Antibody Response 3 Months after 2 Doses of BNT162b2 mRNA COVID-19 Vaccine in Residents of Long-Term Care Facilities.

BACKGROUND: Older adults living in long-term care facilities (LTCFs) are at increased risk for severe outcomes from COVID-19 and were identified as a priority group in COVID-19 vaccination strategies. Emerging evidence suggests vaccine effectiveness in LTCF populations, but data about median and long-term durability of immune response after vaccination are still limited. OBJECTIVES: In this study, we assessed the humoral response to BNT162b2 mRNA COVID-19 vaccine 3 months after the second dose, in a cohort of 495 residents aged ≥65 years from 11 LTCF in Granada, Spain. METHOD: Between April 19 and April 30, 2021, we measured anti-SARS-CoV-2 Spike IgG to evaluate the humoral vaccination response. Antibody titers were reported in binding antibody units (BAU/mL). Bivariate and multivariate logistic regression models were performed to investigate the impact of age, sex, underlying health conditions, and prior COVID-19 infection on the antibody levels. RESULTS: Over 96% of the participants developed an adequate humoral response. We detected higher antibody titers in previously infected individuals, compared with those previously uninfected (B: 1,150.059 BAU/mL, p < 0.001). Moreover, we found a significant inverse association between age and antibody levels (B: -7.943 BAU/mL, p < 0.05). This negative age-dependent response was more noticeable among residents over 85 years old. In contrast, baseline health conditions and cognitive status were not associated with different antibody levels. CONCLUSIONS: These findings support monitoring COVID-19 vaccination response trend in older adults, in order to optimize future disease prevention and control strategies in this vulnerable population.

Comparison between Aptima® assays (Hologic) and the CoBAS® 6800 system (Roche) for the diagnosis of sexually transmitted infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium.

Nowadays, it is of utmost importance to use fully validated assays for molecular-based diagnosis. In the field of sexually transmitted disease (STD), Roche and Hologic provide assays for diagnosing Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG), and Trichomonas vaginalis (TV). A total of 212 clinical samples were tested. Aptima® Combo 2 (detecting CT and NG), Aptima® M. genitalium and the Aptima® T. vaginalis on the Panther® system were compared to CoBAS® CT/NG and CoBAS® TV/MG running on the CoBAS® 6800 system. To solve the discrepancies, Allplex™ STI Essential assay (Seegene®) and/or Sanger DNA sequencing were used. The diagnostic performance was calculated by mean of the sensitivity and specificity parameters. Aptima® (sensitivity: 98.90%, specificity: 100%), CoBAS® (sensitivity 100%, specificity: 96.67%). The CoBAS® combo (CT/NG) failed detecting NG from an anal/rectum specimen, which is not included into the validated specimens of the assay. Aptima® combo 2 produced two false positives (CT and NG), not detected by the third tests. All the assays showed an optimal diagnostic capacity, meeting the requirements for IVD DNA-based assays. All products work optimally on automatic platforms, minimizing time and risk of contamination during handling.

Detection of sexually transmitted disease-causing pathogens from direct clinical specimens with the multiplex PCR-based STD Direct Flow Chip Kit.

Pathogens causing sexually transmitted diseases (STDs) include viruses, bacteria, and parasites. The ability to rapidly and efficiently detect these pathogens in a single reaction still remains a health challenge. The aim of this study was to evaluate the clinical reliability and accuracy of the STD Direct Flow Chip Kit (Vitro, IVD-EC approved), which can simultaneously detect up to 9 different species of STD pathogens at once. This kit enables direct analysis-direct-PCR-of clinical specimens (urine, semen, endocervical, urethral, nasopharyngeal, and perianal swabs) without DNA purification for the following pathogens: Chlamydia trachomatis (serovars A-K and L1-L3), Haemophilus ducreyi, Herpes Simplex Virus (Types I and II), Mycoplasma genitalium, Mycoplasma hominis, Neisseria gonorrhoeae, Treponema pallidum, Trichomonas vaginalis, and Ureaplasma. The Anyplex™ II STI-7 Detection Kit (Seegene, IVD-EC) was used as the reference's method. Existing discordances were resolved using either a third molecular assay or DNA sequencing. Clinical performance was evaluated at two different stages: (i) from purified DNA of three hundred and fifty-eight clinical specimens with a diagnostic sensitivity (SE) and specificity (SP) of 99.4% and 100%, respectively, and an agreement of 99% (kappa index, κ = 0.97) with the reference's method and; (ii) by direct-PCR from six hundred and thirty-three specimens rendering SE, SP, and agreement values of 98.4%, 99.9%, and 98.0% (κ = 0.95), respectively. The STD Direct Flow Chip Kit constitutes a promising alternative to routine procedures in diagnostic, allowing direct analysis of specimens and enabling the detection of a broad panel of pathogens.

Validación de un método seguro y sencillo para la elaboración de secuencias consenso del virus de la inmunodeficiencia humana a partir de los datos de secuenciación masiva 454 / A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data

Objetivo: Generar una secuencia consenso a partir de los datos de secuenciación masiva obtenidos en estudios de resistencias a antiretrovirales, que sea representativa de la secuencia Sanger y que sirva para estudios de epidemiología molecular. Material y métodos: En 62 pacientes se obtuvo la secuencia de transcriptasa reversa-proteasa, mediante Sanger (Trugene-Siemens), y NGS (454GSJunior-Roche). Las secuencias consenso NGS se generaron con Mesquite, seleccionando umbrales 10%, 15% y 20%. Para el estudio filogenético se empleó MEGA. Resultados: Utilizando el umbral 10%, 17/62 pacientes presentaron secuencias pareadas NGS-Sanger, con una mediana de bootstrap del 88% (IQR83,5-95,5). La asociación aumenta a 36/62 pacientes y el bootstrap, a 94% (IQR85,5-98), y alcanza el máximo al 20% en 61/62 pacientes, bootstrap 99% (IQR98-100). Conclusión: Mostramos un método seguro para generar secuencias consenso NGS para su uso en estudios de epidemiología molecular procesadas con umbral 20%, de fácil uso y aplicación en los servicios de microbiología clínica (AU)

Objective: To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Material and methods: Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. Results: At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). Conclusion: A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies (AU)

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data. / Validación de un método seguro y sencillo para la elaboración de secuencias consenso del virus de la inmunodeficiencia humana a partir de los datos de secuenciación masiva 454.

OBJECTIVE: To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. MATERIAL AND METHODS: Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. RESULTS: At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). CONCLUSION: A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies.

Los estudios de resistencias a antirretrovirales como herramienta para el análisis de los clusters de transmisión del virus de la inmunodeficiencia humana / Study of human immunodeficiency virus transmission chains in Andalusia: Analysis from baseline antiretroviral resistance sequences

INTRODUCCIÓN Y OBJETIVO: Las secuencias de proteasa y transcriptasa reversa del VIH-1 aportan una información muy valiosa para el manejo de la infección por VIH, más allá de la información de resistencias a los antirretrovirales. En nuestro estudio la hemos utilizado para evaluar las cadenas de transmisión, la transmisión de resistencias entre ellos, y para conocer la distribución espacial de los diferentes subtipos utilizando técnicas de georreferenciación. MÉTODOS: Hemos estudiado 693 pacientes diagnosticados de VIH-1 durante el periodo 2005-2012, todos ellos residentes en Andalucía Oriental. La secuencia del gen pol (transcriptasa reversa y proteasa) se generó utilizando Trugene® HIV Genotyping Kit (Siemens, NAD). La historia evolutiva fue inferida a través de MEGA 5.2 mediante el método de Neighbor-Joining. Para la filogeografía y el estudio de resistencias utilizamos ArcGIS y REGA. RESULTADOS: Doscientos noventa y ocho pacientes se asociaron en 77 clusters diferentes. La mayoría de los cluster estaban formados por parejas (n = 49), de hombres que practican sexo con hombres (n = 26), de nacionalidad española (n = 37), con una edad menor a 45 años (73,5%). Las áreas de mayor heterogeneidad de subtipos fueron el área metropolitana de Granada y las zonas de costa de Almería y Granada. Hemos encontrado 5 cluster con más de 10 individuos. En 15 cluster detectamos mutaciones de resistencia. CONCLUSIONES: Presentamos datos que demuestran que el estudio epidemiológico de los diferentes clusters de transmisión de VIH mediante análisis filogenético se presenta como una herramienta potente y de gran utilidad para la vigilancia y control epidemiológico de la propagación del VIH, que puede ayudar a diseñar actuaciones eficaces para prevenir la diseminación del VIH

INTRODUCTION AND OBJECTIVE: Protease and reverse transcriptase HIV-1 sequences provide useful information for patient clinical management, as well as information on resistance to antiretrovirals. The aim of this study is to evaluate transmission events, transmitted drug resistance, and to georeference subtypes among newly diagnosed patients referred to our center. METHODS: A study was conducted on 693 patients diagnosed between 2005 and 2012 in Southern Spain. Protease and reverse transcriptase sequences were obtained for resistance to cART analysis with Trugene® HIV Genotyping Kit (Siemens, NAD). MEGA 5.2, Neighbor-Joining, ArcGIS and REGA were used for subsequent analysis. RESULTS: The results showed 298 patients clustered into 77 different transmission events. Most of the clusters were formed by pairs (n = 49), of men having sex with men (n = 26), Spanish (n = 37), and below 45 years of age (73.5%). Urban areas from Granada, and the coastal areas of Almeria and Granada showed the greatest subtype heterogeneity. Five clusters were formed by more than 10 patients, and 15 clusters had transmitted drug resistance. CONCLUSIONS: The study data demonstrate how the phylogenetic characterization of transmission clusters is a powerful tool to monitor the spread of HIV, and may contribute to design correct preventive measures to minimize it

Diagnóstico microbiológico de la infección por el virus de la inmunodeficiencia humana / Microbiological diagnosis of human immunodeficiency virus infection

El presente documento intenta reflejar y actualizar las principales tareas y cometidos que un laboratorio de microbiología debería tener para realizar el diagnóstico y seguimiento de los pacientes infectados por el VIH. Se distribuye en 3 apartados: en el primero se trata el diagnóstico serológico, que en los últimos años ha sufrido una importante renovación, y en el que hemos procurado adecuarnos a las demandas diagnósticas y epidemiológicas actuales, para que desde los laboratorios podamos contribuir a no perder oportunidades de diagnóstico. En una segunda parte se describe la determinación de la carga viral plasmática, y se hace una exhaustiva revisión de los avances tecnológicos y de las recomendaciones actuales, además de abordar un tema de enorme interés clínico, la significación de la viremia persistente de bajo grado. Finalmente, en el tercer apartado se desarrolla el tema de las resistencias a los fármacos antirretrovirales tanto en pacientesnaive como en fracaso, analizando la transcriptasa reversa, la proteasa y la integrasa, e incorporando como novedades las técnicas de determinación del tropismo viral, y el papel de las variantes minoritarias

This document attempts to update the main tasks and roles of the Clinical Microbiology laboratory in HIV diagnosis and monitoring. The document is divided into three parts. The first deals with HIV diagnosis and how serological testing has changed in the last few years, aiming to improve diagnosis and to minimize missed opportunities for diagnosis. Technological improvements for HIV Viral Load are shown in the second part of the document, which also includes a detailed description of the clinical significance of low-level and very low-level viremia. Finally, the third part of the document deals with resistance to antiretroviral drugs, incorporating clinical indications for integrase and tropism testing, as well as the latest knowledge on minority variants

[Study of human immunodeficiency virus transmission chains in Andalusia: analysis from baseline antiretroviral resistance sequences]. / Los estudios de resistencias a antirretrovirales como herramienta para el análisis de los clusters de transmisión del virus de la inmunodeficiencia humana.

INTRODUCTION AND OBJECTIVE: Protease and reverse transcriptase HIV-1 sequences provide useful information for patient clinical management, as well as information on resistance to antiretrovirals. The aim of this study is to evaluate transmission events, transmitted drug resistance, and to georeference subtypes among newly diagnosed patients referred to our center. METHODS: A study was conducted on 693 patients diagnosed between 2005 and 2012 in Southern Spain. Protease and reverse transcriptase sequences were obtained for resistance to cART analysis with Trugene(®) HIV Genotyping Kit (Siemens, NAD). MEGA 5.2, Neighbor-Joining, ArcGIS and REGA were used for subsequent analysis. RESULTS: The results showed 298 patients clustered into 77 different transmission events. Most of the clusters were formed by pairs (n=49), of men having sex with men (n=26), Spanish (n=37), and below 45 years of age (73.5%). Urban areas from Granada, and the coastal areas of Almeria and Granada showed the greatest subtype heterogeneity. Five clusters were formed by more than 10 patients, and 15 clusters had transmitted drug resistance. CONCLUSIONS: The study data demonstrate how the phylogenetic characterization of transmission clusters is a powerful tool to monitor the spread of HIV, and may contribute to design correct preventive measures to minimize it.

[Microbiological diagnosis of human immunodeficiency virus infection]. / Diagnóstico microbiológico de la infección por el virus de la inmunodeficiencia humana.

This document attempts to update the main tasks and roles of the Clinical Microbiology laboratory in HIV diagnosis and monitoring. The document is divided into three parts. The first deals with HIV diagnosis and how serological testing has changed in the last few years, aiming to improve diagnosis and to minimize missed opportunities for diagnosis. Technological improvements for HIV Viral Load are shown in the second part of the document, which also includes a detailed description of the clinical significance of low-level and very low-level viremia. Finally, the third part of the document deals with resistance to antiretroviral drugs, incorporating clinical indications for integrase and tropism testing, as well as the latest knowledge on minority variants.

Baja prevalencia de resistencias primarias frente al virus de la hepatitis B en el sur de España / Low prevalence of hepatitis B virus primary drug resistance in Southern Spain

Introducción Para decidir si es necesario investigar resistencias primarias en pacientes naïve con hepatitis B crónica es necesario conocer su prevalencia. Pacientes y métodos Hemos analizado la secuencia genética de la polimerasa en 105 pacientes naïve. Resultados En 2 pacientes (1,9%) detectamos el cambio rtV173L, mutación compensatoria para lamivudina, en un caso la mutación rtI233V y en otro la «mutación de escape» sG145R.ConclusiónNuestro estudio demuestra que, por el momento, no está justificado realizar estudio de resistencias frente al VHB en pacientes naïve (AU)

Introduction: To know the prevalence of primary resistance in chronic hepatitis B naïve patients isessential to decide on the need of routine laboratory testing. Patients and methods: The genetic sequence of the HBV polymerase from 105 naïve patients was analysed. Results: rtV173L, a lamivudine compensatory mutation, was detected in two patients (1.9%), rtI233V inone patient, and another one carried the sG145R vaccine escape mutation. Conclusion: Our study shows that studying HBV resistance in naïve patients should not be recommended in the routine laboratory setting, for the time being (AU)

[Low prevalence of hepatitis B virus primary drug resistance in Southern Spain]. / Baja prevalencia de resistencias primarias frente al virus de la hepatitis B en el sur de España.

INTRODUCTION: To know the prevalence of primary resistance in chronic hepatitis B naïve patients is essential to decide on the need of routine laboratory testing. PATIENTS AND METHODS: The genetic sequence of the HBV polymerase from 105naïve patients was analysed. RESULTS: rtV173L, a lamivudine compensatory mutation, was detected in two patients (1.9%), rtI233V in one patient, and another one carried the sG145R vaccine escape mutation. CONCLUSION: Our study shows that studying HBV resistance in naïve patients should not be recommended in the routine laboratory setting, for the time being.

[Update on hepatitis C therapy. New drugs, treatment response monitoring and emergence of resistance]. / Actualización en la terapia de la hepatitis C. Nuevos fármacos, monitorización de la respuesta y resistencias.

The development of novel direct antiviral agents (DAAs) against hepatitis C virus (HCV) has represented a breakthrough in the treatment of chronic hepatitis C. Telaprevir and boceprevir are the first two protease inhibitor (PI) DAAs to be approved for combination therapy with pegylated interferon (PEG-IFN) and ribavirin (RBV). In genotype 1 monoinfected patients, triple PI therapy has increased sustained viral response (SVR) rates by approximately 30% compared with conventional combination therapy. The introduction of these drugs into clinical practice will modify the timing of monitoring parameters in diagnostic laboratories, especially with regard to stopping rules and to faster delivery of results. In the near future, new DAAs, directed against different targets of the HCV cycle (polymerase inhibitors, viral replication complex inhibitors and cyclophilin inhibitors), which are currently in various stages of clinical development, will be available. Some of these DAAs have already reached advanced phases of development, both in combination with PEG-IFN and RBV and in interferon-free therapy, with very high rates of SVR.

Quantification of viral loads lower than 50 copies per milliliter by use of the Cobas AmpliPrep/Cobas TaqMan HIV-1 test, version 2.0, can predict the likelihood of subsequent virological rebound to >50 copies per milliliter.

After 1 year of follow-up, patients on HAART with a baseline viral load (VL) of <20 copies/ml showed significantly lower odds of virological rebound to two consecutive VLs of >50 copies/ml than those with baseline VLs of 20 to 39 and 40 to 49 (P < 0.001). The time to virological rebound was also significantly shorter (P < 0.001) for the groups with baseline VLs of 20 to 39 and 40 to 49.

Actualización en la terapia de la hepatitis C. Nuevos fármacos, monitorización de la respuesta y resistencias / Update on hepatitis C therapy. New drugs, treatment response monitoring and emergence of resistance

El desarrollo de nuevas moléculas de acción antiviral directa (AAD) frente al virus de la hepatitis C (VHC) ha supuesto un gran avance en el tratamiento de la hepatitis crónica por VHC. Boceprevir y telaprevir son los 2 primeros AAD, pertenecientes a los inhibidores de la proteasa, autorizados para el tratamiento en combinación con interferón pegilado (INF-PEG) y ribavirina (RBV). En pacientes monoinfectados con genotipo 1, esta terapia triple consigue un incremento aproximado de un 30% en las tasas de respuesta viral sostenida con respecto a la biterapia. La introducción de estos fármacos en la práctica clínica supone una modificación de los parámetros de monitorización en los laboratorios, en especial en lo que se refiere a reglas de parada y a rapidez en la entrega de resultados. En un futuro cercano, dispondremos de nuevos fármacos AAD dirigidos frente a diferentes dianas del ciclo del VHC (polimerasa viral, complejo de replicación o ciclofilinas), que en la actualidad se encuentran en distintas fases de desarrollo clínico. Algunos de ellos ya han alcanzado fases avanzadas de desarrollo, tanto en combinación con INF-PEG y RBV como en terapias libres de interferón, con muy elevadas tasas de respuesta viral sostenida

The development of novel direct antiviral agents (DAAs) against hepatitis C virus (HCV) has represented a breakthrough in the treatment of chronic hepatitis C. Telaprevir and boceprevir are the first two protease inhibitor (PI) DAAs to be approved for combination therapy with pegylated interferon (PEG-IFN) and ribavirin (RBV). In genotype 1 monoinfected patients, triple PI therapy has increased sustained viral response (SVR) rates by approximately 30% compared with conventional combination therapy. The introduction of these drugs into clinical practice will modify the timing of monitoring parameters in diagnostic laboratories, especially with regard to stopping rules and to faster delivery of results. In the near future, new DAAs, directed against different targets of the HCV cycle (polymerase inhibitors, viral replication complex inhibitors and cyclophilin inhibitors), which are currently in various stages of clinical development, will be available. Some of these DAAs have already reached advanced phases of development, both in combination with PEG-IFN and RBV and in interferon-free therapy, with very high rates of SVR

Características químicas, mecanismo de acción y actividad antiviral de etravirina / Chemical characteristics, mechanism of action and antiviral activity of etravirine

Etravirina (ETR) es un derivado diarilpirimidínico. Se trata de una molécula policíclica, constituida por 3 anillos aromáticos unidos por enlaces sencillos (C20H15BrN60). Ejerce su acción mediante un mecanismo de inhibición no competitiva, al unirse a un bolsillo hidrofóbico (binding pocket), muy cercano al centro activo de la enzima, provocando un cambio alostérico hacia una conformación que distorsiona su estructura e impide la polimerización del ADN. Al tratarse de 3 anillos unidos por enlaces sencillos, la molécula está dotada de una enorme flexibilidad y capacidad de torsión. Debido a estas características, ETR puede "acomodarse" a cambios conformacionales en el binding pocket, incluidas un gran número de las conformaciones provocadas por las mutaciones de resistencia que aparecen tras el fracaso a regímenes que incluyen efavirenz o nevirapina. Esta particular estructura química explicará gran parte de sus peculiaridades y diferencias en cuanto a su potencia antiviral y su elevada barrera genética. ETR es una molécula muy activa frente a VIH-1. Presenta una elevada barrera genética y ha demostrado actividad antiviral frente a un amplio panel de virus recombinantes que incorporan mutaciones de resistencia a los no análogos de primera generación. De igual modo, ha demostrado ser eficaz frente a diversos subtipos del grupo M del virus de la inmunodeficiencia humana (VIH) 1 (A, B, C, D, F y H y formas recombinantes CRF01_AE, CRF02_AG, CRF05_ DF) y frente a aislados de VIH-1 grupo O. ETR, como el resto de no análogos, no ha demostrado actividad antiviral frente a VIH-2

Etravirine (ETR) is a diarylpyrimidine derivative with a polycyclic molecule composed of 3 aromatic rings with single bonds between the rings (C20H15BrN60). The drug acts through a mechanism of noncompetitive inhibition on binding to a hydrophobic binding pocket, very close to the active center of the enzyme, provoking an allosteric transition to a conformation that distorts its structure and impedes DNA polymerization. The 3 rings with single bonds between the rings confer the molecule with great flexibility and torsion. Because of these characteristics, etravirine can adapt to conformational changes in the binding pocket, including a large number of the conformations provoked by the resistance mutations that appear after failure to regimens that include efavirenz or nevirapine. This specific chemical structure largely explains the drug's distinguishing features in terms of its antiviral potency and high genetic barrier. ETR is a highly active molecule against HIV-1. This drug has a high genetic barrier to resistance and has demonstrated antiviral activity against a wide panel of recombinant viruses that incorporate resistance mutations to first-generation non-nucleoside analogues. Equally, ETR has demonstrated efficacy against several subtypes of the M group of HIV-1 (A, B, C, D, F and H, and recombinant forms CRF01_AE, CRF02_AG, CRF05_DF), as well as against isolates of HIV-1 group O. ETR, as the rest of non-nucleoside analogues, does not have demonstrated antiviral activity against HIV-2