Late Identification of Perinatal Transmission of HIV in an Infant at High Risk.

The focus of this case study is the delayed diagnosis of a perinatal HIV transmission, which was identified when the infant reached 4 months of age, and the social conditions and structural determinants that contributed to the increased transmission risk. Despite adhering to the diagnostic testing protocols and neonatal antiretroviral (ARV) guidelines of the New York State Department of Health, this transmission still occurred. This transmission event prompted strategies to address criminalization of substance use during pregnancy and a reevaluation of the HIV testing and treatment protocols, including the timing of testing. Obtaining a diagnostic specimen at birth before initiating prophylactic or presumptive therapy, without causing delays in therapy, and incorporating HIV-1 DNA or RNA testing 2 to 6 weeks after discontinuing ARV therapy might have facilitated earlier detection and a quicker resumption of ARV therapy for this high-risk infant. Subsequently, the New York State HIV perinatal testing guidelines were updated. These changes included the recommendation to obtain a diagnostic specimen at birth before initiating ARV medications, whenever feasible, without causing delays in ARV initiation. Additionally, an extra virologic diagnostic test is recommended at 2 to 6 weeks after discontinuing ARVs for infants at high risk of perinatal HIV transmission, especially those with possible DNA or RNA suppression due to ARV prophylaxis or presumptive HIV therapy.

Impact of HIV preexposure prophylaxis prescriptions on HIV diagnoses in New York City.

BACKGROUND: HIV preexposure prophylaxis (PrEP) has proven to be efficacious and effective in preventing HIV infections, but few studies have reported its impact in the real world. METHODS: We conducted an ecological analysis and compared the trends in HIV PrEP prescriptions with the trends in age-adjusted HIV diagnosis rates in New York City (NYC). Joinpoint regression analyses were used to identify any temporal trends in HIV diagnosis rates in NYC. RESULTS: The number of people filling at least one PrEP prescription in NYC increased from 2551 in 2014 to 35 742 in 2022. The overall age-adjusted HIV diagnosis rate steadily decreased from 48.1 per 100 000 in 2003 to 17.1 per 100 000 in 2022. After the rollout of PrEP, accelerated decreases were detected in some subpopulations including white men [2014-2019 annual percentage change (APC): -16.6%; 95% confidence interval (CI) -22.7 to -10.0], Asian/Pacific Islander men (2016-2022 APC: -9.8%), men aged 20-29 years (2017-2020 APC: -9.4%) and 40 -49 years (2014-2020 APC: -12.2%), Latino/Hispanic people aged 40-49 years (2015-2020 APC: -13.0%), white people aged 20-29 years (2012-2022 APC: -11.4%) and 40-49 years (2014-2018 APC: -27.8%), and Asian/Pacific Islander people aged 20-29 years (2017-2022 APC: -13.0%). CONCLUSION: With a high coverage, PrEP can have a long-term impact in reducing HIV infections in a population, but if preexisting social determinants that contribute to racial, ethnic, and gender inequities are not well addressed, the implementation of PrEP can exacerbate these inequalities.

Pre-exposure prophylaxis (PrEP) use history in people with antiretroviral resistance at HIV diagnosis: Findings from New York City HIV surveillance and partner services, 2015-2022.

BACKGROUND: Drug resistance may be acquired in people starting HIV pre-exposure prophylaxis (PrEP) during undiagnosed infection. Population-based estimates of PrEP-related resistance are lacking. METHODS: We used New York City surveillance and partner services data to measure the effect of PrEP use (tenofovir disoproxil fumarate/tenofivir alafenamide fumarate with emtricitabine) history on baseline prevalence of M184I/V mutations in people diagnosed with HIV, 2015-2022. PrEP use was categorized as "Recent" defined as PrEP stopped ≤ 90 days before diagnosis, "Past" as PrEP stopped >90 days before diagnosis, and "No known use". Resistance associated mutations were determined using the Stanford Algorithm. We used log binomial regression to generate adjusted relative risk (aRR) of M184I/V by PrEP use history in people with and without acute HIV infection (AHI). RESULTS: Of 4,246 newly diagnosed people with a genotype ≤30 days of diagnosis, 560 (13%) had AHI, 136 (3%) reported recent, and 124 (35%) past PrEP use; 98 (2%) harbored M184I/V. In people with AHI, recent PrEP use was associated with 6 times greater risk of M184I/V than no known use (aRR: 5.86; 95% confidence interval [CI]: 2.49-13.77). In people without AHI, risk of M184I/V in recent users was 7 times (aRR:7.26; 95% CI: 3.98-13.24), and in past users, 4 times that of people with no known use (aRR: 4.46; 95% CI: 2.15-9.24). CONCLUSIONS: PrEP use was strongly associated with baseline M184I/V in NYC, regardless of AHI. Ordering a nucleic acid test when indicated after assessment of exposure, antiretroviral history and AHI symptoms can decrease PrEP initiation in people with undetected infection.

Improvement in CD4+ cell count among people with HIV in New York City, 2007-2021.

BACKGROUND: A higher CD4+ cell count among people with HIV (PWH) is associated with improved immune function and reduced HIV-related morbidity and mortality. The purpose of this analysis is to report the trend in CD4+ cell count among PWH in New York City (NYC). METHODS: We conducted a serial cross-sectional analysis using the NYC HIV registry data and reported the proportion of PWH with a CD4+ cell count of 500 cells/µl or above, overall and by sex, race or ethnicity, and age. RESULTS: The overall proportion of PWH in NYC with a CD4+ cell count of 500 cells/µl or above increased from 38.1% in 2007 to 63.8% in 2021. Among men, the proportion increased from 36.7% in 2007 to 62.3% in 2021 with an annual percentage change (APC) of 6.6% [95% confidence interval (95% CI): 5.8-7.5] in 2007-2013 and 2.6% (95% CI: 0.7-4.4) in 2013-2017, and no changes in 2017-2021 (APC: 0.0%; 95% CI: -1.1 to 1.0); among women, the proportion increased from 41.0% in 2007 to 67.6% in 2021 with an APC of 7.5% (95% CI: 5.2-9.8) in 2007-2010, 4.5% (95% CI: 3.5-5.4) in 2010-2015, and 0.8% (95% CI: 0.4-1.2) in 2015-2021. White people had a higher proportion than other racial/ethnic groups, 70.9, 59.3, 60.9, and 61.7%, respectively, among white, black, Latino/Hispanic, and Asian/Pacific Islander men, and 69.8, 68.0, 66.3, and 69.3%, respectively, among white, black, Latina/Hispanic, and Asian/Pacific Islander women in 2021. CONCLUSION: CD4+ cell count among PWH in NYC improved during 2007-2021, but the improvement slowed in recent years.

An Exploratory Study to Describe Transgender People with HIV Who Accessed Medicaid and Their Viral Suppression Over Time in New York City, 2013-2017.

Purpose: Although HIV surveillance contains information on HIV outcomes among transgender persons with HIV (TPWH), it does not include other important data, for example, gender-affirming health care, which may influence viral suppression (VS). We describe TPWH accessing Medicaid and the association of gender-affirming surgery with VS. Methods: Through matching Medicaid claims with HIV registry data, a cohort of previously identified TPWH in Medicaid was compared to cisgender women and men in terms of VS in 2013-2017 in New York City. Medicaid claims were used to identify TPWH who obtained gender-affirming surgery (e.g., chest, genital surgeries). We described the VS of those who had surgery and examined temporal trends in VS pre- and postsurgery and by surgery type. Results: 1730 TPWH were enrolled in Medicaid and in HIV care in 2013-2017. Overall for VS at last laboratory, TPWH in Medicaid had lower VS (76.0%) than cisgender women (80.4%) and men (83.3%). The exception was the 185 TPWH who obtained gender-affirming surgery (86.5%). Among 160 TPWH in Medicaid who obtained gender-affirming surgery and achieved VS, VS increased presurgery (66.3% 2 years prior, 76.9% 1 year prior) and remained high 1 year after (86.3%) and 2 years after (87.7%) (the last percentage is only among those who had surgery before 2017, N=81). Conclusion: Gender-affirming surgery may be an important motivator to becoming virally suppressed and was associated with sustained high VS, which can lead to improved survival and quality of life. Medicaid and other insurers should consider improving access to gender-affirming surgery among TPWH.

Years Since Diagnosis Among People Living With Diagnosed HIV in New York City.

Antiretroviral treatment has greatly improved the survival of people living with diagnosed HIV (PLWDH), but little information is available on the time since diagnosis among them. Using New York City HIV surveillance data, we described the trend in the number of years since diagnosis among PLWDH during 2010-2019 and reported the mean, median, and interquartile range (IQR) of years since diagnosis among PLWDH in New York City in 2019, overall and by gender, race and ethnicity, and transmission risk. The median number of years since diagnosis among PLWDH in New York City increased from 10.5 years (IQR, 6.3-15.6) in 2010 to 16.3 years (IQR, 8.9-22.1) in 2019. By gender, transgender people had the shortest time since diagnosis, with a median of 11.4 years (IQR, 5.6-17.9), compared with men (median = 15.2 years; IQR, 8.1-21.6) and women (median, 18.5 years; IQR, 12.0-23.0). By race and ethnicity, non-Hispanic White people had been living with the diagnosis for the longest time (median = 17.4 years; IQR, 9.5-23.5), and Asian/Pacific Islander people had been living with the diagnosis for the shortest time (median = 10.1 years; IQR, 4.7-17.0). With an expected and continuing increase in the number of years since HIV diagnosis among PLWDH, programs that provide treatment and support services will need to be expanded, updated, and improved.

Life Expectancy Among People With HIV in New York City, 2009-2018.

OBJECTIVE: To conduct a population-based analysis and compare life expectancy between people with HIV and the general population in New York City (NYC). METHODS: We obtained the annual total number and age, sex, and race/ethnicity distributions of people with HIV from the NYC HIV registry and generated comparable numbers for the NYC general population from the Census 2000 and 2010 data using linear interpolation. RESULTS: Life expectancy at age 20 among people with HIV increased from 38.5 years [95% confidence interval (CI): 37.4 to 39.5] in 2009 to 50.6 (95% CI: 48.5 to 52.7) in 2018, whereas it increased from 62.0 years (95% CI: 61.8 to 62.1) to 63.6 (95% CI: 63.5 to 63.7) among the NYC general population. The gap between the 2 populations narrowed from 23.5 years (95% CI: 22.4 to 24.6) in 2009 to 13.0 (95% CI: 10.9 to 15.1) in 2018. By sex and race/ethnicity, life expectancy at age 20 among people with HIV increased from 36.7 years in 2009 to 47.9 in 2018 among Black men; 37.5 to 50.5 years among Black women; 38.6 to 48.9 years among Hispanic men; 46.0 to 51.0 years among Hispanic women; 44.7 to 59.7 years among White men; and 38.0 years in 2009-2013 to 50.4 years in 2014-2018 among White women. CONCLUSIONS: Life expectancy among people with HIV improved greatly in NYC in 2009-2018, but the improvement was not equal across sex and racial/ethnic groups. The gap in life expectancy between people with HIV and the general population narrowed but remained.

Improving Data on the HIV Epidemic in New York City by Identifying Transgender Persons in Medicaid in 2013-2017.

Purpose: Undercounting of transgender people with HIV (PWH) in New York City (NYC) remains prevalent. We sought to improve our ability to accurately enumerate transgender PWH and address their needs for gender-affirming health care. Methods: We enhance previous algorithms used to identify transgender beneficiaries, using diagnoses, prescriptions, and sex at birth from Medicaid claims in 2013-2017. We then matched beneficiaries to individuals diagnosed with HIV in the HIV surveillance registry to identify transgender PWH. Results: Our algorithm identified 6043 transgender persons who accessed Medicaid in 2013-2017, with 1472 (24%) reported to the HIV registry, 1168 (79%) of whom were accurately identified as transgender in the registry. We found 292 transgender persons in the registry that had accessed Medicaid but were not identified by our algorithm, for a total of 6335 transgender persons accessing Medicaid (0.1% of the NYC Medicaid population), including 1764 transgender PWH (28% of transgender persons accessing Medicaid). From 2013 to 2017, there was a 35% increase in transgender persons identified in Medicaid claims using our algorithm. Conclusion: We identified a large number of transgender persons in Medicaid, many of whom were PWH. We saw a sizeable increase over the 5-year period, likely due, in part, to expansion of Medicaid policy to cover gender-affirming health care. Given the high proportion of transgender PWH accessing Medicaid, Medicaid claims data are a valuable source of health information for the transgender population, a group that is often difficult to identify due to issues of underreporting, stigma, reduced access to appropriate care, and misgendering by health care personnel.

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.

Using molecular epidemiology to trace the history of the injection-related HIV epidemic in New York City, 1985-2019.

OBJECTIVE: Unintentional drug poisoning and overdose deaths in New York City (NYC) increased 175% between 2010 and 2017, partly due to the transition from noninjectable opioids to heroin injection. This transition has led to concern of a resurgent HIV epidemic among persons who inject drugs (PWID) in NYC. Thus, we sought to characterize HIV transmission dynamics in PWID. DESIGN: Genetic network analysis of HIV-1 public health surveillance data. METHODS: We analyzed HIV diagnoses reported to public health surveillance to determine the trajectory of the HIV epidemic among PWID in NYC, from 1985 through 2019. Genetic distance-based clustering was performed using HIV-TRACE to reconstruct transmission patterns among PWID. RESULTS: The majority of the genetic links to PWID diagnosed in the 1980s and 1990s are to other PWID. However, since 2011, there has been a continued decline in new diagnoses among PWID, and genetic links between PWID have become increasingly rare, although links to noninjecting MSM and other people reporting sexual transmission risk have become increasingly common. However, we also find evidence suggestive of a resurgence of genetic links among PWID in 2018-2019. PWID who reported male-male sexual contact were not preferentially genetically linked to PWID over the surveillance period, emphasizing their distinct risk profile from other PWID. CONCLUSION: These trends suggest a transition from parenteral to sexual transmission among PWID in NYC, suggesting that harm reduction, syringe exchange programs, and legalization of over-the-counter syringe sales in pharmacies have mitigated HIV risk by facilitating well tolerated injection among new PWID.

Survival Among New Yorkers with HIV from 1981 to 2017: Inequities by Race/Ethnicity and Transmission Risk Persist into the Post-HAART Era.

Data on long-term survival among people with HIV (PWH) can inform the development of services for this population. An estimated 90,000 PWH live in New York City (NYC). Using HIV surveillance data, we conducted survival analysis of PWH diagnosed in NYC before and after introduction of highly active antiretroviral therapy (HAART) (pre-HAART cohort: 1981-1994; post-HAART cohort: 1995-2016). We created Kaplan-Meier curves by cohort and demographic factors, and Cox proportional hazards models to evaluate adjusted mortality risk by cohort. 205,584 adults and adolescents were diagnosed with HIV in NYC from 1981 to 2016, half each in the pre-HAART and post-HAART eras. The pre-HAART cohort had significantly poorer survival compared with the post-HAART cohort. Adjusted mortality risk in the pre-HAART cohort was almost threefold that in the post-HAART cohort (HR 2.84, 95% confidence interval [CI] 2.80-2.88). In sex- and risk-stratified models, men who have sex with men (MSM) had the largest difference in mortality risk pre-HAART versus post-HAART (HR 5.41, 95% CI 5.23-5.59). Race/ethnic disparities were pronounced among MSM, with Latino/Hispanic and White MSM having lower mortality than Black MSM. Females with heterosexual risk born outside the US had lower mortality than US-born women. The improvement in survival post-HAART was most pronounced for White people. Survival among persons diagnosed with HIV in NYC increased significantly since the introduction of HAART. However, among MSM and among PWH overall, improvements even post-HAART lagged for Black and Latino/Hispanic people, underscoring the need to address structural barriers, including racism, to achieve optimal health outcomes among people with HIV.

Sorting by Race/Ethnicity Across HIV Genetic Transmission Networks in Three Major Metropolitan Areas in the United States.

An important component underlying the disparity in HIV risk between race/ethnic groups is the preferential transmission between individuals in the same group. We sought to quantify transmission between different race/ethnicity groups and measure racial assortativity in HIV transmission networks in major metropolitan areas in the United States. We reconstructed HIV molecular transmission networks from viral sequences collected as part of HIV surveillance in New York City, Los Angeles County, and Cook County, Illinois. We calculated assortativity (the tendency for individuals to link to others with similar characteristics) across the network for three candidate characteristics: transmission risk, age at diagnosis, and race/ethnicity. We then compared assortativity between race/ethnicity groups. Finally, for each race/ethnicity pair, we performed network permutations to test whether the number of links observed differed from that expected if individuals were sorting at random. Transmission networks in all three jurisdictions were more assortative by race/ethnicity than by transmission risk or age at diagnosis. Despite the different race/ethnicity proportions in each metropolitan area and lower proportions of clustering among African Americans than other race/ethnicities, African Americans were the group most likely to have transmission partners of the same race/ethnicity. This high level of assortativity should be considered in the design of HIV intervention and prevention strategies.

Neighborhood social cohesion and viral suppression after HIV diagnosis.

Social cohesion has varying effects on health. We investigated the association of perceived neighborhood social cohesion with HIV viral suppression using individual-level data from the New York City HIV registry and surveillance-based interviews (n = 92). Suppression was achieved within 12 months of HIV diagnosis by 60 percent of persons perceiving low cohesion and 71 percent of those perceiving high (p = 0.31). Controlling for demographic and clinical characteristics and neighborhood poverty, per proportional hazards regression, cohesion was not associated with suppression (adjusted hazards ratio (95% confidence interval) for high versus low cohesion: 0.79 (0.49-1.28)). Cohesion may have heterogeneous effects on HIV medication adherence.

Calculating Age-Standardized Death Rates Among People With HIV Comparable Across Jurisdictions and Over Time.

The Centers for Disease Control and Prevention (CDC) and local health jurisdictions have been using HIV surveillance data to monitor mortality among people with HIV in the United States with age-standardized death rates, but the principles of age standardization have not been consistently followed, making age standardization lose its purpose-comparison over time, across jurisdictions, or by other characteristics.We review the current practices of age standardization in calculating death rates among people with HIV in the United States, discuss the principles of age standardization including those specific to the HIV population whose age distribution differs markedly from that of the US 2000 standard population, make recommendations, and report age-standardized death rates among people with HIV in New York City.When we restricted the analysis population to adults aged between 18 and 84 years in New York City, the age-standardized death rate among people with HIV decreased from 20.8 per 1000 (95% confidence interval [CI] = 19.2, 22.3) in 2013 to 17.1 per 1000 (95% CI = 15.8, 18.3) in 2017, and the age-standardized death rate among people without HIV decreased from 5.8 per 1000 in 2013 to 5.5 per 1000 in 2017.

Addressing Ethical Challenges in US-Based HIV Phylogenetic Research.

In recent years, phylogenetic analysis of HIV sequence data has been used in research studies to investigate transmission patterns between individuals and groups, including analysis of data from HIV prevention clinical trials, in molecular epidemiology, and in public health surveillance programs. Phylogenetic analysis can provide valuable information to inform HIV prevention efforts, but it also has risks, including stigma and marginalization of groups, or potential identification of HIV transmission between individuals. In response to these concerns, an interdisciplinary working group was assembled to address ethical challenges in US-based HIV phylogenetic research. The working group developed recommendations regarding (1) study design; (2) data security, access, and sharing; (3) legal issues; (4) community engagement; and (5) communication and dissemination. The working group also identified areas for future research and scholarship to promote ethical conduct of HIV phylogenetic research.

Estimating the probability of diagnosis within 1 year of HIV acquisition.

BACKGROUND: Early diagnosis of HIV is important for the prevention of ongoing transmission and development of HIV-related illness. The purpose of this study is to develop an outcome indicator to monitor the progress in early HIV diagnosis. METHODS: Persons diagnosed with HIV in New York City and their first CD4 test results were used to estimate the distribution of HIV diagnosis delay, based on a CD4 count depletion model. The distribution was then used to estimate the probability of diagnosis within 1 year of HIV acquisition, which is the number of cases diagnosed in a given calendar year for which diagnosis occurred within 1 year of acquisition divided by the number of incident cases in that calendar year. RESULTS: In 2012-2016, the estimated annual probability of diagnosis within 1 year of HIV acquisition in New York City was 43.0% [95% confidence interval (CI): 37.9-48.2%), 42.5% (95% CI: 36.8--48.3%), 42.8% (95% CI: 36.3--49.2%), 42.9% (95% CI: 35.4--50.3%), and 42.2% (95% CI: 33.1--51.2%), respectively. CONCLUSION: National and local health jurisdictions should consider using this new outcome indicator, the probability of diagnosis within 1 year of HIV acquisition, to monitor their progress in early HIV diagnosis.

An expanded HIV screening strategy in the Emergency Department fails to identify most patients with undiagnosed infection: insights from a blinded serosurvey.

Screening for HIV in Emergency Departments (EDs) is recommended to address the problem of undiagnosed HIV. Serosurveys are an important method for estimating the prevalence of undiagnosed HIV and can provide insight into the effectiveness of an HIV screening strategy. We performed a blinded serosurvey in an ED offering non-targeted HIV screening to determine the proportion of patients with undiagnosed HIV who were diagnosed during their visit. The study was conducted in a high-volume, urban ED and included patients who had blood drawn for clinical purposes and had sufficient remnant specimen to undergo deidentified HIV testing. Among 4752 patients not previously diagnosed with HIV, 1403 (29.5%) were offered HIV screening and 543 (38.7% of those offered) consented. Overall, undiagnosed HIV was present in 12 patients (0.25%): six among those offered screening (0.4%), and six among those not offered screening (0.2%). Among those with undiagnosed HIV, two (16.7%) consented to screening and were diagnosed during their visit. Despite efforts to increase HIV screening, more than 80% of patients with undiagnosed HIV were not tested during their ED visit. Although half of those with undiagnosed HIV were missed because they were not offered screening, the yield was further diminished because a substantial proportion of patients declined screening. To avoid missed opportunities for diagnosis in the ED, strategies to further improve implementation of HIV screening and optimize rates of consent are needed.

Use of molecular HIV surveillance data and predictive modeling to prioritize persons for transmission-reduction interventions.

BACKGROUND: To develop a predictive model to prioritize persons with a transmissible HIV viral load for transmission-reduction interventions. METHODS: New York City (NYC) HIV molecular surveillance data from 2010 to 2013 were used to build a model to predict the probability that the partial pol gene of the virus of a person with a transmissible HIV viral load (>1500 copies/ml) would be genetically similar to that of a person with a new HIV infection (diagnosis at stage 0 or 1 according to the revised Centers for Disease Control and Prevention classification system). Data from 2013 to 2016 were then used to validate the model and compare it with five other selection strategies that can be used to prioritize persons for transmission-reduction interventions. RESULTS: A total of 10 609 persons living with HIV (PLWH) were included in the development dataset, and 8257 were included in the validation dataset. Among the six selection strategies, the predictive model had the highest area under the receiver operating characteristic curve (AUC) [0.86, 95% confidence interval (CI) 0.84--0.88], followed by the 'Young MSM' (0.79, 95% CI 0.77--0.82), 'MSM with high viral loads' (0.74, 95% CI 0.72--0.76), 'Random sample of MSM' (0.73, 95% CI 0.71--0.76), 'Persons with high viral loads' (0.56, 95% CI 0.54--0.59), and 'Random sample' (0.50, 95% CI 0.48--0.53) strategies. CONCLUSIONS: Jurisdictions should consider applying predictive modeling to prioritize persons with a transmissible viral load for transmission-reduction interventions and to evaluate its feasibility and effectiveness.