HIV behind bars: human immunodeficiency virus cluster analysis and drug resistance in a reference correctional unit from southern Brazil

Molecular Epidemiology of HIV-1 among Prisoners in Central Brazil and Evidence of Transmission Clusters

Higher rates of human immunodeficiency virus (HIV) infection have been detected in prisoners when compared with the general population, but research into HIV molecular epidemiology and its transmission network has been lacking among them. Thus, this study aimed to verify potential HIV molecular transmission networks among prisoners. In addition, we aimed to describe the mutations related to antiretroviral resistance in these isolates. Thus, we conducted a cross-sectional survey from 2013 to 2018 in prisons in Central-Western Brazil, and the final sampling composed of 84 prisoners. Proviral DNA was extracted from each whole blood sample followed by amplification of the partial polymerase gene and sequencing. Forty-nine sequences (58.3%) were classified as subtype B, followed by C (14.3%), D, and F1 (2.4% each). A complex and dynamic HIV-1 epidemic is observed in the prisons, as 25% of the sequences were recombinant forms. We detected 15 HIV transmission clusters composed of at least two sequences, that included not only prisoners but also individuals from the general population from the same State with a variety of risk behaviors. Thirty-two percent (32.0%) of treatment-experienced prisoners had at least one drug resistance mutation (DRM), while transmitted DRMs were found in 5.9% of the prisoners. We highlight the urgent need for routine surveillance of HIV-1 infection including resistance genotypic tests considering the high disease burden, risky behaviors inside prisons, and the dynamic relationship of prisoners with the outside community.

HIV Drug Resistance and Transmission Networks Among a Justice-Involved Population at the Time of Community Reentry in Washington, D.C

Justice-involved (JI) populations bear a disproportionate burden of HIV infection and are at risk of poor treatment outcomes. Drug resistance prevalence and emergence, and phylogenetic inference of transmission networks, understudied in vulnerable JI populations, can inform care and prevention interventions, particularly around the critical community reentry period. We analyzed banked blood specimens from CARE+ Corrections study participants in Washington, D.C. (DC) across three time points and conducted HIV drug resistance testing using next-generation sequencing (NGS) at 20% and 5% thresholds to identify prevalent and evolving resistance during community reentry. Phylogenetic analysis was used to identify molecular clusters within participants, and in an extended analysis between participants and publicly available DC sequences. HIV sequence data from 54 participants (99 specimens) were analyzed. The prevalence of transmitted drug resistance was 14% at both thresholds, and acquired drug resistance was 47% at 20%, and 57% at 5% NGS thresholds, respectively. The overall prevalence of drug resistance was 43% at 20%, and 52% at 5% NGS thresholds, respectively. Among 34 participants sampled longitudinally, 21%–35% accumulated 10–17 new resistance mutations during a mean 4.3 months. In phylogenetic analysis within the JI population, 11% were found in three molecular clusters. The extended phylogenetic analysis identified 46% of participants in 22 clusters, of which 21 also included publicly-available DC sequences, and one JI-only unique dyad. This is the first study to identify a high prevalence of HIV drug resistance and its accumulation in a JI population during community reentry and suggests phylogenetic integration of this population into the non-JI DC HIV community. These data support the need for new, effective, and timely interventions to improve HIV treatment during this vulnerable period, and for JI populations to be included in broader surveillance and prevention efforts.

[Mortality and causes of deaths in prisons in Rio de Janeiro, Brazil]

Mortality in prisons, a basic indicator of the right to health for incarcerated persons, has never been studied extensively in Brazil. An assessment of all-cause and cause-specific mortality in prison inmates was conducted in 2016-2017 in the state of Rio de Janeiro, based on data from the Mortality Information System and Prison Administration. Mortality rates were compared between prison population and general population after standardization. The leading causes of death in inmates were infectious diseases (30%), cardiovascular diseases (22%), and external causes (12%). Infectious causes featured HIV/AIDS (43%) and TB (52%, considering all deaths with mention of TB). Only 0.7% of inmates who died had access to extramural health services. All-cause mortality rate was higher among prison inmates than in the state's general population. Among inmates, mortality from infectious diseases was 5 times higher, from TB 15 times higher, and from endocrine diseases (especially diabetes) and cardiovascular diseases 1.5 and 1.3 times higher, respectively, while deaths from external causes were less frequent in prison inmates. The study revealed important potentially avoidable excess deaths in prisons, reflecting lack of care and exclusion of this population from the Brazilian Unified National Health System. This further highlights the need for a precise and sustainable real-time monitoring system for deaths, in addition to restructuring of the prison staff through implementation of the Brazilian National Policy for Comprehensive Healthcare for Persons Deprived of Freedom in the Prison System in order for inmates to fully access their constitutional right to health with the same quality and timeliness as the general population.

Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems

BACKGROUND

Human immunodeficiency virus (HIV) remains a public health priority in Latin America. While the burden of HIV is historically concentrated in urban areas and high-risk groups, subnational estimates that cover multiple countries and years are missing. This paucity is partially due to incomplete vital registration (VR) systems and statistical challenges related to estimating mortality rates in areas with low numbers of HIV deaths. In this analysis, we address this gap and provide novel estimates of the HIV mortality rate and the number of HIV deaths by age group, sex, and municipality in Brazil, Colombia, Costa Rica, Ecuador, Guatemala, and Mexico.

METHODS

We performed an ecological study using VR data ranging from 2000 to 2017, dependent on individual country data availability. We modeled HIV mortality using a Bayesian spatially explicit mixed-effects regression model that incorporates prior information on VR completeness. We calibrated our results to the Global Burden of Disease Study 2017.

RESULTS

All countries displayed over a 40-fold difference in HIV mortality between municipalities with the highest and lowest age-standardized HIV mortality rate in the last year of study for men, and over a 20-fold difference for women. Despite decreases in national HIV mortality in all countries-apart from Ecuador-across the period of study, we found broad variation in relative changes in HIV mortality at the municipality level and increasing relative inequality over time in all countries. In all six countries included in this analysis, 50% or more HIV deaths were concentrated in fewer than 10% of municipalities in the latest year of study. In addition, national age patterns reflected shifts in mortality to older age groups-the median age group among decedents ranged from 30 to 45 years of age at the municipality level in Brazil, Colombia, and Mexico in 2017.

CONCLUSIONS

Our subnational estimates of HIV mortality revealed significant spatial variation and diverging local trends in HIV mortality over time and by age. This analysis provides a framework for incorporating data and uncertainty from incomplete VR systems and can help guide more geographically precise public health intervention to support HIV-related care and reduce HIV-related deaths.

Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions

The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9^th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.

Defining HIV-1 transmission clusters based on sequence data

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.

Controle da tuberculose nas prisões, da pesquisa à ação: a experiência do Rio de Janeiro, Brasil

Resumo As altas taxas de tuberculose (TB) observadas na população carcerária brasileira evidenciam a necessidade, de medidas mais efetivas para o controle da doença nesta população, especialmente no Estado de Rio de Janeiro, onde as taxas de detecção de casos nas prisões são 30 vezes superiores as da população geral. Apresentamos resultados de pesquisas realizadas neste estado no campo da epidemiologia, modelagem matemática, biologia molecular, psicossociologia, arquitetura e direito, a fim de avaliar a situação e desenvolver estratégias de controle da TB adaptadas às especificidades do contexto carcerário. A implementação dessas estratégias implica em considerar o dia a dia da vida na prisão e tornar mais efetiva a fiscalização do sistea de saúde prisional por entidades encarregadas do acompanhamento do cumprimento da pena, de modo a garantir o acesso dos presos à saúde de acordo com leis internacionais e nacionais.

Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis

BACKGROUND

HIV transmitted drug resistance (TDR) remains at moderate level in Latin America and the Caribbean (LAC). However, different epidemiologic scenarios could influence national and sub-regional TDR levels and trends.

METHODS AND FINDINGS

We performed a systematic review of currently available publications on TDR in antiretroviral treatment-naïve adults in LAC. Ninety-eight studies published between January 2000 and June 2015 were included according to critical appraisal criteria and classified by sub-region: Brazil (50), Mesoamerica (17), Southern Cone (16), Andean (8) and Caribbean (7). From these, 81 studies encompassing 11,441 individuals with data on DR mutation frequency were included in a meta-analysis. Overall TDR prevalence in LAC was 7.7% (95% CI: 7.2%-8.2%). An increasing trend was observed for overall TDR when comparing 2000-2005 (6.0%) and 2006-2015 (8.2%) (p<0.0001), which was associated with significant NNRTI TDR increase (p<0.0001). NRTI TDR decreased (4.5% vs. 2.3%, p<0.0001). NNRTI TDR increase was associated mainly with K101E, K103N and G190A. NRTI TDR decrease was associated mainly with M184V, K70R and T215Y. All sub-regions reached moderate overall TDR levels. The rapid increase in TDR to all antiretroviral classes in the Caribbean is notable, as well as the significant increase in NNRTI TDR reaching moderate levels in the Southern Cone. NRTI TDR was dominant in 2000-2005, mainly in the Caribbean, Mesoamerica and Brazil. This dominance was lost in 2006-2015 in all sub-regions, with the Southern Cone and the Caribbean switching to NNRTI dominance. PI TDR remained mostly constant with a significant increase only observed in the Caribbean.

CONCLUSIONS

Given the high conceptual and methodological heterogeneity of HIV TDR studies, implementation of surveys with standardized methodology and national representativeness is warranted to generate reliable to inform public health policies. The observed increasing trend in NNRTI TDR supports the need to strengthen TDR surveillance and programme monitoring and evaluation in LAC.

Public health and international drug policy

In September 2015, the member states of the United Nations endorsed sustainable development goals (SDG) for 2030 that aspire to human rights-centered approaches to ensuring the health and well-being of all people. The SDGs embody both the UN Charter values of rights and justice for all and the responsibility of states to rely on the best scientific evidence as they seek to better humankind. In April 2016, these same states will consider control of illicit drugs, an area of social policy that has been fraught with controversy, seen as inconsistent with human rights norms, and for which scientific evidence and public health approaches have arguably played too limited a role.

The previous UN General Assembly Special Session (UNGASS) on drugs in 1998 – convened under the theme “a drug-free world, we can do it!” – endorsed drug control policies based on the goal of prohibiting all use, possession, production, and trafficking of illicit drugs. This goal is enshrined in national law in many countries. In pronouncing drugs a “grave threat to the health and well-being of all mankind,” the 1998 UNGASS echoed the foundational 1961 convention of the international drug control regime, which justified eliminating the “evil” of drugs in the name of “the health and welfare of mankind.” But neither of these international agreements refers to the ways in which pursuing drug prohibition itself might affect public health. The “war on drugs” and “zero-tolerance” policies that grew out of the prohibitionist consensus are now being challenged on multiple fronts, including their health, human rights, and development impact.

The Johns Hopkins – Lancet Commission on Drug Policy and Health has sought to examine the emerging scientific evidence on public health issues arising from drug control policy and to inform and encourage a central focus on public health evidence and outcomes in drug policy debates, such as the important deliberations of the 2016 UNGASS on drugs.

The Johns Hopkins-Lancet Commission is concerned that drug policies are often colored by ideas about drug use and drug dependence that are not scientifically grounded. The 1998 UNGASS declaration, for example, like the UN drug conventions and many national drug laws, does not distinguish between drug use and drug abuse. A 2015 report by the UN High Commissioner for Human Rights, by contrast, found it important to emphasize that “[d]rug use is neither a medical condition nor does it necessarily lead to drug dependence.” The idea that all drug use is dangerous and evil has led to enforcement-heavy policies and has made it difficult to see potentially dangerous drugs in the same light as potentially dangerous foods, tobacco, alcohol for which the goal of social policy is to reduce potential harms.

Improvement in human immunodeficiency virus-1/acquired immune deficiency syndrome patients’ well-being following administration of “Phyto V7”

AIM: To corroborate the capacity of Phyto V7, a complex of phytochemicals, to improve the physical well-being of human immunodeficiency virus-1 (HIV-1) infected and acquired immune deficiency syndrome (AIDS) patients not undergoing antiretroviral treatment.

METHODS: Two hundred and thirty nine HIV-1 seropositive male and female voluntary inmates were recruited through the Uruguay National Program of AIDS. The study participants received for 90 consecutive days every eight hours two tablets (760 mg/each) of Phyto V7, containing a mix of the following phytochemicals: flavonols (Kaempferol, Quercetin), flavones (Apigenin, Luteolin), hydroxy-cinnamic acids (ferrulic acid), carotenoids (Lutein, Lycopene, Beta carotene) and organosulfur compounds, all from vegetal origin. The participants did not receive any antiretroviral treatment during the study. At days 0, 30, 60 and 90 (± 2 d) the participants were evaluated for body mass index (BMI), tolerance to Phyto V7 and Index of Quality of Life based on the Karfnosky scale. ANOVA, Tukey Post-test, χ² test and Wilcoxon Signed Rank test were used to analyze the effect of treatment.

RESULTS: One hundred and nighty nine study participants finished the study. Already after 30 d of Phyto V7 consumption, the weight, BMI and Karnofsky score statistically significantly improved (P < 0.001), and continued to improve until the end of the study. The mean weight gain per participant during the 90 d was of 1.21 kg (approximately 2% of body weight). The overall increase in the mean Karnofsky score after 90 d was 14.08%. The lower the BMI and Karnofsky score of the participants were at the beginning of the study, the more notorious was the improvement over time. For example, the mean increment of Index of Quality of Life, among the participants with an initial Karnofsky score of 5 or below (n = 33) from day 0 to day 90, was of 35.67% (0.476 ± 0.044 vs 0.645 ± 0.09; P < 0.001). The tolerability to Phyto V7 was very good and no adverse reactions were recorded or reported.

CONCLUSION: Administration of the Phyto V7 can be an important tool to improve the well-being of HIV-1 seropositive individuals and AIDS patients, not undergoing antiretroviral treatment.

Incarceration of people living with HIV/AIDS: implications for treatment-as-prevention

Contact with the criminal justice system, including incarceration, is a common experience for many people living with HIV/AIDS. Optimism has recently been expressed that correctional facilities could be important locations for treatment-as-prevention (TasP)-based initiatives. We review recent findings regarding the effect of incarceration on patterns of HIV transmission, testing, treatment initiation and retention. We found that the prevalence of HIV infection among incarcerated individuals remains higher than analogous non-incarcerated populations. Recent studies have shown that voluntary HIV/AIDS testing is feasible in many correctional facilities, although the number of previously undiagnosed individuals identified has been modest. Studies have implied enhanced linkage to HIV/AIDS treatment and care in jails in the United States was associated with improvements in the HIV cascade of care. However, for many individuals living with HIV/AIDS, exposure to the correctional system remains an important barrier to retention in HIV/AIDS treatment and care. Future research should evaluate structural interventions to address these barriers and facilitate the scale-up of TasP-based efforts among individuals living in correctional settings.

The changing face of HIV in Latin America and the Caribbean

Latin America and the Caribbean (LAC) is a region with similarities and important disparities. In recent years LAC has witnessed achievements, with HIV prevalence rates relatively stable for LA and decreasing for the Caribbean. However average values hide differences. General population HIV prevalence in LAC is 0.4 % on average. In the Caribbean there are fewer new HIV infections but HIV prevalence among adults exceeds 1 % in several countries. It is estimated that 31 % of adults living with HIV in LA and 52 % of adults in the Caribbean are women. Unprotected sex is the main route of HIV transmission in LAC. Men who have sex with men and transgender women are the populations with the highest prevalence (10.6 % and 17.7 % respectively); however other key populations such as female sex workers (4.9 %), drug users (range 1 %-49.7 % for intravenous drug users), prisoners and indigenous populations are also important. LAC has the highest anti-retroviral treatment coverage of any low- and middle-income region in the world, but women and children are less likely than men to receive treatment. There is an important pending agenda to address the gaps in information, prevention, and care for HIV in LAC.