RESUMEN
This study aimed to analyse the existence of an association between social class (categorized by type of occupation) and the occurrence of A(H1N1)pmd09 infection and hospitalization for two seasons (2009-2010 and 2010-2011). This multicentre study compared ambulatory A(H1N1)pmd09 confirmed cases with ambulatory controls to measure risk of infection, and with hospitalized A(H1N1)pmd09 confirmed cases to asses hospitalization risk. Study variables were: age, marital status, tobacco and alcohol use, pregnancy, chronic obstructive pulmonary disease, chronic respiratory failure, cardiovascular disease, diabetes, chronic liver disease, body mass index >40, systemic corticosteroid treatment and influenza vaccination status. Occupation was registered literally and coded into manual and non-manual worker occupational social class groups. A conditional logistic regression analysis was performed. There were 720 hospitalized cases, 996 ambulatory cases and 1062 ambulatory controls included in the study. No relationship between occupational social class and A(H1N1)pmd09 infection was found [adjusted odds ratio (aOR) 0·97, 95% confidence interval (CI) 0·74-1·27], but an association (aOR 1·53, 95% CI 1·01-2·31) between occupational class and hospitalization for A(H1N1)pmd09 was observed. Influenza vaccination was a protective factor for A(H1N1)pmd09 infection (aOR 0·41, 95% CI 0·23-0·73) but not for hospitalization. We conclude that manual workers have the highest risk of hospitalization when infected by influenza than other occupations but they do not have a different probability of being infected by influenza.
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Hospitalización , Subtipo H1N1 del Virus de la Influenza A/fisiología , Gripe Humana/epidemiología , Ocupaciones , Clase Social , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Hospitalización/estadística & datos numéricos , Humanos , Gripe Humana/virología , Masculino , Persona de Mediana Edad , Prevalencia , Factores de Riesgo , Estaciones del Año , España/epidemiología , Adulto JovenRESUMEN
The objective of this paper was to develop a prognostic index for severe complications among hospitalized patients with influenza A (H1N1) 2009 virus infection. We conducted a prospective observational cohort study of 618 inpatients with 2009 H1N1 virus infection admitted to 36 Spanish hospitals between July 2009 and February 2010. Risk factors evaluated included host-related factors and clinical data at admission. We developed a composite index of severe in-hospital complications (SIHC), which included: mortality, mechanical ventilation, septic shock, acute respiratory distress syndrome, and requirement for resuscitation maneuvers. Six factors were independently associated with SIHC: age >45 years, male sex, number of comorbidities, pneumonia, dyspnea, and confusion. From the ß parameter obtained in the multivariate model, a weight was assigned to each factor to compute the individual influenza risk score. The score shows an area under the receiver operating characteristic (ROC) curve of 0.77. The SIHC rate was 1.9 % in the low-risk group, 10.3 % in the intermediate-risk group, and 29.6 % in the high-risk group. The odds ratio for complications was 21.8 for the high-risk group compared with the low-risk group. This easy-to-score influenza A (H1N1) 2009 virus infection risk index accurately stratifies patients hospitalized for H1N1 virus infection into low-, intermediate-, and high-risk groups for SIHC.
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Hospitalización , Subtipo H1N1 del Virus de la Influenza A/patogenicidad , Gripe Humana/diagnóstico , Índice de Severidad de la Enfermedad , Adulto , Anciano , Índice de Masa Corporal , Estudios de Casos y Controles , Comorbilidad , Biología Computacional/métodos , Femenino , Humanos , Gripe Humana/virología , Masculino , Persona de Mediana Edad , Análisis Multivariante , Oportunidad Relativa , Embarazo , Pronóstico , Estudios Prospectivos , Curva ROC , Respiración Artificial/métodos , Síndrome de Dificultad Respiratoria/virología , Factores de Riesgo , Choque Séptico/virologíaRESUMEN
Limonium narbonense Miller is a fertile tetraploid species with a sporophytic self-incompatibility system. This sea lavender is found in coastal salt marshes which have been under intense human pressure during the past decades resulting in significant habitat fragmentation. Eleven microsatellite loci specifically designed for this species were amplified in 135 individuals from five populations. These markers were used to investigate the polyploid nature, the levels of genetic diversity and population structure in this species. L. narbonense showed high levels of genetic diversity (A = 7.82, P = 100% H (T) = 0.446), consistent with its likely autotetraploid origin revealed in this study and obligate outcrossing breeding system. Inbreeding (F (IS)) values were low in the three southern populations (mean F (IS) = 0.062), and higher in the northern populations (mean F (IS) = 0.184). Bayesian analysis of population structure revealed that populations could be grouped into two genetic clusters, one including three southern populations and the other the two northernmost ones. Individuals from the two northernmost populations showed higher admixture of the two genetic clusters than individuals from the three southern ones. A thorough analysis of microsatellite electrophoretic patterns suggests an autotetraploid origin for L. narbonense. The genetic structure revealed in this study is attributed to a recent migration from the southern area. This result suggests a net gene flow from the south to the north, likely facilitated by migratory movements of birds visiting the temporary flooded ponds occupied by L. narbonense.
Asunto(s)
Variación Genética , Plumbaginaceae/genética , Tetraploidía , Análisis de Varianza , Teorema de Bayes , Especies en Peligro de Extinción , EspañaRESUMEN
BACKGROUND: Serratia marcescens frequently causes outbreaks in healthcare settings. There are few studies using high-throughput sequencing (HTS) that analyse S. marcescens outbreaks. We present the analysis of two outbreaks in neonatal intensive care units (NICUs) in hospitals from the Comunitat Valenciana (CV, Spain) and the impact of using different reference genomes. METHODS: DNA from cultured isolates was extracted and sequenced by HTS using Illumina NextSeq. Reads were mapped against two reference genomes, strains UMH9 and Db11, and the unmapped fraction of the genomes was assembled to fully genetically characterize the isolates. FINDINGS: Isolates from the first outbreak were identical to the UMH9 reference, an unrelated isolate obtained three years earlier in the USA. This did not occur when the Db11 strain, a standard reference for S. marcescens, was used as the reference for mapping. To check whether UMH9 was a widely distributed clone spreading in the CV, the second outbreak isolates were mapped against this reference. They were not closely related to this strain, and this outbreak could be defined as such regardless of the reference used for mapping the reads. CONCLUSIONS: The choice of the reference for genomic analysis of outbreaks is a critical decision. In the case of the first outbreak, this choice changed the interpretation of the results drastically, allowing or preventing the definition of the outbreak according to the reference used. Although HTS is a powerful tool for epidemiological analysis, it is still essential to collect microbiological and epidemiological data for the correct interpretation of the results.
Asunto(s)
Infección Hospitalaria , Brotes de Enfermedades , Infecciones por Serratia , Serratia marcescens/clasificación , Células Clonales , Infección Hospitalaria/epidemiología , Humanos , Recién Nacido , Unidades de Cuidado Intensivo Neonatal , Pruebas de Sensibilidad Microbiana , Infecciones por Serratia/epidemiología , EspañaRESUMEN
BACKGROUND: Whole-genome sequencing (WGS) of Mycobacterium tuberculosis allows rapid, accurate inferences about the sources, location and timing of transmission. However, in an era of heightened concern for personal privacy and science distrust, such inferences could result in unintended harm and undermine the public´s trust.METHODS: We held interdisciplinary stakeholder discussions and performed ethical analyses of real-world illustrative cases to identify principles that optimise benefit and mitigate harm of M. tuberculosis WGS-driven TB source investigations.RESULTS: The speed and precision with which real-time WGS can be used to associate M. tuberculosis strains with sensitive information has raised important concerns. While detailed understanding of transmission events could mitigate harm to vulnerable patients and communities when otherwise unfairly blamed for TB outbreaks, the precision of WGS can also identify transmission events resulting in social blame, fear, discrimination, individual or location stigma, and the use of defaming language by the public, politicians and scientists. Public health programmes should balance the need to safeguard privacy with public health goals, transparency and individual rights, including the right to know who infects whom or where.CONCLUSIONS: Ethical challenges raised by real-time WGS-driven TB source investigation requires public health authorities to move beyond their current legal mandate and embrace transparency, privacy and community engagement.
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Mycobacterium tuberculosis , Salud Pública , Tuberculosis , Humanos , Personal Administrativo , Brotes de Enfermedades , Mycobacterium tuberculosis/genética , Secuenciación Completa del Genoma , Tuberculosis/epidemiología , Tuberculosis/microbiologíaRESUMEN
Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.
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Proteínas Bacterianas/genética , Genoma Bacteriano , Interacciones Huésped-Patógeno/genética , Mycobacterium tuberculosis/genética , Mycobacterium/genética , Tuberculosis/microbiología , Factores de Virulencia/genética , Proteínas Bacterianas/metabolismo , Conjuntos de Datos como Asunto , Expresión Génica , Sitios Genéticos , Especiación Genética , Historia del Siglo XXI , Historia Antigua , Humanos , Mutación , Mycobacterium/clasificación , Mycobacterium/metabolismo , Mycobacterium/patogenicidad , Mycobacterium tuberculosis/clasificación , Mycobacterium tuberculosis/metabolismo , Mycobacterium tuberculosis/patogenicidad , Filogenia , Recombinación Genética , Selección Genética , Tuberculosis/epidemiología , Tuberculosis/genética , Tuberculosis/historia , Virulencia , Factores de Virulencia/metabolismoRESUMEN
Hepatitis C virus (HCV) infects approximately 3% of the world population. The chronicity of hepatitis C seems to depend on the level of genetic variability. We have recently (Torres-Puente et al., J Viral Hepat, 2008; 15: 188) reported genetic variability estimates from a large-scale sequence analysis of 67 patients infected with HCV subtypes 1a (23 patients) and 1b (44 patients) and related them to response, or lack of, to alpha-interferon plus ribavirin treatment.. Two HCV genome regions were analysed in samples prior to antiviral therapy, one compressing the three hypervariable regions of the E2 glycoprotein and another one including the interferon sensitive determining region and the V3 domain of the NS5A protein. Haplotype and nucleotide diversity measures showed a clear tendency to higher genetic variability levels in nonresponder than in responder patients. Here, we have refined the analysis of genetic variability (haplotype and nucleotide diversity, number of haplotypes and mutations) by considering their distribution in each of the biologically meaningful subregions mentioned above, as well as in their surrounding and intervening regions. Variability levels are very heterogeneous among the different subregions, being higher for nonresponder patients. Interestingly, significant differences were detected in the biologically relevant regions, but also in the surrounding regions, suggesting that the level of variability of the whole HCV genome, rather than exclusively that from the hypervariable regions, is the main indicator of the treatment response. Finally, the number of haplotypes and mutations seem to be better discriminators than haplotype and nucleotide diversity, especially in the NS5A region.
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Antivirales/uso terapéutico , Variación Genética , Hepacivirus/genética , Hepatitis C Crónica/tratamiento farmacológico , Interferones/uso terapéutico , Ribavirina/uso terapéutico , Antivirales/farmacología , Farmacorresistencia Viral , Haplotipos , Hepacivirus/efectos de los fármacos , Hepacivirus/aislamiento & purificación , Hepatitis C Crónica/virología , Humanos , Interferones/farmacología , Mutación Missense , Ribavirina/farmacología , Resultado del Tratamiento , Proteínas del Envoltorio Viral/genética , Proteínas no Estructurales Virales/genéticaRESUMEN
For about half of all Chagas disease cases T. infestans has been the responsible vector. Contributing to its genetic knowledge will increase our understanding of the capacity of geographic expansion and domiciliation of triatomines. Populations of all infestans subcomplex species, T. infestans, T. delpontei, T. platensis and T. melanosoma and the so-called T. infestans "dark morph", from many South American countries were studied. A total of 10 and 7 different ITS-2 and ITS-1 haplotypes, respectively, were found. The total intraspecific ITS-2 nucleotide variability detected in T. infestans is the highest hitherto known in triatomines. ITS-1 minisatellites, detected for the first time in triatomines, proved to be homologous and thus become useful markers. Calculations show that ITS-1 evolves 1.12-2.60 times faster than ITS-2. Despite all species analyzed presenting the same n=22 chromosome number, a large variation of the haploid DNA content was found, including a strikingly high DNA content difference between Andean and non-Andean specimens of T. infestans (mean reduction of 30%, with a maximum of up to 40%) and a correlation between presence/absence of minisatellites and larger/smaller genome size. Population genetics analysis of the eight composite haplotypes of T. infestans and net differences corroborate that there are clear differences between western and eastern populations (60%), and little genetic variation among populations (1.3%) and within populations (40%) within these two groups with migration rates larger than one individual per generation corresponding only to pairs of populations one from each of these groups. These values are indicative either of a large enough gene flow to prevent population differentiation by drift within each geographic area or a very recent spread, the latter hypothesis fitting available data better. Phylogenetic trees support a common ancestor for T. infestans and T. platensis, an origin of T. infestans in Bolivian highlands and two different dispersal lines, one throughout Andean regions of Bolivia and Peru and another in non-Andean lowlands of Chile, Paraguay, Argentina, Uruguay and Brazil.
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Enfermedad de Chagas/transmisión , ADN Espaciador Ribosómico/análisis , ADN Ribosómico/genética , ARN Ribosómico 5.8S/análisis , Triatoma/genética , Animales , Enfermedad de Chagas/genética , ADN Espaciador Ribosómico/genética , Vectores de Enfermedades/clasificación , Genética de Población , Insectos Vectores/genética , Filogenia , ARN Ribosómico 5.8S/genética , Triatoma/clasificaciónRESUMEN
This work was aimed to study the HIV-1 subtype B epidemics in the Basque Country, Spain. 1727 HIV-1 subtype B sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2001 and 2008, were analyzed. 156 transmission clusters were detected by means of phylogenetic analyses. Most of them comprised less than 4 individuals and, in total, they included 441 patients. Six clusters comprised 10 or more patients and were further analyzed in order to study their origin and diversification. Four clusters included men who had unprotected homosexual sex (MSM), one group was formed by intravenous drug users (IDUs), and another included both IDUs and people infected through unprotected heterosexual sex (HTs). Most of these clusters originated from the mid-1980s to the mid-1990s. Only one cluster, formed by MSM, originated after 2000. The time between infections was significantly lower in MSM groups than in those containing IDUs (P-value <0.0001). Nucleoside RT and non-nucleoside RT inhibitor (NRTI and NNRTI)-resistance mutations to antiretroviral treatment were found in these six clusters except the most recent MSM group, but only the IDU clusters presented protease inhibitor (PI)-resistance mutations. The most prevalent mutations for each inhibitor class were PI L90M, NRTI T215D/Y/F, and NNRTI K103N, which were also among the most prevalent resistant variants in the whole dataset. In conclusion, while most infections occur as isolated introductions into the population, the number of infections found to be epidemiologically related within the Basque Country is significant. Public health control measures should be reinforced to prevent the further expansion of transmission clusters and resistant mutations occurring within them.
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Farmacorresistencia Viral , Infecciones por VIH/transmisión , Proteasa del VIH/genética , Transcriptasa Inversa del VIH/genética , VIH-1/clasificación , Consumidores de Drogas/estadística & datos numéricos , Genotipo , VIH-1/genética , Homosexualidad Masculina/estadística & datos numéricos , Humanos , Masculino , Mutación , Filogenia , Análisis de Secuencia de ARN/métodos , España/epidemiología , Factores de TiempoRESUMEN
The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait "fitness" in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of Muller's ratchet and genetic drift as opposed to the appearance of beneficial mutations.
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Cómputos Matemáticos , Modelos Genéticos , Virus de la Estomatitis Vesicular Indiana/genética , Adaptación Fisiológica , Animales , Evolución Biológica , Línea Celular , Cricetinae , Células HeLa , HumanosRESUMEN
The intraspecific variability of Vibrio splendidus, V. harveyi and V. tubiashii recovered from oysters (Ostrea edulis) collected at the Mediterranean coast near Valencia, Spain, was analyzed by ribotyping. The two former species represented the most abundant ones, and the third one was the only species described as pathogenic for oysters. A total of 115 environmental strains were studied, 84 of V. splendidus, 23 of V. harveyi and 8 of V. tubiashii. Chromosomal DNA was digested with KpnI and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Ribotyping among natural populations of the three species rendered 5 to 9 bands, and showed a high genetic diversity, with a ratio no. of strains/no. of ribotypes between 1.1 and 1.5. Cluster analysis of V. splendidus ribotypes suggests a seasonal pattern of incidence, with those ribotypes corresponding to winter and spring samples being maintained in the oysters over the year.
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Acuicultura , Ostreidae/microbiología , Ribotipificación/métodos , Vibrio/clasificación , Vibrio/genética , Animales , Análisis por Conglomerados , ADN Bacteriano/genética , Variación Genética , Estaciones del AñoRESUMEN
BACKGROUND: Hepatitis C virus infection (HCV) is not infrequent among haemodialysis patients. Most published reports suggest that patient-to-patient spread, either directly or indirectly, is the most common mode of transmission in renal units. AIM: To investigate the source of an outbreak, and the route of transmission, of acute HCV infection in two Scottish patients occurring within eight weeks of receiving haemodialysis in the same unit while on holiday in Majorca. METHODS: This was an international epidemiological and molecular investigation of HCV infection among a cohort of haemodialysis patients from nine countries. FINDINGS: No further HCV-positive infections were observed among residents and holidaymakers receiving haemodialysis at the unit in Majorca. Molecular investigations confirmed that a Spanish healthcare worker (HCW) was the source of infection for the two Scottish patients. The investigators were unable to determine the route of transmission. CONCLUSIONS: This outbreak is the first reported case of HCW-to-patient transmission of HCV in a renal unit, and the third reported case of transmission involving a HCW who had not performed invasive procedures. The issue of whether renal units are an exceptional case with regards to the risk of transmission associated with non-invasive procedures should be considered, in conjunction with the need to improve surveillance of blood-borne virus transmissions in renal units in the UK and abroad.
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Brotes de Enfermedades , Hepatitis C/epidemiología , Hepatitis C/virología , Diálisis Renal/efectos adversos , Infección Hospitalaria/epidemiología , Infección Hospitalaria/transmisión , Infección Hospitalaria/virología , Genotipo , Hepacivirus/clasificación , Hepacivirus/genética , Hepacivirus/aislamiento & purificación , Hepatitis C/transmisión , Vacaciones y Feriados , Humanos , Epidemiología Molecular , ARN Viral/genética , Escocia/epidemiología , EspañaRESUMEN
BACKGROUND: Epidemiological surveys have revealed outbreaks of pandemic influenza A (H1N1) 2009 in several different contexts. Molecular characterization of the influenza virus could help to provide a more accurate description of these outbreaks. OBJECTIVE: To genotype pandemic influenza A (H1N1) 2009 isolates from an epidemiologically defined nosocomial outbreak. STUDY DESIGN: We sequenced the neuraminidase (NA) and hemagglutinin (HA) influenza A (H1N1) 2009 genes from ten HIV-positive patients involved in an epidemiologically defined outbreak in the Clinical Microbiology and Infectious Diseases (CMID) Department. Sequences were aligned to search for specific genetic features of the involved strain. We also analyzed 37 unrelated influenza A (H1N1) 2009 cases from other hospital departments. All the sequences were used to obtain phylogenetic trees. RESULTS: Identical genotypic features were shared by nine of the 10 cases initially considered to be involved in the outbreak, but not by the remaining case. These features involved two silent mutations at N385 and V407 in the NA gene and three amino acid substitutions in the HA gene (D225E, A189T, and P300S). Searching for these substitutions in patients with influenza A (H1N1) 2009 hospitalized in other departments during the same period allowed us to identify an additional unsuspected immunocompetent case. The five outbreak-specific substitutions were absent in the remaining 36 unrelated controls. One of the substitutions (P300S) rendered detection of this variant by the CDC protocol inefficient. The other outbreak-specific substitutions (D225E and A189T) were identified at codons that have been analyzed in the context of virulence. CONCLUSIONS: Genotyping is essential to ensure a more accurate description of pandemic influenza A (H1N1) 2009 outbreaks.
Asunto(s)
Infección Hospitalaria/epidemiología , Genotipo , Subtipo H1N1 del Virus de la Influenza A/genética , Gripe Humana/epidemiología , Pandemias , Sustitución de Aminoácidos , Coinfección , Infección Hospitalaria/complicaciones , Infección Hospitalaria/virología , Brotes de Enfermedades , Técnicas de Genotipaje , Seropositividad para VIH/complicaciones , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Humanos , Subtipo H1N1 del Virus de la Influenza A/clasificación , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Gripe Humana/complicaciones , Gripe Humana/virología , Datos de Secuencia Molecular , Mutación , Neuraminidasa/genética , Filogenia , Proteínas Virales/genéticaRESUMEN
Hepatitis C virus (HCV) is a major health problem worldwide, infecting an estimated 170 million people. The high genetic variability of HCV contributes to the chronicity of hepatitis C. Here, we report results from a large-scale sequence analysis of 67 patients infected with HCV genotype 1, 23 with subtype 1a and 44 with subtype 1b. Two regions of the HCV genome were analysed in samples prior to combined therapy with alpha interferon plus ribavirin, one compressing the hypervariable regions (HVR1, HVR2 and HVR3) of the E2 glycoprotein and another one including the interferon-sensitive determining region (ISDR) and the V3 domain of the NS5A protein. Genetic diversity measures showed a clear tendency to higher genetic variability levels in nonresponder patients to antiviral treatment than in responder patients, although highly disperse values were present within each response group for both subtypes. A more detailed analysis of amino acid composition revealed the presence of several subtype-specific variants in a few positions, but no discriminating positions between responder and nonresponder patients were detected. Our results also revealed that most amino acid positions were highly conserved, especially for subtype 1a. We conclude that the outcome of the antiviral treatment might depend not only on the nature of one or a few independent positions, but more likely on the combination of several positions along the HCV genome. Moreover, the own host's ability to generate an appropriate systemic response, in combination with the action of antivirals, is also likely to be essential for treatment outcome.
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Antivirales/uso terapéutico , Hepacivirus/efectos de los fármacos , Hepacivirus/genética , Hepatitis C/tratamiento farmacológico , Hepatitis C/virología , Sustitución de Aminoácidos , Secuencia Conservada , Hepacivirus/clasificación , Hepacivirus/aislamiento & purificación , Humanos , Interferón-alfa/uso terapéutico , Datos de Secuencia Molecular , Mutación Missense , ARN Viral/genética , Ribavirina/uso terapéutico , Análisis de Secuencia de ADN , Proteínas del Envoltorio Viral/genética , Proteínas no Estructurales Virales/genéticaRESUMEN
Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed.
Asunto(s)
Evolución Molecular , Variación Genética , Plumbaginaceae/genética , Alelos , Genoma de Planta , Genotipo , Geografía , Hibridación Genética , Repeticiones de Microsatélite , Plumbaginaceae/clasificación , Análisis de Secuencia de ADN , EspañaRESUMEN
We have studied the genetic variability in two genes (p18 and p20) from two groups of Citrus tristeza virus (CTV) isolates. One group (isolates T385, T317, T318, and T305) was derived from a Spanish source by successive host passages while the other (isolates T388 and T390) was obtained after aphid transmission from a Japanese source. A total of 274 sequences were obtained for gene p18 and 451 for p20. In the corresponding phylogenetic trees, sequences derived from the severe isolates (T318, T305, and T388) clustered together and separately from those derived from mild or moderate isolates (T385, T317, and T390), regardless of their geographic origin. Hierarchical analyses of molecular variance showed that up to 53% of the total genetic variability in p18 and up to 87% of the variation in p20 could be explained by differences in the pathogenicity features of the isolates. Neutrality tests revealed that different selection forces had been acting between isolates and between genes, with purifying selection being suggested for p18 from isolates T385 and T390 and for p20 from isolates T385, T317, and T388, and balancing selection for p18 from isolates T318, T305, and T388 and for p20 from isolates T318 and T390. Furthermore, several models of codon selection were observed, with purifying selection being the most notable one, compatible with low effective population size of the virus populations resulting from transmission bottlenecks. We found no evidence of recombination playing a significant role during p18 and p20 evolution in these isolates. These results suggest that hosts can be an important evolutionary factor for CTV isolates.
Asunto(s)
Closterovirus/crecimiento & desarrollo , Closterovirus/genética , Evolución Molecular , Variación Genética , Mutación , Animales , Citrus/virología , Closterovirus/aislamiento & purificación , ADN Complementario , Frecuencia de los Genes , Genes Virales , Haplotipos , Filogenia , ARN Viral/genética , Recombinación Genética , Selección Genética , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
The effect of hepatitis C virus (HCV) genetic heterogeneity on clinical features of post-transplantation hepatitis C is controversial. Different regions of the HCV genome have been associated with apoptosis, fibrosis, and other pathways leading to liver damage in chronic HCV infection. Besides, differences in immunodominant regions, such as NS3, may influence HCV-specific immune responses and disease outcome. In the liver transplant setting, a recent study has reported a positive association between HCV-1b Core region genetic relatedness 5-year post-transplantation and histological severity of recurrent hepatitis C. We have compared nucleotide sequences of HCV Core, NS3 and NS5b regions in HCV-1b-infected patients 3 years post-transplantation (n = 22). A cohort of nontransplanted patients (n = 22) was used as control of natural chronic HCV-1b infection. Histological evaluation was used to define the rate of fibrosis progression. Molecular variance analysis did not show significant differences in HCV sequences between transplanted and nontransplanted patients, or between those with fast or slow fibrosis progression. The same results were obtained when analysing phylogenetic trees for Core, NS3 and NS5b regions. A more appropriate clustering method (using minimum spanning networks) revealed a significant positive relationship between HCV genetic similarity in Core (r = 0.550, P < 0.01) and NS5b regions (r = 0.847, P < 0.01) and the yearly rate of fibrosis progression in nontransplanted patients which, in contrast, was not observed in transplanted patients. Our results indicate that some strains of HCV-1b might be more pathogenic in the natural course of chronic infection by this virus subtype. In the liver transplant setting, when the immune response is severely compromised, other mechanisms are probably more important in determining hepatitis C progression.
Asunto(s)
Hepacivirus/genética , Hepatitis C Crónica/diagnóstico , Hepatitis C Crónica/etiología , Cirrosis Hepática/diagnóstico , Trasplante de Hígado/efectos adversos , Biopsia , Estudios de Cohortes , Progresión de la Enfermedad , Femenino , Genoma Viral , Hepatitis C Crónica/patología , Hepatitis C Crónica/virología , Humanos , Hígado/patología , Cirrosis Hepática/etiología , Cirrosis Hepática/patología , Masculino , Persona de Mediana Edad , Recurrencia , Análisis de Secuencia de ARN , España , Especificidad de la Especie , Proteínas del Núcleo Viral/genética , Proteínas no Estructurales Virales/genéticaRESUMEN
Borderea chouardii is a relictual and dioecious, strictly sexually reproducing, long-living geophyte of the Dioscoreaceae family. Previous biological and demographic studies have indicated the existence of a uniformly distributed panmictic population of this taxon at the southernmost Spanish pre-Pyrenean mountain ranges where it occurs in rather inaccessible crevices of a single limestone cliff. However, individuals of B. chouardii are spatially subdivided into two subpopulations located, respectively, on the upper and lower parts of the cliff, and vertically separated 150 m. Because of its extreme rarity, B. chouardii was the first Iberian taxon to have a specific conservation plan and has been included in several red lists under the category of critically endangered (CR). However, no previous attempts have been conducted to analyse the fine scale evolutionary mechanisms involved in its present microspatial distribution. Genetic diversity and population structure have been investigated through the analysis of neutral hypervariable markers such as simple sequence repeats (SSRs) and randomly amplified polymorphic DNAs (RAPDs) to unravel the impact of life history traits in the differentiation of the two subpopulations. Both types of molecular markers were unequivocal in distinguishing two genetically distinct groups of individuals corresponding to their spatial separation. However, SSRs detected a higher level of subpopulation differentiation (F(ST) = 0.35, R(ST) = 0.32) than RAPDs (F(ST) = 0.21). SSR data indicated significant deviation from random dispersal of genes and genotypes between the two groups, suggesting that mating occurs mainly among individuals within subpopulations, thus, favouring the divergence between the two groups. This microevolutionary differentiation scenario might have been caused by a coupled effect of past genetic drift and reproductive isolation, as a result of strong glacial age bottlenecks and inefficient dispersal system of pollen and seeds, respectively. The identification of such genetic structure in this narrow endemic prompts a modification of the management strategies of its single extant population.
Asunto(s)
Conservación de los Recursos Naturales , ADN de Plantas/genética , Dioscoreaceae/genética , Variación Genética , Genotipo , Repeticiones de Microsatélite , Hojas de la Planta/genética , Densidad de Población , Técnica del ADN Polimorfo Amplificado Aleatorio , EspañaRESUMEN
Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii. The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii, which is a requisite in order to establish efficient conservation measures for this species.