RESUMEN
The Vibrio genus contains a large number of closely related bacterial species differing, in some cases, less than 1% in 16S rRNA gene sequence. The present study evaluated the usefulness of toxR gene for phylogenetic and evolution analysis on Vibrio isolates of environmental or clinical origin belonging to the two closely related species V. parahaemolyticus and V. alginolyticus. The phylogenetic analysis based on toxR gene, contrary to 16S rRNA gene, allowed a clear differentiation of the isolates belonging to the two species and showed the presence of two separate, statistically supported clusters in V. alginolyticus (subgroup A and B). Such division, partially reflected in the biochemical features of the isolates, could not be explained by spatial and/or temporal distance in the isolation, leading to the hypothesis of two distinct, co-existing clusters in the V. alginolyticus isolates analysed. The evolutionary analysis on the toxR sequence showed that while the substitutions inferred from the alignment of V. parahaemolyticus are best explained by the negative/neutral selection model, in V. alginolyticus--and particularly in subgroup B--is acting a positive evolutionary pressure. The site detected as under diversifying selection (P164L) could be related to conformational changes of ToxR protein.
Asunto(s)
Proteínas Bacterianas/genética , Proteínas de Unión al ADN/genética , Evolución Molecular , Factores de Transcripción/genética , Vibrio alginolyticus/clasificación , Vibrio parahaemolyticus/clasificación , Animales , Técnicas de Tipificación Bacteriana , Secuencia de Bases , Explotaciones Pesqueras , Peces/microbiología , Microbiología de Alimentos , Humanos , Italia , Proteínas de la Membrana/genética , Datos de Secuencia Molecular , Filogenia , Agua de Mar/microbiología , Mariscos/microbiología , Vibrio alginolyticus/genética , Vibrio parahaemolyticus/genética , Microbiología del AguaRESUMEN
Little information is available about the prevalence of resistance mutations to reverse transcriptase (RT) and protease (PR) inhibitors of HIV-1, after the introduction of antiretroviral treatment in Bulgaria. To fill this gap, we analyzed 80 plasma samples from HIV-1-infected Bulgarian patients, 22 naive at antiretroviral treatment (ARV) and 58 ARV experienced. The subtypes B and A resulted in the two most prevalent (41 patients and 18 patients, respectively). The proportion of subtype B among naive and treated patients was similar in each group (57% vs. 47%, p = 0.62), while a major proportion of subtypes A was present in drug-naive patients rather than in treated patients [8/22 (36.4%) vs. 10/58 (17.2%), p = 0.08]. Two (9.1%) naive patients and 40 (70.1%) drug-experienced patients had viruses carrying at least one mutation conferring resistance to ARV drugs. Of 57 patients having experience with nucleoside reverse transcriptase inhibitors (NRTI), 32 (56.1%) had NRTI resistance mutations; 8/14 (57.2%) patients having experience with non-NRTI (NNRTI) had viruses carrying NNRTI resistance mutations; and 21/46 (45.7%) patients having experience with protease inhibitors (PI) had PI resistance mutations. The commonest resistance mutations resulted in the NRTI mutation M184V (42.1%) and the PI mutation L90M (24.1%). In conclusion, due to the detection of the substantial transmission of resistant variants to newly infected individuals, continuous surveillance is required, since greater access to highly active antiretroviral therapy (HAART) will be expected in Bulgaria. Furthermore, surveillance of PR and RT sequences is also convenient to monitor the introduction of nonsubtype B HIV-1 strains in Bulgaria.
Asunto(s)
Antirretrovirales/uso terapéutico , Farmacorresistencia Viral , Infecciones por VIH/virología , VIH-1/efectos de los fármacos , Mutación Missense , Sustitución de Aminoácidos/genética , Bulgaria , Femenino , Infecciones por VIH/tratamiento farmacológico , Proteasa del VIH/genética , Inhibidores de la Proteasa del VIH/uso terapéutico , Transcriptasa Inversa del VIH/genética , VIH-1/genética , VIH-1/aislamiento & purificación , Humanos , Masculino , Datos de Secuencia Molecular , Plasma/virología , ARN Viral/genética , Inhibidores de la Transcriptasa Inversa/uso terapéutico , Análisis de Secuencia de ADNRESUMEN
In Italy, the prevalence of non-B HIV-1 subtypes ranges reportedly from 5.4% to 12.6%, yet there are no data on their circulation in prisons, where the prevalence of HIV infection is high. A retrospective study was conducted to evaluate the circulation of non-B subtypes and to characterize their determinants in five Italian prisons. To this end an aliquot of samples of blood was taken in the period 2001-2006 from all 262 HIV-positive inmates in whom antiretroviral treatment had failed. Complete HIV-1 PR and RT regions were sequenced for all samples and subjected to phylogenetic analysis; 250 (95.4%) sequences clustered with subtype B. The non-B subtype was found in 4% of Italian prison inmates and 16.7% of non-Italian prison inmates; the overall percentage increased from 1.8% for inmates infected in 1982-1990 to 4.4% in 1991-1999 and 21.9% in 2000-2006. Factors significantly associated with non-B subtypes were an exposure to other than injecting drug use and a first positive HIV test in 2000-2006. Non-B subtypes were distributed within five monophyletic clades. In all cases but one, it was possible to correlate the history of HIV-exposure to the origin of the clade, with high bootstrap values. In conclusion, although the sample may not be representative of the prison inmate population in Italy, the data suggest strongly that the circulation of non-B subtypes has apparently increased. Non-B subtypes were found to have been associated with heterosexual contact and time of the first HIV-positive test. Knowledge of the different subtypes circulating in prisons may be useful for tracking the epidemiology of HIV infection and for choosing antiretroviral therapy.
Asunto(s)
Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/clasificación , Adulto , Femenino , Proteasa del VIH/genética , Transcriptasa Inversa del VIH/genética , VIH-1/genética , VIH-1/aislamiento & purificación , Heterosexualidad , Humanos , Italia/epidemiología , Masculino , Datos de Secuencia Molecular , Filogenia , Prisioneros , Prisiones , Estudios Retrospectivos , Factores de Riesgo , Abuso de Sustancias por Vía IntravenosaRESUMEN
Little is known about the HIV-1 epidemic in Balkan countries. To fill the gap, we investigated the viral genetic diversity in Bulgaria, by sequencing and phylogenetic characterization of 86 plasma samples collected between 2002 and 2006 from seropositive individuals diagnosed within 1986-2006. Analysis of pol gene sequences assigned 51% of the samples to HIV-1 subtype B and 27% to subtype A1. HIV-1 subtype C, F, G, H, and a few putative recombinant forms were also found. Phylogenetic and molecular clock analysis showed a continuous exchange of subtype A and B between Bulgaria and Western as well as other Eastern European countries. At least three separate introductions of HIV-1 subtype A and four of HIV-1 subtype B have occurred within the past 25 years in Bulgaria. The central geographic location of Bulgaria, the substantial genetic heterogeneity of the epidemic with multiple subtypes, and the significant viral flow observed to and from the Balkan countries have the potential to modify the current HIV-1 epidemiological structure in Europe and highlight the importance of more extensive and continuous monitoring of the epidemic in the Balkans.
Asunto(s)
Brotes de Enfermedades , Flujo Génico , VIH-1/genética , Productos del Gen pol del Virus de la Inmunodeficiencia Humana/genética , Adulto , Secuencia de Bases , Teorema de Bayes , Bulgaria/epidemiología , Estudios de Cohortes , Emigración e Inmigración , Femenino , Variación Genética , Infecciones por VIH/epidemiología , Infecciones por VIH/genética , Humanos , Funciones de Verosimilitud , Masculino , Epidemiología Molecular , Datos de Secuencia Molecular , Método de Montecarlo , Filogenia , ARN Viral/sangre , Alineación de Secuencia , Análisis de Secuencia de ARN , Factores de TiempoRESUMEN
Enfuvirtide is the first of a new class of antiretroviral drugs that inhibits HIV entry. It is a 36 amino acid synthetic peptide that mimics the HR2 region of the HIV-1 gp41, preventing the fusion of viral and cellular membranes. Up to now, enfuvirtide was designed based on the HIV-1 B-subtype gp41, and resistance mutations to the fusion inhibitor have been investigated primarily in individuals infected with this subtype. To fill the gap, we analyzed the full length gp41 protein sequence of HIV-1 non-B strains from individuals receiving enfuvirtide-containing regimens. No primary resistance to the enfuvirtide binding domain (36-45 residues) was found. Resistance mutations were detected at follow-up visits and were comparable to those described among B-subtype HIV-1-infected patients; no sequence changes were detected in crucial HR1/HR2 gp41 sites such as the cytotoxic T lymphocyte epitope, cysteine loop, ectodomain, and 5-helix interaction and binding region.
Asunto(s)
Proteína gp41 de Envoltorio del VIH/química , Proteína gp41 de Envoltorio del VIH/uso terapéutico , Inhibidores de Fusión de VIH/uso terapéutico , Infecciones por VIH/tratamiento farmacológico , VIH-1/química , Fragmentos de Péptidos/uso terapéutico , Adulto , Secuencia de Aminoácidos , Farmacorresistencia Viral/genética , Enfuvirtida , Femenino , Proteína gp41 de Envoltorio del VIH/genética , Proteína gp41 de Envoltorio del VIH/farmacología , Inhibidores de Fusión de VIH/metabolismo , Inhibidores de Fusión de VIH/farmacología , Infecciones por VIH/virología , VIH-1/clasificación , VIH-1/efectos de los fármacos , Humanos , Masculino , Persona de Mediana Edad , Datos de Secuencia Molecular , Mutación , Fragmentos de Péptidos/farmacología , FilogeniaRESUMEN
H5N1 avian influenza viruses circulating in early 2004 in eastern Asia appeared to be under strong purifying selection, except for the hemagglutinin (HA) and nonstructural 1 (NS1) genes, where few amino acid positions were found under positive selection pressure. To evaluate whether the widespread circulation of the H5N1 viruses in the following years was accompanied by a change in the evolution of the HA and NS1, phylogenetic and positive selection analyses were performed on 89 HA and 57 NS1 sequences. Results showed that the number of HA positively selected sites decreased compared to 2004; no selection pressure for NS1 was found. These findings suggest a possible change in the adaptation of the H5N1 virus to birds.
Asunto(s)
Brotes de Enfermedades/veterinaria , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Subtipo H5N1 del Virus de la Influenza A/genética , Gripe Aviar/virología , Proteínas no Estructurales Virales/genética , Animales , Aves/virología , Evolución Molecular , Genes Virales , Filogenia , Factores de TiempoRESUMEN
We describe an outbreak of subtype G among injecting drug users (IDU) in northern Italy newly infected with HIV. We analysed pol gene sequences from samples of 139 individuals from different risk groups. Non-B subtypes were more frequently detected among IDU than in homosexual or heterosexual contacts. All G subtypes but one were found among IDU. The phylogenetic analysis indicated that the outbreak was of monophyletic origin and was caused by HIV-1 strains similar to those from western Africa.
Asunto(s)
Brotes de Enfermedades , Infecciones por VIH/epidemiología , VIH-1/genética , Abuso de Sustancias por Vía Intravenosa/epidemiología , Secuencia de Bases , Femenino , Genes pol/genética , Infecciones por VIH/complicaciones , Infecciones por VIH/genética , VIH-1/clasificación , Humanos , Italia/epidemiología , Masculino , Filogenia , Estudios Prospectivos , Sexualidad , Abuso de Sustancias por Vía Intravenosa/complicaciones , Abuso de Sustancias por Vía Intravenosa/genéticaRESUMEN
Twenty-seven strains of Toscana virus, collected over a period of 23 years and isolated from several localities and from different hosts (humans, arthropods and a bat), were investigated by sequencing of a portion of the M genomic segment comprising the G(N) glycoprotein coding region. Sequence data indicated that the divergence among isolates ranged from 0 to 5.7 % at the nucleotide level and from 0 to 3.4 % at the amino acid level. Phylogenetic analysis revealed four main clusters. A close correspondence between viral strains and area/year of isolation could not be demonstrated, whilst co-circulation of different viral strains in the same area and in the same time period was observed for both patients and environmental viral isolates. Alignment of the deduced amino acid sequences and evolutionary analysis indicated that most of the sites along the gene may be invariable because of purifying and/or neutral selection.
Asunto(s)
Infecciones por Bunyaviridae/virología , Genoma Viral , Glicoproteínas/genética , Polimorfismo Genético , Virus de Nápoles de la Fiebre de la Mosca de los Arenales/genética , Proteínas Virales/genética , Adolescente , Adulto , Anciano , Animales , Artrópodos , Secuencia de Bases , Quirópteros , Femenino , Geografía , Humanos , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Datos de Secuencia Molecular , Filogenia , Virus de Nápoles de la Fiebre de la Mosca de los Arenales/clasificación , Virus de Nápoles de la Fiebre de la Mosca de los Arenales/aislamiento & purificación , Selección Genética , Homología de Secuencia de Aminoácido , Homología de Secuencia de Ácido Nucleico , Factores de TiempoRESUMEN
The evolutionary analysis of OrcPI, the orchid homologue to the PISTILLATA/GLOBOSA gene, was conducted on some Mediterranean orchid species, measuring mean pairwise Ka/Ks ratios and nucleotide variability. Evidence for positive selection was tested using a maximum likelihood approach implemented in PAML, and neutrality tests were conducted to assess deviation from neutral evolution. Data were also examined partitioning the coding region into four regions, corresponding to different functional domains of the protein. The results show that OrcPI is subjected to different evolutionary forces: diffuse purifying selection, localized positive selection or selective sweep, and different partitions of selective constraints.
Asunto(s)
Evolución Molecular , Proteínas de Homeodominio/genética , Orchidaceae/genética , Proteínas de Plantas/genética , Secuencia de Aminoácidos , Secuencia de Bases , ADN Complementario/análisis , Región Mediterránea , Datos de Secuencia Molecular , Homología de Secuencia de AminoácidoRESUMEN
BACKGROUND: Asparagus acutifolius L. is a dioecious and native plant species, widely distributed in the Mediterranean Basin. It is known for its fine flavour and could represent an important resource for cultivation programs in desert areas. Few molecular studies have been performed on this species. In the present paper, the ISSR technique was employed to study genetic diversity in Italian A. acutifolius. RESULTS: Twenty-three primers produced a total of 228 polymorphic fragments used to evaluate genetic variation. FST (0.4561) and Theta B (0.4776) values indicate a wide genetic variation among the samples examined. The distance UPGMA tree grouped together the genotypes strictly according to their geographical origin, showing that each sample is genetically structured and can be considered a distinct population. AMOVA analysis further confirmed genetic structuring of the populations. Population-specific fragments were also detected. CONCLUSION: The results suggest that ISSR markers are useful in distinguishing the populations of A. acutifolius according to geographical origin, and confirm the importance of genetic studies for designing germplasm conservation strategies.
Asunto(s)
Asparagus/genética , Variación Genética , Secuencias Repetitivas de Ácidos Nucleicos , ADN de Plantas/genética , Marcadores Genéticos , Geografía , Italia , Reacción en Cadena de la Polimerasa/métodos , Polimorfismo GenéticoRESUMEN
It has been suggested that the evolutionary analysis of floral development genes could explain the divergences between the rates of morphological and molecular evolution. The LEAFY (LFY) gene of Arabidopsis thaliana is one of the central regulatory genes in the control of flower development. We have identified the homologue of this gene (OrcLFY) in Orchis italica using 5'/3'RACE and primer walking, and compared the coding sequences of several orchid species. We analyzed nonsynonymous and synonymous substitution rates between the OrcLFY coding regions of 14 species, and performed a McDonald-Kreitman test on Orchis morio and Orchis laxiflora populations, showing that purifying selection is acting on this gene in these orchids. We have performed a phylogenetic analysis showing that OrcLFY is a new useful marker to reconstruct molecular phylogenies at low taxonomic levels.