RESUMEN
OBJECTIVE: Short-read next-generation sequencing (NGS) has been implemented to study the resistance profile of HIV as it provides a higher sensitivity than Sanger sequencing. However, short-reads only generates a consensus view of the viral population rather than a reconstruction of the viral haplotypes. In this study, we evaluated the resistance profile of HIV quasispecies in patients undergoing treatment failure using SMRT sequencing. DESIGN: Whole-pol RT-PCR was performed on viral RNA extracted from plasma samples of 38 HIV-positive individuals undergoing treatment failure, and sequenced in the RSII instrument. Error correction and viral haplotype phasing was performed with the Multilayer Directed Phasing and Sequencing (MDPSeq) algorithm. Presence of resistance mutations reported by the IAS-USA in 2017 was assessed using an in-house script. RESULTS: The SMRT sequencing-based test detected 131/134 resistance mutations previously detected using a Sanger sequencing-based test. However, the SMRT test also identified seven additional mutations present at an estimated frequency lower than 30%. The intra-host phylogenetic analysis showed that seven samples harbored at least one resistance variant at 20--80% frequency. The haplotype-resolved sequencing revealed viral diversification and selection of new resistance during suboptimal treatment, an overall trend toward selection and accumulation of new resistance mutations, as well as the co-existence of resistant and susceptible variants. CONCLUSION: Our results validate the SMRT sequencing-based test for detection of HIV drug resistance. In addition, this method unraveled the complex dynamic of HIV quasispecies during treatment failure, which might have several implications on clinical management.
Asunto(s)
Infecciones por VIH , VIH-1 , Fármacos Anti-VIH/farmacología , Farmacorresistencia Viral , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/virología , VIH-1/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mutación , Filogenia , Cuasiespecies , Reacción en Cadena en Tiempo Real de la Polimerasa , Insuficiencia del TratamientoRESUMEN
The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity.
Asunto(s)
Variación Genética , Infecciones por VIH/genética , VIH-1/genética , Filogenia , Enfermedad Aguda , Adulto , Antirretrovirales , Femenino , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/metabolismo , VIH-1/metabolismo , Humanos , Masculino , Persona de Mediana Edad , ZambiaRESUMEN
The influence of biological sex on disease progression in HIV-1-infected individuals has been focused on the chronic stage of infection, but little is known about how sex differences influence acute HIV-1 infection. We observed profound differences in viral load and CD4+ T cell activation from the earliest time points in men and women in a Zambian heterosexual acute infection cohort. Women exhibited a >2-fold higher rate of CD4+ T cell loss despite significantly lower viral loads (VL) than men. The importance of studying acute infection was highlighted by the observation that very early in infection, women exhibited significantly higher levels of CD4+ T cell activation, a difference that was lost over the first 3 years of infection as activation in men increased. In women, activation of CD4+ T cells in the acute phase was significantly correlated with plasma levels of 17ß-estradiol (E2). However, unlike in men, higher CD4+ T cell activation in women was not associated with higher VL. In contrast, a higher E2 level in early infection was associated with lower early and set-point VL in women. We attribute this to an inhibitory effect of estradiol on virus replication, which we were able to observe with relevant transmitted/founder viruses in vitro Thus, estradiol plays a key role in defining major differences between men and women during early HIV-1 infection by contributing to both viral control and CD4+ T cell loss, an effect that extends into the chronic phase of the disease.IMPORTANCE Previous studies have identified sex-specific differences during chronic HIV-1 infection, but little is known about sex differences in the acute phase, or how disparities in the initial response to the virus may affect disease. We demonstrate that restriction of viral load in women begins during acute infection and is maintained into chronic infection. Despite this, women exhibit more rapid CD4+ T cell loss than men. These profound differences are influenced by 17ß-estradiol, which contributes both to T cell activation and to reduced viral replication. Thus, we conclude that estradiol plays a key role in shaping responses to early HIV-1 infection that influence the chronic phase of disease.
Asunto(s)
Estradiol/farmacología , Infecciones por VIH/tratamiento farmacológico , Carga Viral/efectos de los fármacos , Adulto , Recuento de Linfocito CD4 , Linfocitos T CD4-Positivos/inmunología , Estudios de Cohortes , Progresión de la Enfermedad , Estradiol/metabolismo , Femenino , Hormonas Esteroides Gonadales/farmacología , Infecciones por VIH/metabolismo , Infecciones por VIH/virología , VIH-1/metabolismo , VIH-1/patogenicidad , Humanos , Activación de Linfocitos , Masculino , Replicación Viral , Zambia/epidemiologíaRESUMEN
HIV-1 frequently escapes from CD8 T cell responses via HLA-I restricted adaptation, leading to the accumulation of adapted epitopes (AE). We previously demonstrated that AE compromise CD8 T cell responses during acute infection and are associated with poor clinical outcomes. Here, we examined the impact of AE on CD8 T cell responses and their biological relevance in chronic HIV infection (CHI). In contrast to acute infection, the majority of AE are immunogenic in CHI. Longitudinal analyses from acute to CHI showed an increased frequency and magnitude of AE-specific IFNγ responses compared to NAE-specific ones. These AE-specific CD8 T cells also were more cytotoxic to CD4 T cells. In addition, AE-specific CD8 T cells expressed lower levels of PD1 and CD57, as well as higher levels of CD28, suggesting a more activated and less exhausted phenotype. During CHI, viral sequencing identified AE-encoding strains as the dominant quasispecies. Despite increased CD4 T cell cytotoxicity, CD8 T cells responding to AE promoted dendritic cell (DC) maturation and CD4 T cell trans-infection perhaps explaining why AE are predominant in CHI. Taken together, our data suggests that the emergence of AE-specific CD8 T cell responses in CHI confers a selective advantage to the virus by promoting DC-mediated CD4 T cell trans-infection.
Asunto(s)
Linfocitos T CD4-Positivos/inmunología , Linfocitos T CD8-positivos/inmunología , Células Dendríticas/inmunología , Epítopos de Linfocito T/inmunología , Infecciones por VIH/virología , VIH-1/inmunología , Linfocitos T Citotóxicos/inmunología , Estudios Transversales , Femenino , Infecciones por VIH/inmunología , Humanos , Interferón gamma/metabolismo , Estudios Longitudinales , Masculino , Carga ViralRESUMEN
HIV-1 adapts to a new host through mutations that facilitate immune escape. Here, we evaluate the impact on viral control and disease progression of transmitted polymorphisms that were either preadapted to or nonassociated with the new host's HLA. In a cohort of 169 Zambian heterosexual transmission pairs, we found that almost one-third of possible HLA-linked target sites in the transmitted virus Gag protein are already adapted, and that this transmitted preadaptation significantly reduced early immune recognition of epitopes. Transmitted preadapted and nonassociated polymorphisms showed opposing effects on set-point VL and the balance between the two was significantly associated with higher set-point VLs in a multivariable model including other risk factors. Transmitted preadaptation was also significantly associated with faster CD4 decline (<350 cells/µl) and this association was stronger after accounting for nonassociated polymorphisms, which were linked with slower CD4 decline. Overall, the relative ratio of the two classes of polymorphisms was found to be the major determinant of CD4 decline in a multivariable model including other risk factors. This study reveals that, even before an immune response is mounted in the new host, the balance of these opposing factors can significantly influence the outcome of HIV-1 infection.
Asunto(s)
Adaptación Fisiológica/inmunología , Progresión de la Enfermedad , Infecciones por VIH/genética , Infecciones por VIH/patología , Antígenos de Histocompatibilidad Clase I/genética , Polimorfismo Genético , Alelos , Linfocitos T CD4-Positivos/inmunología , Epítopos/inmunología , Femenino , Infecciones por VIH/inmunología , Humanos , Inmunidad , Masculino , Modelos Biológicos , Análisis Multivariante , Linfocitos T Citotóxicos/inmunología , Carga Viral/inmunología , Productos del Gen gag del Virus de la Inmunodeficiencia HumanaRESUMEN
Heterosexual transmission of HIV-1 is characterized by a genetic bottleneck that selects a single viral variant, the transmitted/founder (TF), during most transmission events. To assess viral characteristics influencing HIV-1 transmission, we sequenced 167 near full-length viral genomes and generated 40 infectious molecular clones (IMC) including TF variants and multiple non-transmitted (NT) HIV-1 subtype C variants from six linked heterosexual transmission pairs near the time of transmission. Consensus-like genomes sensitive to donor antibodies were selected for during transmission in these six transmission pairs. However, TF variants did not demonstrate increased viral fitness in terms of particle infectivity or viral replicative capacity in activated peripheral blood mononuclear cells (PBMC) and monocyte-derived dendritic cells (MDDC). In addition, resistance of the TF variant to the antiviral effects of interferon-α (IFN-α) was not significantly different from that of non-transmitted variants from the same transmission pair. Thus neither in vitro viral replicative capacity nor IFN-α resistance discriminated the transmission potential of viruses in the quasispecies of these chronically infected individuals. However, our findings support the hypothesis that within-host evolution of HIV-1 in response to adaptive immune responses reduces viral transmission potential.
Asunto(s)
Farmacorresistencia Viral , Variación Genética , Infecciones por VIH/transmisión , Seropositividad para VIH/transmisión , VIH-1/fisiología , Interferón-alfa/farmacología , Replicación Viral , Antivirales/farmacología , Células Cultivadas , Estudios de Cohortes , Células Dendríticas/inmunología , Células Dendríticas/patología , Células Dendríticas/virología , Composición Familiar , Femenino , Infecciones por VIH/inmunología , Infecciones por VIH/patología , Infecciones por VIH/virología , Seropositividad para VIH/inmunología , Seropositividad para VIH/patología , Seropositividad para VIH/virología , VIH-1/clasificación , VIH-1/efectos de los fármacos , VIH-1/genética , Heterosexualidad , Humanos , Leucocitos Mononucleares/inmunología , Leucocitos Mononucleares/patología , Leucocitos Mononucleares/virología , Masculino , Datos de Secuencia Molecular , Tipificación Molecular , Filogenia , Virión/clasificación , Virión/efectos de los fármacos , Virión/genética , Virión/fisiología , Internalización del Virus/efectos de los fármacos , ZambiaRESUMEN
Single Molecule, Real-Time (SMRT) Sequencing (Pacific Biosciences, Menlo Park, CA, USA) provides the longest continuous DNA sequencing reads currently available. However, the relatively high error rate in the raw read data requires novel analysis methods to deconvolute sequences derived from complex samples. Here, we present a workflow of novel computer algorithms able to reconstruct viral variant genomes present in mixtures with an accuracy of >QV50. This approach relies exclusively on Continuous Long Reads (CLR), which are the raw reads generated during SMRT Sequencing. We successfully implement this workflow for simultaneous sequencing of mixtures containing up to forty different >9 kb HIV-1 full genomes. This was achieved using a single SMRT Cell for each mixture and desktop computing power. This novel approach opens the possibility of solving complex sequencing tasks that currently lack a solution.
Asunto(s)
Variación Genética , Genoma Viral , VIH-1/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis de Secuencia de ADN/métodos , Algoritmos , Análisis por Conglomerados , Humanos , Alineación de SecuenciaRESUMEN
OBJECTIVE: Our objective was to estimate primary resistance in an urban setting in a developing country characterized by high antiretroviral (ARV) coverage over the diagnosed population and also by an important proportion of undiagnosed individuals, in order to determine whether any change in primary resistance occurred in the past five years. DESIGN: We carried out a multi-site resistance surveillance study according to WHO HIV resistance guidelines, using a weighted sampling technique based on annual HIV case reports per site. METHODS: Blood samples were collected from 197 drug-naive HIV-1-infected individuals diagnosed between March 2010 and August 2011 at 20 HIV voluntary counselling and testing centres in Buenos Aires. Clinical records of enrolled patients at the time of diagnosis were compiled. Viral load and CD4 counts were performed on all samples. The pol gene was sequenced and the resistance profile determined. Phylogenetic analysis was performed by neighbour-joining (NJ) trees and bootscanning analysis. RESULTS: We found that 12 (7.9%) of the 152 successfully sequenced samples harboured primary resistance mutations, of which K103N and G190A were the most prevalent. Non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance mutations were largely the most prevalent (5.9%), accounting for 75% of all primary resistance and exhibiting a significant increase (p=0.0072) in prevalence during the past 10 years as compared to our previous study performed in 1997-2000 and in 2003-2005. Nucleoside reverse transcriptase inhibitor (NRTI) and protease inhibitor primary resistance were low and similar to the one previously reported. CONCLUSIONS: Levels of primary NNRTI resistance in Buenos Aires appear to be increasing in the context of a sustained ARV coverage and a high proportion of undiagnosed HIV-positive individuals.
Asunto(s)
Fármacos Anti-VIH/uso terapéutico , Farmacorresistencia Viral , Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/efectos de los fármacos , Adulto , Fármacos Anti-VIH/farmacología , Argentina/epidemiología , Femenino , Genotipo , Infecciones por VIH/tratamiento farmacológico , VIH-1/aislamiento & purificación , Humanos , Incidencia , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Análisis de Secuencia de ADN , Población Urbana , Adulto Joven , Productos del Gen pol del Virus de la Inmunodeficiencia Humana/genéticaRESUMEN
BACKGROUND: In HIV infection, initiation of treatment is associated with improved clinical outcom and reduced rate of sexual transmission. However, difficulty in detecting infection in early stages impairs those benefits. We determined the minimum testing rate that maximizes benefits derived from early diagnosis. METHODS: We developed a mathematical model of HIV infection, diagnosis and treatment that allows studying both diagnosed and undiagnosed populations, as well as determining the impact of modifying time to diagnosis and testing rates. The model's external consistency was assessed by estimating time to AIDS and death in absence of treatment as well as by estimating age-dependent mortality rates during treatment, and comparing them with data previously reported from CASCADE and DHCS cohorts. RESULTS: In our model, life expectancy of patients diagnosed before 8 years post infection is the same as HIV-negative population. After this time point, age at death is significantly dependent on diagnosis delay but initiation of treatment increases life expectancy to similar levels as HIV-negative population. Early mortality during HAART is dependent on treatment CD4 threshold until 6 years post infection and becomes dependent on diagnosis delay after 6 years post infection. By modifying testing rates, we estimate that an annual testing rate of 20% leads to diagnosis of 90% of infected individuals within the first 8.2 years of infection and that current testing rate in middle-high income settings stands close to 10%. In addition, many differences between low-income and middle-high incomes can be predicted by solely modifying the diagnosis delay. CONCLUSIONS: To increase testing rate of undiagnosed HIV population by two-fold in middle-high income settings will minimize early mortality during initiation of treatment and global mortality rate as well as maximize life expectancy. Our results highlight the impact of achieving early diagnosis and the importance of strongly work on improving HIV testing rates.
Asunto(s)
Infecciones por VIH/diagnóstico , Infecciones por VIH/terapia , Adulto , Recuento de Linfocito CD4 , Simulación por Computador , Diagnóstico Precoz , VIH/aislamiento & purificación , Infecciones por VIH/mortalidad , Humanos , Esperanza de Vida , Persona de Mediana Edad , Modelos Biológicos , Tasa de Supervivencia , Resultado del Tratamiento , Adulto JovenRESUMEN
We studied drug resistance mutations (DRMs) in 2623 pol sequences. Out of 94,828 amino acid substitutions that were detected, 8749 corresponded to nucleoside reverse transcriptase inhibitor (NRTI), 3765 to nonnucleoside reverse transcriptase inhibitor (NNRTI), and 7141 to protease inhibitor (PI) resistance-associated mutations. The most common DRMs were L10I, I54V, L90M, V82A, A71V, L10V, M46I, M184V, M41L, T215Y, D67N, L210W, K70R, N348I, V118I, K103N, Y181C, G190A, K101E, V108I, L100I, V90I, K101Q, and A98G. As expected, DRMs frequencies depended on viral genotype. The amounts of NRTI and PI resistance mutations among B and BF sequences from children were higher than among sequences from adults. The frequencies of PI and NRTI resistance mutations among B and BF sequences from adult men were higher than among sequences from women. Some of these observations can be explained in light of the available epidemiological information, but some cannot, indicating that further studies are needed to understand the antiretroviral resistance epidemics in Argentina.
Asunto(s)
Antirretrovirales/farmacología , Farmacorresistencia Viral/genética , Infecciones por VIH/tratamiento farmacológico , VIH/genética , Mutación , Inhibidores de la Transcriptasa Inversa/farmacología , Adolescente , Adulto , Secuencia de Aminoácidos , Antirretrovirales/uso terapéutico , Argentina , Niño , Preescolar , Femenino , Identidad de Género , VIH/efectos de los fármacos , Infecciones por VIH/virología , Humanos , Lactante , Masculino , Inhibidores de la Transcriptasa Inversa/uso terapéuticoRESUMEN
HIV-1 epidemics in South America are believed to have originated in part from the subtype B epidemic initiated in the Caribbean/North America region. However, circulation of BF recombinants in similar proportions was extensively reported. Information currently shows that many BF recombinants share a recombination structure similar to that found in the CRF12_BF. In the present study, analyzing a set of 405 HIV sequences, we identified the most likely origin of the BF epidemic in an early event of recombination. We found that the subtype B epidemics in South America analyzed in the present study were initiated by a founder event that occurred in the early 1970s, a few years after the introduction of these strains in the Americas. Regarding the F/BF recombinant epidemics, by analyzing a subtype F genomic segment within the viral gene gag present in the majority of the BF recombinants, we found evidence of a geographic divergence very soon after the introduction of subtype F strains in South America. Moreover, through analysis of a subtype B segment present in all the CRF12_BF-like recombination structure, we estimated the circulation of the subtype B strain that gave rise to that recombinant structure around the same time period estimated for the introduction of subtype F strains. The HIV epidemics in South America were initiated in part through a founder event driven by subtype B strains coming from the previously established epidemic in the north of the continent. A second introduction driven by subtype F strains is likely to have encountered the incipient subtype B epidemic that soon after their arrival recombined with them, originating the BF epidemic in the region. These results may explain why in South America the majority of F sequences are found as BF recombinants.
Asunto(s)
Evolución Molecular , Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/clasificación , VIH-1/genética , Recombinación Genética , Análisis por Conglomerados , Genoma Viral , Genotipo , VIH-1/aislamiento & purificación , Humanos , Epidemiología Molecular , Filogenia , Análisis de Secuencia de ADN , América del Sur/epidemiología , Factores de TiempoRESUMEN
In Argentina, HIV diagnosis is reached by voluntary testing or symptom-based case findings. However, because of the high proportion of infected individuals unaware of their serologic status new strategies are required. In this article we show how a mathematic model predicts the impact of expanding HIV testing in Argentina. The model is based on time-dependent Markov matrixes and applies parameters-dependent transition-probabilities obtained from both national and international cohort studies. Outputs include time on clinical stages and therapy regime, CD4-count, viral-load, infection-state and age; mortality rates and proportion of unidentified infection at a population-level. Simulations were performed for current testing strategy and for a theoretical scenario with earlier diagnosis. We show how our prediction suggests that diagnosis before onset of symptoms would increase life expectancy by 10.7 years. Also, we show how a reduction of time to diagnosis to 5 or less years from infection would reduce mortality rates in the first year of HAART from 7.6% to 2.1%, the proportion of unrecognized infection from 43.2% to 23.8% and the proportion of individuals with unaware infection needing treatment from 12% to 0.2%. Based on this prediction we stress the importance of implementing health policies aimed at detecting HIV infection in early stages in Argentina.
Asunto(s)
Infecciones por VIH/diagnóstico , Esperanza de Vida , Terapia Antirretroviral Altamente Activa , Argentina , Diagnóstico Tardío/efectos adversos , Diagnóstico Precoz , Infecciones por VIH/mortalidad , Humanos , Cadenas de Markov , Tasa de Supervivencia , Factores de TiempoRESUMEN
Jujuy province, in Northwest Argentina, is known to be endemic for HTLV-1 infection. Moreover, foci of HTLV-1 associated pathologies have also been described in this region. To gain an insight into the current situation of HTLV-1/2 in this endemic area, a seroprevalence and phylogenetic study was performed among a Kolla community from Abra Pampa city and surroundings. Out of 112 individuals, 11 (9.8%) were confirmed as HTLV-1 positive and no HTLV-2 infection was detected. The phylogenetic analysis of the LTR region showed that all the HTLV-1 sequences belonged to the Cosmopolitan subtype a/transcontinental subgroup A, and were closely related to reference sequences from Peru, Argentina, and the South of Brazil (P = 0.82). Considering the cultural and historical features of this community and in spite of the mandatory detection of anti-HTLV-1/2 antibodies in blood banks since 2005, it would be important to implement new public health measures focused on decreasing HTLV-1 transmission in this endemic area.
Asunto(s)
Enfermedades Endémicas , Infecciones por HTLV-I/etnología , Infecciones por HTLV-I/epidemiología , Virus Linfotrópico T Tipo 1 Humano/genética , Indígenas Sudamericanos , Adulto , Anciano de 80 o más Años , Anticuerpos Antivirales/sangre , Argentina/epidemiología , Argentina/etnología , Femenino , Genotipo , Infecciones por HTLV-I/virología , Infecciones por HTLV-II/epidemiología , Infecciones por HTLV-II/etnología , Infecciones por HTLV-II/virología , Virus Linfotrópico T Tipo 1 Humano/clasificación , Virus Linfotrópico T Tipo 1 Humano/inmunología , Virus Linfotrópico T Tipo 1 Humano/aislamiento & purificación , Virus Linfotrópico T Tipo 2 Humano/clasificación , Virus Linfotrópico T Tipo 2 Humano/genética , Virus Linfotrópico T Tipo 2 Humano/inmunología , Virus Linfotrópico T Tipo 2 Humano/aislamiento & purificación , Humanos , Masculino , Persona de Mediana Edad , Filogenia , Análisis de Secuencia de ADN , Estudios SeroepidemiológicosRESUMEN
The South American HIV-1 epidemic is characterized by the co-circulation of subtype B and BF recombinant variants. Together with the B and BF genotypes, HIV-1 subtype C (HIV-1C), F1, and several other recombinants have been reported. The epidemiological significance and immune correlates of these "non-B-non-BF" strains circulating in South America are still uncertain and therefore are increasingly attracting the interest of the scientific community. In this study, the South American HIV-1C epidemic was studied using new technologies for the phylogenetic analysis of large datasets. Our results indicate that there is a major clade encompassing most of the South American HIV-1C strains. These analyses also agreed that some strains do not group inside this major clade, suggesting that there could be HIV-1C sequences of different origins circulating in South America. Others have proposed different hypotheses about the origins of HIV-1C strains from South America. This study shows that an exact single origin cannot be determined, a fact that could be attributed to sampling problems, phylogenetic uncertainty, and the shortage of historical and epidemiological data. Currently, the reported data indicate that HIV-1C strains were introduced in Brazil and afterward spread to other regions of South America. By using character optimization on the obtained phylogenetic trees, we observed that Argentina could also be a point in which the HIV-1C epidemic entered South America.
Asunto(s)
Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/clasificación , VIH-1/genética , Análisis por Conglomerados , VIH-1/aislamiento & purificación , Humanos , Epidemiología Molecular , Datos de Secuencia Molecular , Filogenia , Análisis de Secuencia de ADN , Homología de Secuencia , América del Sur/epidemiologíaRESUMEN
HTLV-1 Cosmopolitan subtype Transcontinental subgroup A has been described among aboriginal communities from the northwest endemic area of Argentina. Moreover, Transcontinental subgroup A and the Japanese subgroup B were reported among blood donors from the nonendemic central region of the country. We carried out the first HTLV-1 phylogenetic study in individuals residing in Buenos Aires capital city. Phylogenetic analysis performed on the LTR region showed that all 44 new strains clustered within the Cosmopolitan subtype, with 42 (95.4%) belonging to Transcontinental subgroup A. Of them, 20 (45.5%) strains grouped in the large Latin American cluster and 4 (9.1%) in the small Latin American cluster. The majority of them belonged to individuals of nonblack origin, grouped with Amerindian strains. Three (6.8%) were closely related to South African references and two monophyletic clusters including only HIV/HTLV-1 coinfected individuals were observed. Interestingly, two (4.5%) new sequences (divergent strains) branched off from all five known Cosmopolitan subgroups in a well-supported clade. In summary, these findings show that HTLV-1 Cosmopolitan subtype Transcontinental subgroup A is infecting residents of Buenos Aires, a nonendemic area of Argentina, and confirm the introduction of divergent strains in the country.
Asunto(s)
Infecciones por HTLV-I/epidemiología , Infecciones por HTLV-I/virología , Virus Linfotrópico T Tipo 1 Humano/clasificación , Virus Linfotrópico T Tipo 1 Humano/aislamiento & purificación , Adulto , Anciano , Argentina/epidemiología , Análisis por Conglomerados , Femenino , Genoma Viral , Genotipo , Virus Linfotrópico T Tipo 1 Humano/genética , Humanos , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Datos de Secuencia Molecular , Filogenia , Mujeres Embarazadas , Análisis de Secuencia de ADN , Homología de Secuencia , Secuencias Repetidas Terminales/genética , Población UrbanaRESUMEN
To perform a diversity surveillance study we characterized viral subtypes among newly diagnosed individuals in Buenos Aires city. Plasma samples were collected from 322 drug-naive newly diagnosed HIV-1 individuals attending two voluntary counseling and testing centers. Sequences of pol and vpu genes were obtained from 283 samples and viral subtype was characterized by Neighbor-joining trees and Bootscanning analysis. BF recombinants were found in 56.9% followed by subtype B strains (39.2%). CRF12_BF structure was found in 27% of BF while another 27% had that structure only in one of both genes analyzed. Unusual non-B-non-BF strains were found in 3.9% (11/283). They were further analyzed by database searching and maximum likelihood trees in order to track their origin. Two subtype C sequences were found to be related to South American isolates while another two subtype C sequences and the subtype C segment of a BC recombinant were found to be related to isolates from Senegal. We also identified the CRF16_A2D previously found in Argentina and the CRF06_cpx commonly prevalent in Africa. The B segment of a BD recombinant was also found to be related to the Argentinean Bs suggesting a recombination between an African and a local strain. We also found a BK and two BA recombinants. In conclusion, CRF16_A2D and a new line of subtype C (of Senegalese origin) seem to be successfully established and are now spreading in Buenos Aires. BF recombinants keep recombining with local strains losing the CRF12_BF structure. Altogether they are changing the diversity of HIV in Argentina.
Asunto(s)
Variación Genética , Infecciones por VIH/virología , VIH-1/genética , Vigilancia de la Población , Adolescente , Adulto , Argentina/epidemiología , Femenino , Infecciones por VIH/epidemiología , VIH-1/clasificación , VIH-1/aislamiento & purificación , Humanos , Masculino , Persona de Mediana Edad , FilogeniaRESUMEN
OBJECTIVE: Our objective was to estimate primary resistance in an urban setting in a developing country with a long history of antiretroviral delivery and high coverage levels. DESIGN: We carried out a resistance surveillance study according to WHO HIV-Resistance Guidelines. METHODS: Blood samples were collected from 323 drug-naive HIV-1 infected individuals diagnosed at two HIV voluntary counselling and testing centers in Buenos Aires. Viral-load, CD4 cell counts and detuned assays were performed on all samples. The pol gene was sequenced and the resistance profile determined. Phylogenetic analysis was performed by neighbor-joining trees and bootscanning analysis. RESULTS: We found that 12 (4.2%) of the 284 samples sequenced harbored primary resistance mutations, of which K103N, M41L and V108I were most prevalent. Phylogenetic analysis revealed evidence for the transmission of the K103N mutation among the drug-naive population. The proportion of recent infections identified by the detuned assay was 10.1%. CONCLUSIONS: Levels of primary resistance in Buenos Aires are still low, despite a long history of ARV delivery and high coverage levels.