clusters demonstrate HLA enrichment, and viruses in these HLA-associated clusters often show evidence of escape to enriched alleles. Interestingly, HLA discordance was associated with clustering in our predominantly MSM population.

Cost savings associated with testing of antibodies, antigens, and nucleic acids for diagnosis of acute HIV infection

Efforts to identify all persons infected with HIV in the United States are driven by the hope that early diagnosis will lower risk behaviors and decrease HIV transmission. Identification of HIV-infected people earlier in the course of their infection with HIV antigen/antibody (Ag/Ab) combination assays (4th-generation HIV assays) should help achieve this goal. We compared HIV RNA nucleic acid test (NAT) results to the results of a 4th-generation Ag/Ab assay (Architect HIV Ag/Ab Combo [HIV Combo] assay; Abbott Diagnostics) in 2,744 HIV antibody-negative samples. Fourteen people with acute HIV infection (HIV antibody negative/NAT positive) were identified; the HIV Combo assay detected nine of these individuals and was falsely negative in the remaining five. All five persons missed by the HIV Combo assay were in the stage of exponential increase in plasma virus associated with acute HIV infection (3, 7, 20, 35, 48). In contrast, most acutely infected persons detected by the HIV Combo assay demonstrated either a plateauing or decreasing plasma viral load. The HIV Combo assay also classified as positive five other samples which were negative by NAT. Taken together, the HIV Combo assay had a sensitivity of 73.7% and a specificity of 99.8%. Using published data, we estimated secondary transmission events had HIV infection in these five individuals remained undiagnosed. Screening of our population with NAT cost more than screening with the HIV Combo assay but achieved new diagnoses that we predict resulted in health care savings that far exceed screening costs. These findings support the use of more sensitive assays, like NAT, in HIV screening of populations with a high prevalence of acute HIV infection.

Protocol for the use of a rapid real-time PCR method for the detection of HIV-1 proviral DNA using double-stranded primer

This chapter describes a real-time PCR method for the detection of HIV-1 proviral DNA in whole blood samples using a novel double-stranded primer system. The assay utilizes a simple commercially available DNA extraction method and a rapid and easy-to-perform real-time PCR protocol to consistently detect a minimum of four copies of HIV-1 group M proviral DNA in as little as 90 min after sample (whole blood) collection. Co-amplification of the human RNase P gene serves as an internal control to monitor the efficiency of both the DNA extraction and amplification. Once the assay is validated properly, it may be suitable as an alternative confirmation test for HIV-1 infections in a variety of HIV testing venues including the mother-to-child transmission testing sites, clinics, and diagnostic testing centers.

Use of the Internet for the surveillance and prevention of sexually transmitted diseases

The Internet is a relatively new tool in the surveillance and prevention of sexually transmitted infections, and this review examines its global use in this regard. Much use has been made in the form of information collection and dissemination; targeted population engagement through chat rooms, partner notification and other mechanisms; and the provision of testing services and other products. Internet users may need education concerning reputable websites, and public health practitioners need proficiency in the use of social media and marketing.

Evaluation of pooled rapid HIV antibody screening of patients admitted to a San Diego Hospital

Current HIV screening guidelines in the United States recommend expanding the scope of HIV screening to include routine screening in health care settings; however, this will require increased resources. Since testing of pooled samples can decrease costs, the test characteristics of pooled rapid antibody testing were determined and optimal pool sizes were estimated for populations with HIV prevalence ranging from 0.25% to 10%. Based on these results, pooled testing methods were evaluated for screening patients admitted to hospital in San Diego, California. Evaluation of pooled antibody testing on samples collected from individuals with known HIV infection found only a modest reduction in sensitivity. These false negative results were only found among samples with very low optical density readings (<0.125 by the ADVIA Centaur® HIV assay). These readings are considered as HIV negative by the ADVIA Centaur® HIV assay, and therefore likely correspond to samples collected during acute infection. Further evaluation of pooled testing of samples collected from individuals during recent infection, found that mini-pool testing of five samples detected HIV antibody in 86% of samples taken within 60 days of the initial infection and 92% of samples taken within 90 days of the initial infection. Based on estimations of optimal pool sizes for low prevalence populations, it was decided to evaluate mini-pools consisting of 10 samples to screen the study's hospitalized patients. During this evaluation, the HIV prevalence among hospitalized patients was 0.8%, and the 10 sample mini-pool testing had 100% sensitivity and specificity. Additionally, pooled testing resulted in an 84.5% reduction in the number of rapid HIV antibody tests needed, as compared to testing each sample individually. Even when incorporating the increased costs of technician time, mini-pooled tested would have resulted in a net savings of 8760 USD for the 523 samples tested in the study. Taken together, these results indicate that pooled rapid antibody testing may reduce substantially the costs for HIV screening in low prevalence populations without a loss in accuracy.