Molecular characteristics of HIV type 1 infection among prisoners from Central Western 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.

Human immunodeficiency virus infection and syphilis among homeless people in a large city of Central-Western Brazil: prevalence, risk factors, human immunodeficiency virus-1 genetic diversity, and drug resistance mutations

Homeless people are at high risk for sexually transmitted infections (STIs), such as human immunodeficiency virus (HIV) infection and syphilis. We investigated the epidemiology of HIV-1 infection and syphilis among homeless individuals in a large city in Central-Western Brazil. In this cross-sectional study, we interviewed and tested 355 individuals from September 2014 to August 2015. Rapid test samples positive for syphilis were retested using the Venereal Disease Research Laboratory (VDRL) test. Blood samples from HIV-infected participants were collected for POL sequencing using HIV-1 RNA extracted from plasma, reverse transcription, and nested polymerase chain reaction. Anti-HIV-1-positive samples were subtyped by sequencing the nucleotides of HIV-1 protease and part of the HIV-1 reverse transcriptase genes. Transmitted and acquired drug resistance mutations and susceptibility to antiretroviral drugs were also analyzed. Anti-HIV was positive in 14 patients (3.9%; 95% confidence interval [CI]: 2.3–6.4). HIV-1 RNA was detected in 8 of the 14 samples. Two of the eight (25%) isolates showed HIV-1 drug resistance mutations. Furthermore, 78 (22%; 95% CI: 17.9–26.5) and 29 (8.2%; 95% CI: 5.6–11.4) homeless individuals tested positive for syphilis using the rapid test and VDRL test, respectively. Two individuals were anti-HIV-1 and VDRL test positive. Daily alcohol use (adjusted odds ratio [AOR]: 3.2, 95% CI: 1.0–10.4), sex with people living with HIV (PLWH) infection (AOR: 6.8, 95% CI: 1.9–25.0), and sex with people of the same sex (AOR: 5.4, 95% CI: 1.7–17.5) were predictors of HIV infection. Age ≤35 years (AOR: 3.8, 95% CI: 1.4–10.8), previous syphilis testing (AOR: 3.5, 95% CI: 1.4–8.4), history of genital lesions (AOR: 4.9, 95% CI: 1.3–19.1), and crack use in the last six months (AOR: 3.1, 95% CI: 1.3–7.6) were predictors of syphilis. Our findings highlight the importance of STI prevention and control strategies among the homeless.

Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms

Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous pol region studies (2003-2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in pol were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B (n = 629), 6.4% subtype C (n = 53), 4.2% subtype F1 (n = 35), 13.4% intersubtype recombinants: 10.5% BF1 (n = 87), 2.3% BC (n = 19), 0.4% F1CB (n = 3), and 0.2% CF1 (n = 2). Two full and one partial BF1C genomes allowed the characterization of the CRF81_cpx that has 9 breakpoints dividing the genome into 10 subregions. Basic Local Alignment Search Tool searches (Los Alamos HIV Sequence Database) identified six other sequences with the same recombination profile in pol, five from Brazil, and one from Italy. The estimated median TMRCA of CRF81_cpx was 1999 (1992-2003). CRF60_BC-like sequences, originally described in Italy, were also found. Two full and one near full-length BF1 genomes led to the characterization of the new CRF99_BF1 that has six recombination breakpoints dividing the genome into seven subregions. Two new URFs BF1, with six recombination breakpoints and seven subregions were also characterized. The description of the first Brazilian BF1C CRF81_cpx and of the new CRF99_BF1 corroborate the important role of CRFs in the HIV/AIDS epidemic throughout Brazil. Our data also highlight the value of HIV-1 full-genome sequence studies in order to fully reveal the complexity of the epidemic in a huge country as Brazil.

HIV-1 Molecular Epidemiology, Transmission Clusters and Transmitted Drug Resistance Mutations in Central Brazil

We aimed to characterize HIV-1 molecular epidemiology and transmission clusters among heterosexual (HET) and men who have sex with men (MSM) individuals, as well as transmitted drug resistance mutations (TDRM) in Central-Western Brazil. This cross-sectional survey was conducted among 190 antiretroviral naïve HIV-1 infected individuals. Proviral DNA was extracted, and nested PCR amplified partial polymerase gene (PR/RT). After sequencing, subtypes were assigned, and the sequences were analyzed for the occurrence of possible transmission networks. Calibrated Population Resistance (CPR) tool from Stanford HIV Database was used to investigate the presence of TDRM. Among 150 individuals whose samples were successfully sequenced, the most prevalent HIV-1 subtype was B, followed by recombinant forms. The occurrence of twenty transmission clusters composed by at least two sequences was verified, suggesting the existence of transmission clusters among individuals from the same or distinct sexual orientations. Intermediate level of TDRM (12%) was found in the study population, and almost half of the subjects with TDRM had more than one resistance mutation. No correlations between sexual orientation and the presence of TDRM, HIV-1 subtypes/recombinants forms were verified. Taken together, the necessity of the continuous monitoring of the TDRM to verify the importance of pre-genotyping and to delineate future strategies in primary antiretroviral therapy. Likewise, the knowledge of the HIV-1 transmission networks in Brazil would allow the implementation of effective HIV-1 prevention strategies in local settings.

HIV-1 infection among crack cocaine users in a region far from the epicenter of the HIV epidemic in Brazil: Prevalence and molecular characteristics

Brazil has the largest cocaine market in South America, and crack cocaine use is closely associated with HIV-1 infection. This study investigated the prevalence, risk factors, and HIV-1 subtypes, including recombinant forms and mutations associated with drug resistance, among crack cocaine users in Central-West Brazil. We recruited 600 crack cocaine users admitted to a referral hospital in Goiânia for psychiatric disorders. The participants were interviewed; blood samples were collected for anti-HIV-1/2 serological screening. HIV-1 pol gene sequences (entire protease [PR] and partial reverse transcriptase [RT]) were obtained from plasma RNA. HIV-1 subtypes, recombinant viruses, transmitted drug resistance (TDR), and secondary drug resistance mutations were investigated. The median participant age was 30 years (range, 18-68 years); most were male, single, unemployed, and of mixed races. Among them, 2.8% (17/600) were HIV-1 positive: 2.2% of men (11/507) and 6.5% of women (6/93). The main predictors of HIV-1 seropositivity were a sexual partner with HIV infection, irregular condom use, and previous homelessness. HIV-1 pol sequences (12/17) indicated the predominance of subtype B (n = 7), followed by recombinant forms FPR/BRT (n = 1) and BPR/FRT (n = 2) and subtypes F1 (n = 1) and C (n = 1). TDR prevalence was 58.3% (7/12). Isolates from two participants showed mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTI) only (M41L, T125C, T125F, M184V), while an isolate from one patient who had received antiretroviral therapy (ART) since 2008 had a mutation associated with resistance to non-NRTI (G190S). Five isolates had secondary mutations to protease inhibitors (K20M, L10V, L33I, A71T, A71V). In conclusion, the findings of HIV-1 circulation, TDR to NRTI, and secondary mutations to protease inhibitors in ART-naïve crack cocaine users support the importance of monitoring this population in regions far from the epicenter of the HIV epidemic.

Spatiotemporal and demographic history of the HIV-1 circulating recombinant form CRF31_BC in Brazil

CRF31_BC is an HIVs-1 recombinant form very prevalent in the southernmost capital city of Brazil, Porto Alegre. Recent studies have been describing a growing number of cases of infection by CRF31_BC in other Brazilian cities and countries, suggesting a process of expansion of this strain. Aiming to describe the city of origin, dispersion routes and demographic history of CRF31_BC, this study analyzed all HIV-1 CRF31_BC and Brazilian BC mosaic publicly available sequences. CRF31_BC classification was performed by bootscanning and tree reconstruction methods. Bayesian phylogeographic and phylodynamic model approaches were used to reconstruct the spatiotemporal and demographic history of 95 sequences identified as CRF31_BC-like. Porto Alegre was estimated to be the origin and center of the dispersion of the CRF31_BC for most of the analyzed locations. However, some viral transitions independent from Porto Alegre were observed in other cities from the Rio Grande do Sul state and also in other Brazilian states. The estimated CRF31_BC epidemic growth rate was similar to subtype C and B in Brazil. Our findings suggest that CRF31_BC, although mostly prevalent in south region, is circulating nation-wide with some localities presenting autochthonous transmissions.

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.

Incident and long-term HIV-1 infection among pregnant women in Brazil: Transmitted drug resistance and mother-to-child transmission

Primary infection, seroconversion, and transmitted drug resistance (TDR) during pregnancy may influence the risk of mother-to-child-transmission (MTCT) of HIV-1 infection. This study estimated recent seroconversion, TDR rates, HIV-1 subtypes and pregnancy outcomes among 95 recently diagnosed, antiretroviral (ARV)-naïve pregnant women recruited during antenatal care in central western Brazil. Recent seroconversion was defined by BED-capture enzyme immunoassay (<155 days) and ambiguous nucleotides base calls (<1 year) in pol sequences (protease-PR and reverse transcriptase-RT regions). TDR was evaluated by the Calibrated Population Resistance tool. HIV-1 subtypes were defined by REGA and phylogenetic analyses. The median age of participants was 25 years; the median gestational age at diagnosis was 20.5 weeks. Based on serology and sequence polymorphism, recent infection was identified in 11.6% (11/95) and, 9 of them (82%), probably seroconverted during pregnancy; one MTCT case was observed among them. Three cases of stillbirth were observed among chronic infected patients (3.6%; 3/84). Moderate rate of TDR was observed (9/90, 10%, CI95% 4.7-18.1%). Subtype B was 60% (54/90), 13.3% (12/90) was subtype C, 6.7% (6/90) was subtype F1. Recombinant B(PR) /F1(RT) and F1(PR) /B(RT) viruses comprised 15.5% (14/90); B(PR) /C(RT) mosaics represented 4.4% (4/90). Seroconversion during pregnancy, late presentation to antenatal care and moderate TDR identified in this study represent significant challenges for the MTCT elimination. J. Med. Virol. 88:1936-1943, 2016. © 2016 Wiley Periodicals, Inc.

HIV-1 transmitted drug resistance and genetic diversity among patients from Piauí State, Northeast Brazil

HIV-1 transmitted-drug-resistance and genetic diversity are dynamic and may differ in distinct locations/risk groups. In Brazil, increased AIDS incidence and related mortality have been detected in the Northeast region, differently from the epicenter in the Southeast. This cross-sectional study describes transmitted-dru- resistance and HIV-1 subtypes in protease/PR and reverse transcriptase/RT regions among antiretroviral naïve patients from Piauí State, Northeast Brazil. Among 96 patients recruited 89 (92.7%) had HIV-1 PR/RT regions sequenced: 44 females and 45 males, 22 self-declared as men who have sex with men. Transmitted-drug-resistance was investigated by CPR tool (Stanford HIV-1 Drug Resistance/SDRM). HIV-1 subtypes were assigned by REGA and phylogenetic inference. Overall, transmitted-drug-resistance rate was 11.2% (10/89; CI 95%: 5.8-19.1%); 22.7% among men who have sex with men (5/22; CI 95%: 8.8-43.4%), 10% in heterosexual men (2/20; CI 95%: 1.7-29.3%) and 6.8% in women (3/44; CI 95%: 1.8-17.4%). Singleton mutations to protease-inhibitor/PI, nucleoside-reverse-transcriptase-inhibitor/NRTI or non-nucleoside-reverse-transcriptase-inhibitor/NNRTI predominated (8/10): PI mutations (M46L, V82F, L90M); NRTI mutations (M41L, D67N) and NNRTI mutations (K103N/S). Dual class resistance mutations to NRTI and NNRTI were observed: T215L (NRTI), Y188L (NNRTI) and T215N (NRTI), F227L (NNRTI). Subtype B prevailed (86.6%; 77/89), followed by subtype F1 (1.1%, 1/89) and subtype C (1.1%, 1/89). B/F1 and B/C intersubtype recombinants represented 11.2% (10/89). In Piauí State extensive testing of incidence and transmitted-drug-resistance in all populations with risk behaviors may help control AIDS epidemic locally.

Tracing the origin and northward dissemination dynamics of HIV-1 subtype C in Brazil

Previous studies indicate that the HIV-1 subtype C epidemic in southern Brazil was initiated by the introduction of a single founder strain probably originating from east Africa. However, the exact country of origin of such a founder strain as well as the origin of the subtype C viruses detected outside the Brazilian southern region remains unknown. HIV-1 subtype C pol sequences isolated in the southern, southeastern and central-western Brazilian regions (n = 209) were compared with a large number (n ~ 2,000) of subtype C pol sequences of African origin. Maximum-likelihood analyses revealed that most HIV-1 subtype C Brazilian sequences branched in a single monophyletic clade (CBR-I), nested within a larger monophyletic lineage characteristic of east Africa. Bayesian analyses indicate that the CBR-I clade most probably originated in Burundi and was introduced into the Paraná state (southern region) around the middle 1970s, after which it rapidly disseminated to neighboring regions. The states of Paraná and Santa Catarina have been the most important hubs of subtype C dissemination, and routine travel and spatial accessibility seems to have been the major driving forces of this process. Five additional introductions of HIV-1 subtype C strains probably originated in eastern (n = 2), southern (n = 2) and central (n = 1) African countries were detected in the Rio de Janeiro state (southeastern region). These results indicate a continuous influx of HIV-1 subtype C strains of African origin into Brazil and also unveil the existence of unrecognized transmission networks linking this country to east Africa.

Combined antiretroviral and anti-tuberculosis drug resistance following incarceration

We describe a case of HIV/tuberculosis (TB) co-infection from KwaZulu-Natal, South Africa, characterised by drug resistance in both pathogens. The development of drug resistance was linked temporally to two periods of incarceration. This highlights the urgent need for improved integration of HIV/TB control strategies within prison health systems and within the broader public health framework.

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

People deprived of liberty in prisons are at higher risk of infection by the human immunodeficiency virus (HIV) due to their increased exposure through intravenous drug use, unprotected sexual activity, tattooing in prison and blood exposure in fights and rebellions. Yet, the contribution of intramural HIV transmission to the epidemic is scarcely known, especially in low- and middle-income settings. In this study, we surveyed 1,667 inmates incarcerated at Presídio Central de Porto Alegre, located in southern Brazil, for HIV infection and molecular characterization. The HIV seroprevalence was 6.6% (110/1,667). Further analyses were carried out on 40 HIV-seropositive inmates to assess HIV transmission clusters and drug resistance within the facility with the use of molecular and phylogenetic techniques. The molecular epidemiology of HIV-1 subtypes observed was similar to the one reported for the general population in southern Brazil, with the predominance of HIV-1 subtypes C, B, CRF31_BC and unique BC recombinants. In particular, the high rate (24%) of URF_BC found here may reflect multiple exposures of the population investigated to HIV infection. We failed to find HIV-infected inmates sharing transmission clusters with each other. Importantly, the analysis of HIV-1 pol genomic fragments evidenced high rates of HIV primary and secondary (acquired) drug resistance and an alarming proportion of virologic failure among patients under treatment, unveiling suboptimal access to antiretroviral therapy (ARV), low ARV adherence and dissemination of drug resistant HIV strains in primary infections. Our results call for immediate actions of public authority to implement preventive measures, serological screening and, for HIV-seropositive subjects, clinical and treatment follow-up in order to control HIV infection and limit the spread of drug resistance strains in Brazilian prisons.

The increasing prevalence of HIV-1 subtype C in Southern Brazil and its dispersion through the continent

The HIV-1 has evolved swiftly and the scenario of HIV-1 genetic diversity is constantly changing. In South America, recombinant forms of subtypes B, F1, and BF1 have historically driven the HIV-1 epidemic. In recent years, however, infection with subtype C has gained prominence as its prevalence increased in Southern Brazil as well as neighboring countries. Current studies point to a single introduction of closely related strains as the beginning of the Brazilian subtype C epidemic. However, the place of origin of these strains, date, and route of introduction are under continuous debate as well as the clinical outcomes of the emergence of subtype C. Therefore, this paper reviews the history of the HIV-1 subtype C in Brazil, particularly in the Southern region, covering its demographic and evolutionary history and the possible implications to the Brazilian AIDS epidemic as well as to neighboring countries.