C-terminal Motifs of HIV-1 gp41 as Possible Determinants of Viral Pathogenesis / Motivos C-terminales de gp41 del VIH-1 como posibles determinantes de la patogénesis viral / Motivos C-terminais do HIV-1 gp41 como Possíveis Determinantes da Patogénese Viral

Abstract: human immunodeficiency virus type 1 (HIV-1) is the etiological agent of acquired immunodeficiency syndrome (AIDS), a pandemic with high economic and social costs. The envelope glycoprotein (ENV) of the virus mediates the infectious process by binding to and entering the host cell, one of the main target components of studies since its discovery. Its endodomain or C-terminal tail (CTT) participates in late replicative cycle processes, such as intracellular trafficking, activation, and cell death, which occurs because it interacts with multiple cellular factors through motifs or signal sequences present throughout its structure. Although these interactions have not been fully understood at specific levels, studies over more than three decades leave no doubtthatthis domain plays a fundamental role in the biology of the virus and probably the development of the disease. This review describes the studies carried out to date that demonstrate the importance of the CTT, focusing on the motifs responsible for its interactions and its possible roles in the pathogenicity of the infection.

Resumen: el virus de la inmunodeficiencia humana tipo 1 (VIH-1) es el agente etiológico del síndrome de inmunodeficiencia adguirida (SIDA), una pandemia con altos costos económicos y sociales. La glicoproteína de la envoltura (ENV) del virus media el proceso infeccioso al unirse a la célula huésped y entrar en ella, uno de los principales componentes objetivo de los estudios desde su descubrimiento. Su endodominio o cola C-terminal (CTT) participa en procesos tardíos del ciclo replicativo, como tráfico intracelular, activación y muerte celular, lo que ocurre porque interactúa con múltiples factores celulares a través de motivos o secuencias señal presentes en toda su estructura. Aunque estas interacciones no se han entendido completamente a niveles específicos, los estudios durante más de tres décadas no dejan dudas de que este campo juega un papel fundamental en la biología del virus y probablemente en el desarrollo de la enfermedad. Esta revisión describe los estudios realizados hasta la fecha que demuestran la importancia de la CTT, centrándose en los motivos responsables de sus interacciones y sus posibles roles en la patogenicidad de la infección.

Resumo: o vírus da imunodeficiência humana tipo 1 (HIV-1) é o agente etiológico da síndrome da imunodeficiência adquirida (AUXILIA), urna pandemia com elevados custos económicos e sociais. A glicoproteína do envelope (ENV) do vírus media o processo infeccioso ligando-se e entrando na célula hospedeira, um dos principais componentes alvo dos estudos desde sua descoberta. Seu endo domínio ou cauda C-terminal (CTT) participa de processos do ciclo replicativo tardio, como tráfego intracelular, ativação e morte celular, que ocorre porque interage com múltiplos fatores celulares por meio de motivos ou sequências-sinal presentes em toda a sua estrutura. Embora essas interações não tenham sido totalmente compreendidas em níveis específicos, estudos ao longo de mais de três décadas não deixam dúvidas de que esse domínio desempenha um papel fundamental na biologia do vírus e provavelmente no desenvolvimento da doença. Esta revisão descreve os estudos realizados até o momento que demonstram a importância da CTT, com foco nos motivos responsáveis por suas interações e seus possíveis papéis na patogenicidade da infecção.

Evaluation of a loop-mediated isothermal amplification method for rapid detection of human respiratory syncytial virus in children with acute respiratory infection / Evaluación de un método de amplificación isotérmica medida por bucle para la detección rápida del virus sincitial respiratorio en niños con infección respiratoria aguda

Introduction: Human respiratory syncytial virus (hRSV) is the most frequent cause of acute respiratory infection of the lower respiratory tract in children under the age of five. The development of molecular techniques able to identify hRSV is one of the current challenges in the field of clinical research. Objective: To evaluate the ability of an isothermal amplification method to rapidly detect hRSV in children with acute respiratory infection. Materials and methods: We collected 304 nasopharyngeal swab samples from children with symptoms of acute respiratory infection who attended the emergency unit at Hospital de la Universidad del Norte in Barranquilla from April, 2016, to July, 2017. After extracting viral RNA from the samples, we evaluated the ability of the reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) M assay to rapidly detect hRSVA and hRSVB compared to other molecular techniques: quantitative PCR (qPCR), reverse transcriptase-LAMP L assay, and as a standard, the multiplex nested reverse transcriptase polymerase chain reaction (nested RT-PCR). Results: The RT-LAMP M assay had a sensitivity of 93.59% and a specificity of 92.92%, and a concordance of 0.83 ± 0.036 as compared with the nested RT-PCR test. While the Kappa index of the RT-LAMP M assay was higher than the values for the RT-LAMP L assay and the qPCR, the values of the latter two methods were in agreement (0.75 ± 0.043 and 0.71 ± 0.045, respectively). Conclusion: Due to the shorter running times, lower costs and better performance of the RT-LAMP M assay, it can be considered as a useful clinical tool for the detection of RSVA.

Introducción. El virus sincicial respiratorio humano (hRSV) es la causa más frecuente de infección respiratoria aguda de las vías respiratorias inferiores en niños menores de cinco años. El desarrollo de técnicas moleculares para identificarlo es uno de los retos actuales en el campo de la investigación clínica. Objetivo. Evaluar un método de amplificación isotérmica para la detección rápida del hRSV en niños con infección respiratoria aguda. Materiales y métodos. Se extrajo el ARN viral de 304 muestras de hisopado nasal en niños con síntomas de infección respiratoria aguda atendidos en el servicio de urgencias del Hospital de la Universidad del Norte en Barranquilla entre abril del 2016 y julio del 2017. Se evaluó la prueba de amplificación isotérmica mediada por bucle mediante transcriptasa inversa de la proteína de la matriz (M) (Reverse Transcription Loop-Mediated Isothermal Amplification, RT-LAMP) comparada con técnicas moleculares como la reacción en cadena de la polimerasa mediante transcriptasa inversa múltiple anidada (Reverse Transcription-Polymerase Chain Reaction, RT-PCR), la cual se empleó como la prueba estándar, la PCR en tiempo real (quantitative PCR, qPCR) y la RT-LAMP de la proteína L (L) para la detección rápida del virus sincicial respiratorio (VSR), subtipo A y subtipo B. Resultados. La prueba de RT-LAMP (M) tuvo una sensibilidad de 93,59 %, una especificidad de 92,92 % y una concordancia de 0,83 ± 0,036 comparada con la prueba de RT-PCR anidada. El índice kappa del RT-LAMP (M) fue superior, y los valores del RTLAMP (L) y la qPCR concordaron (0,75 ± 0,043 y 0,71 ± 0,045, respectivamente).

Evaluación de un método de amplificación isotérmica mediado por bucle para la detección rápida del virus sincicial respiratorio en niños con infección respiratoria aguda / Evaluation of a loop-mediated isothermal amplification method for the rapid detection of human respiratory syncytial virus in children with acute respiratory infection

Resumen Introducción. El virus sincicial respiratorio humano (hRSV) es la causa más frecuente de infección respiratoria aguda de las vías respiratorias inferiores en niños menores de cinco años. El desarrollo de técnicas moleculares para identificarlo es uno de los retos actuales en el campo de la investigación clínica. Objetivo. Evaluar un método de amplificación isotérmica para la detección rápida del hRSV en niños con infección respiratoria aguda. Materiales y métodos. Se extrajo el ARN viral de 304 muestras de hisopado nasal en niños con síntomas de infección respiratoria aguda atendidos en el servicio de urgencias del Hospital de la Universidad del Norte en Barranquilla entre abril del 2016 y julio del 2017. Se evaluó la prueba de amplificación isotérmica mediada por bucle mediante transcriptasa inversa de la proteína de la matriz (M) (Reverse Transcription Loop-Mediated Isothermal Amplification, RT-LAMP) comparada con técnicas moleculares como la reacción en cadena de la polimerasa mediante transcriptasa inversa múltiple anidada (Reverse Transcription- Polymerase Chain Reaction, RT-PCR), la cual se empleó como la prueba estándar, la PCR en tiempo real (quantitative PCR, qPCR) y la RT-LAMP de la proteína L (L) para la detección rápida del virus sincicial respiratorio (VSR), subtipo A y subtipo B. Resultados. La prueba de RT-LAMP (M) tuvo una sensibilidad de 93,59 %, una especificidad de 92,92 % y una concordancia de 0,83 ± 0,036 comparada con la prueba de RT-PCR anidada. El índice kappa del RT-LAMP (M) fue superior, y los valores del RT-LAMP (L) y la qPCR concordaron (0,75 ± 0,043 y 0,71 ± 0,045, respectivamente). Conclusiones. Estos resultados indican que la prueba RT-LAMP (M) puede considerarse como una herramienta de utilidad clínica para detectar el hSRVA, dado que el tiempo requerido para la obtención de resultados, así como los costos, es menor, y su desempeño es mejor que el de las otras pruebas moleculares evaluadas.

Abstract Introduction: Human respiratory syncytial virus (hRSV) is the most frequent cause of acute respiratory infection of the lower respiratory tract in children under the age of five. The development of molecular techniques able to identify hRSV is one of the current challenges in the field of clinical research. Objective: To evaluate the ability of an isothermal amplification method to rapidly detect hRSV in children with acute respiratory infection. Materials and methods: We collected 304 nasopharyngeal swab samples from children with symptoms of acute respiratory infection who attended the emergency unit at Hospital de la Universidad del Norte in Barranquilla from April, 2016, to July, 2017. After extracting viral RNA from the samples, we evaluated the ability of the reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) M assay to rapidly detect hRSVA and hRSVB compared to other molecular techniques: quantitative PCR (qPCR), reverse transcriptase-LAMP L assay, and as a standard, the multiplex nested reverse transcriptase polymerase chain reaction (nested RT-PCR). Results: The RT-LAMP M assay had a sensitivity of 93.59% and a specificity of 92.92%, and a concordance of 0.83 ± 0.036 as compared with the nested RT-PCR test. While the Kappa index of the RT-LAMP M assay was higher than the values for the RT-LAMP L assay and the qPCR, the values of the latter two methods were in agreement (0.75 ± 0.043 and 0.71 ± 0.045, respectively). Conclusion: Due to the shorter running times, lower costs and better performance of the RT-LAMP M assay, it can be considered as a useful clinical tool for the detection of RSVA.

A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America.

HIV infection has a tremendous impact on the immune system's proper functioning. The mucosa-associated lymphoid tissue (MALT) is significantly disarrayed during HIV infection. Compositional changes in the gut microbiota might contribute to the mucosal barrier disruption, and consequently to microbial translocation. We performed an observational, cross-sectional study aimed at evaluating changes in the fecal microbiota of HIV-infected individuals from Colombia. We analyzed the fecal microbiota of 37 individuals via 16S rRNA gene sequencing; 25 HIV-infected patients and 12 control (non-infected) individuals, which were similar in body mass index, age, gender balance and socioeconomic status. To the best of our knowledge, no such studies have been conducted in Latin American countries. Given its compositional nature, microbiota data were normalized and transformed using Aitchison's Centered Log-Ratio. Overall, a change in the network structure in HIV-infected patients was revealed by using the SPIEC-EASI MB tool. Genera such as Blautia, Dorea, Yersinia, Escherichia-Shigella complex, Staphylococcus, and Bacteroides were highly relevant in HIV-infected individuals. Differential abundance analysis by both sparse Partial Least Square-Discriminant Analysis and Random Forest identified a greater abundance of Lachnospiraceae-OTU69, Blautia, Dorea, Roseburia, and Erysipelotrichaceae in HIV-infected individuals. We show here, for the first time, a predominantly Lachnospiraceae-based signature in HIV-infected individuals.

Virus chikungunya: Características virales y evolución genética / Chikungunya Virus: Viral Features and Genetic Evolution

Resumen El virus chikungunya pertenece al género Alphavirus, de la familia de los Togaviridae. Es transmitido por artrópodos, en particular por la picada de especies de mosquitos, tales como Aedes aegypti y Aedes albopictus. El curso clínico característico de la infección incluye fiebres, artralgias y exantema. Desde que fue reportado en 1952 en los límites de Tanzania y Mozambique ha generado brotes de enorme significado epidemiológico. Recientemente fue causado un brote en las Américas por una cepa del virus, aparentemente, asiática. En esta revisión presentamos su filogenia, estructura y organización del genoma. Enfatizaremos en el mecanismo de multiplicación y la expresión genética. Finalmente, la interacción virus-huésped y sus mecanismos de adaptación a vectores específicos también son discutidos.

Abstract Chikungunya virus belongs to the Alphavirus genus of the family Togaviridae. It is transmitted by arthropods, in particular by the biting of mosquito species such as Aedes aegypti and Aedes albopictus. The characteristic clinical course of the infection includes fever, arthralgia, and rash. Since it was reported on 1952 on the borders of Tanzania and Mozambique, it has been triggered outbreaks with tremendous epidemiological significance. Recently an outbreak was caused in the Americas by an apparent Asian strain of this virus. In this review we present its phylogeny, structure and genome organization. We will emphasize the mechanism of replication and gene expression. Finally, the virus-host interaction and its mechanisms of adaptation to specific vectors are also discussed.

Characterization of treatment failure in HIV positive patients in the Colombian Caribbean region.

BACKGROUND: Treatment failure (TF) in patients receiving antiretroviral therapy against human immunodeficiency virus (HIV) is always a concern. OBJECTIVE: To examine the correlates associated with TF in patients living in the Colombian Caribbean city of Barranquilla, an aspect that was poorly studied in this region. METHODS: Treatment failure was evaluated in a cross-sectional study from virological, immunological and clinical standpoints. RESULTS: It was established that 29.5% of patients under highly active antiretroviral therapy (ART) could be considered in TF. Among those, virological failure was most frequent (20.9%), followed by immunological- (14.0%) and clinical failure (4.7%). In patients showing lack of adherence to the treatment, the likelihood of suffering from TF and virogical failure were respectively increased by 6.67-fold and 12.19-fold, compared with patients showing good adherence. Although there was no statistically significant association, TF tended to be more frequent in young adults, in patients with low income and, low level of education. When ART regimens were compared, there was no apparent difference in TF between regimens based on non-nucleoside reverse transcriptase inhibitors and those based on protease inhibitors. This is very important in the context of recent ART strategies, such as early-initiated ART, aimed at achieving long-term infection control. CONCLUSIONS: Is confirmed the importance of treatment adherence to avoid TF and further highlights the importance of educating HIV-infected patients in all parts of the world, especially those individuals with a lower socio-economic status.

OBJETIVOS: El fracaso terapéutico (FT) en pacientes que están recibiendo terapia antirretroviral contra el Virus de la Inmunodeficiencia Humana (VIH) ha sido siempre preocupante. OBJETIVO: Examinar las variables asociadas con el fracaso terapéutico, un problema que ha sido pobremente estudiado en la región, en pacientes que habitan en Barranquilla, ciudad del Caribe colombiano. MÉTODOS: El fracaso terapéutico fue evaluado en un estudio transversal desde los puntos de vista virológico, inmunológico y clínico. RESULTADOS: Se determinó que el 29.5% de los pacientes bajo terapia antirretroviral (TAR) de gran actividad podría considerase en fracaso terapéutico. El fracaso virológico fue el más frecuente (20.9%), seguido por el inmunológico (14.0%) y el clínico (4.7%). En pacientes que mostraron falta de adherencia al tratamiento, las posibilidades de presentar un fracaso terapéutico y virológico fue mayor, 6.67 y 12.19 veces, respectivamente, comparados con pacientes que mostraron buena adherencia. Aun cuando no hubo una asociación estadística significativa, el fracaso terapéutico tendió a ser más frecuente en adultos jóvenes, en pacientes con bajos ingresos y bajo nivel de educación. Cuando se compararon diferentes regímenes de TAR no hubo una diferencia aparente entre el fracaso terapéutico en los regímenes basados en inhibidores no nucleósidos de la transcriptasa inversa y en aquellos basados en inhibidores de la proteasa. Esto es muy importante en el contexto de recientes estrategias de TAR, como es el caso de las iniciadas en forma temprana con el fin de lograr el control de la infección a largo plazo. CONCLUSIONES: Se confirma la importancia de la adherencia al tratamiento para evitar el fracaso terapéutico y la importancia de educar a los pacientes infectados con el VIH, especialmente aquellos individuos con un nivel socioeconómico bajo.

Characterization of HIV type 1 envelope sequence among viral isolates circulating in the northern region of Colombia, South America.

To characterize human immunodeficiency virus (HIV-1) strains circulating in the Northern region of Colombia in South America, sequences of the viral envelope C2V3C3 region were obtained from patients with different high-risk practices. Close to 60% of the sequences were predicted to belong to macrophage-tropic viruses, according to the positions of acidic amino acids and putative N-linked glycosylation sites. This is in agreement with the fact that most of the patients were recently diagnosed individuals. Phylogenic analysis then allowed assignment of all 35 samples to subtype B viruses. This same subtype was found in previous studies carried out in other Colombian regions. This study thus expands previous analyses with previously missing data from the Northern region of the country. The number and the length of the sequences examined also help to provide a clearer picture of the prevailing situation of the present HIV epidemics in this country.

Proteínas del huésped incorporadas en el Virus de la Inmunodeficiencia Humana tipo 1 (VIH 1) / Host proteins incorporated by the Human Immunodeficiency Virus (HIV-1)

El Virus de la Inmunodeficiencia Humana (VIH), como la mayoría de los virus envueltos, toma esta estructura cuando abandona la célula infectada. El virus adquiere durante este proceso, junto con fragmentos de la membrana de la célula huésped, proteínas derivadas de la membrana celular como parte integral de la envoltura madura. Estos componentes de la envoltura viral derivados del huésped pueden ejercer algunos efectos en el ciclo de vida del virus, en la interacción virus-célula, especialmente en la respuesta del huésped a sus propias proteínas incorporadas por el virus y, finalmente, en la patogénesis de la enfermedad inducida por el virus. El rol de estas proteínas ha recibido cada día más atención, específicamente en la importancia que puedan tener en el proceso infeccioso viral y en le desarrollo del Síndrome de la Inmunodeficiencia Adquirida (SIDA). El objetivo de este artículo es hacer una revisión de las proteínas del huésped que son incorporadas por el VIH, haciendo énfasis en el rol potencial de estas proteínas en la patogénesis del SIDA.

The Human Immunodeficiency Virus (HIV), as most of enveloped virus, acquires its envelope during the process of abandoning the infected cell. During this process, the virus acquires, along with segments of the membrane of the host cell, proteins derived from the cellular membrane as an integral part of the mature envelope. These components of the viral envelope derived from the host cell can exert some effects on the virus life cycle; on the virus-cell interaction, especially on the response of the host to its own proteins incorporated by the virus; and, finally, on the pathogenesis of the illness induced by the virus. The role of these proteins is getting more attention every day, specifically due to the importance they may have in the infectious viral process and in the development of the Acquired Immunodeficiency Syndrome (AIDS). The goal of the present article is to revise the host proteins incorporated by the HIV, placing particular emphasis on the potential role of these proteins in the pathogenesis of AIDS...

CD4/CXCR4 co-expression allows productive HIV-1 infection in canine kidney MDCK cells.

The Madin-Darby canine kidney (MDCK) cell line has become the prototypic cell type for studying the mechanisms involved in viral glycoproteins transport and viral assembly in polarized cells. This cell line has been used in our laboratories for studying human immunodeficiency virus (HIV-1), despite the fact that MDCK cells cannot be infected by HIV. In transfected MDCK cells, HIV-1 glycoproteins are specifically transported to the basolateral cell surface where viral budding also mostly occurs. However, this model is of limited use when viral propagation, infection of most cells, or larger production of virions, is needed. The initial objective of this work was thus to establish an MDCK-derived cell line that could be productively infected by HIV-1, in order to pursue our studies on the polarization of viral budding. Expression of both receptor and co-receptor for T-tropic strains of the virus showed that canine cells are rendered permissive once virus binding and entry is allowed. In addition, a reduced infectivity of the viral particles released from the basolateral surface was observed. This observation most likely reflects the interference mediated by CD4 molecules that accumulate at the basolateral domain. Accordingly, this effect was largely prevented when using viruses that down-regulate cell surface CD4 by expression of both viral accessory proteins Vpu and Nef. This is a further evidence that the function of different viral proteins depends of the site of viral budding, which is itself determined by the presence of targeting signal(s) harbored by viral envelope glycoproteins.

Biología molecular de las proteínas accesorias del Virus de la Inmunodeficiencia Humana tipo 1 (VIH-1) / Molecular Biology of accessory proteins of the virus of the human immunodeficiency type 1 (HIV-1)

El Virus de la Inmunodeficiencia Humana tipo 1 (VIH-1) es un retrovirus complejo que codifica15 distintas proteínas. Algunas de estas proteínas no son esenciales para la replicación viral. Noobstante estas proteínas accesorias participan en diferentes estadios del ciclo viral, incluyendo laregulación de la replicación, la infectividad y la salida viral. Los mecanismos por los cuales estasproteínas accesorias orientan ciertos eventos virales y celulares y su interacción con proteínascelulares se ha convertido en un tópico muy importante en investigación. Esta revisión exponeentonces cómo la conformación estructural de las proteínas accesorias del VIH, Nef, Vpr, Vif yVpu está relacionada con sus fenotipos putativos. Finalmente, nuestros resultados de previosestudios serán también presentados y discutidos a la luz de recientes desarrollos en el área.

Human immunodeficiency virus type 1 (HIV-1) is a complex retrovirus encoding 15 distinctproteins. Some of these proteins are not essential for viral replication. However, these accessoryproteins participate in different stages of the viral cycle, including, regulation of the viralreplication, infectivity, and release. The mechanisms by which these accessory proteins drivethe viral and cellular events and their interaction with cellular proteins have become a very hottopic in research. Thus, the present review exposes how the structural conformation of the HIVaccessory proteins Nef, Vpr, Vif and Vpu is related with their putative phenotypes. Finally,our results from previous studies will also be presented and discussed in the light of the recentdevelopments in the field.