RESUMEN

We present a new model to describe DNA interactions with large ligands such as proteins, based on a quenched-disorder equation for ligand binding along the double helix and on Manning's description for the local changes of the persistence length at the binding sites. Such a model allows one to extract the physical chemistry of the interactions from pure mechanical measurements, such as those typically performed with DNA-protein complexes in force spectroscopy assays. We have tested the proposed methodology here to investigate the DNA interaction with the protein lysozyme, determining binding parameters such as the equilibrium association constant, the cooperativity degree of the binding reaction, and the fraction of neutralized charges on the phosphate backbone. The model also allows one to get information on the size and positional conformation of the bound proteins.

Asunto(s)

ADN Viral/química , Muramidasa/química , Química Física , Ligandos , Fenómenos Mecánicos , Modelos Moleculares , Muramidasa/metabolismo

RESUMEN

Currently, bovine papillomavirus types are divided into five genera, namely, Deltapapillomavirus, Epsilonpapillomavirus, Xipapillomavirus, Dyoxipapillomavirus, and Dyokappapapillomavirus. In the recent decades, the characterization of numerous putative and novel bovine papillomavirus types from cattle in several geographic regions, has revealed the occurrence of a high viral diversity. In this study, we describe the identification and characterization of a putative new bovine papillomavirus type within species Xipapillomavirus 1 of Xipapillomavirus genus. The detection of the viral types identified in the skin warts was obtained by polymerase chain reaction assays targeting the L1 gene, followed by direct sequencing of the generated amplicons. The partial L1 sequences revealed that bovine papillomavirus types 6, 10, and 11, the putative new bovine papillomavirus type designated BPV/CHI-SW2, and an unreported putative new bovine papillomavirus type (named BPV/BR-UEL08) were associated with cutaneous papillomatosis in the cows from the dairy herd investigated. Phylogenetic reconstruction based on the L1 gene revealed that the BPV/BR-UEL08 isolate clustered with other bovine papillomaviruses classified in the Xipapillomavirus genus, being closely related to representatives of the species Xipapillomavirus 1. Investigations focusing on the molecular epidemiology of bovine papillomaviruses related to clinical outcomes in cattle are of fundamental importance to determine the actual genetic diversity and prevalent viral types to be included in vaccines for cattle.

Asunto(s)

Enfermedades de los Bovinos/virología , Infecciones por Papillomavirus/veterinaria , Enfermedades Cutáneas Virales/veterinaria , Verrugas/veterinaria , Xipapillomavirus/clasificación , Xipapillomavirus/genética , Animales , Brasil , Bovinos , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , Infecciones por Papillomavirus/virología , Filogenia , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Enfermedades Cutáneas Virales/virología , Verrugas/virología , Xipapillomavirus/aislamiento & purificación

RESUMEN

Antiviral drug resistance is the most important factor contributing to treatment failure using nucleos(t)ide analogs such as lamivudine for chronic infection with hepatitis B virus (HBV). Development of a system supporting efficient replication of clinically resistant HBV strains is imperative, and new antiviral drugs are needed urgently to prevent selection of drug-resistant HBV mutants. A novel fluorinated cytidine analog, NCC (N-cyclopropyl-4'-azido-2'-deoxy-2'-fluoro-ß-d-cytidine), was recently shown to strongly inhibit human HBV in vitro and in vivo. This study was designed to evaluate the antiviral activity of NCC against lamivudine-resistant HBV. We generated a stable cell line encoding the major pattern of lamivudine-resistant mutations rtL180M/M204V and designated it "HepG2.RL1". Immuno-transmission electron microscopic examination and enzyme-linked immunosorbent assay were used to detect secretion of HBV-specific particles and antigens. Quantification of extracellular DNA and intracellular DNA of HepG2.RL1 cells by quantitative real-time polymerase chain reaction revealed >625-fold and >5556-fold increases in the 50% inhibitory concentration of lamivudine, respectively, compared with that for the wild-type virus. The results showed that NCC inhibited DNA replication and HBeAg production in wild-type or lamivudine-resistant HBV in a dose-dependent manner. In conclusion, screening for antiviral compounds active against lamivudine-resistant HBV can be carried out with relative ease using hepG2.RL1 cells. NCC is a potential antiviral agent against wild-type HBV and clinical lamivudine-resistant HBV and deserves evaluation for the treatment of HBV infection.

Asunto(s)

Antivirales/farmacología , Citidina/análogos & derivados , Farmacorresistencia Viral/efectos de los fármacos , Virus de la Hepatitis B/efectos de los fármacos , Lamivudine/farmacología , Replicación Viral/efectos de los fármacos , Línea Celular , ADN Viral/química , Femenino , Virus de la Hepatitis B/aislamiento & purificación , Virus de la Hepatitis B/fisiología , Hepatocitos/virología , Humanos , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Mutación

RESUMEN

ABSTRACT Antiviral drug resistance is the most important factor contributing to treatment failure using nucleos(t)ide analogs such as lamivudine for chronic infection with hepatitis B virus (HBV). Development of a system supporting efficient replication of clinically resistant HBV strains is imperative, and new antiviral drugs are needed urgently to prevent selection of drug-resistant HBV mutants. A novel fluorinated cytidine analog, NCC (N-cyclopropyl-4′-azido-2′-deoxy-2′-fluoro-β-d-cytidine), was recently shown to strongly inhibit human HBV in vitro and in vivo. This study was designed to evaluate the antiviral activity of NCC against lamivudine-resistant HBV. We generated a stable cell line encoding the major pattern of lamivudine-resistant mutations rtL180M/M204V and designated it "HepG2.RL1". Immuno-transmission electron microscopic examination and enzyme-linked immunosorbent assay were used to detect secretion of HBV-specific particles and antigens. Quantification of extracellular DNA and intracellular DNA of HepG2.RL1 cells by quantitative real-time polymerase chain reaction revealed >625-fold and >5556-fold increases in the 50% inhibitory concentration of lamivudine, respectively, compared with that for the wild-type virus. The results showed that NCC inhibited DNA replication and HBeAg production in wild-type or lamivudine-resistant HBV in a dose-dependent manner. In conclusion, screening for antiviral compounds active against lamivudine-resistant HBV can be carried out with relative ease using hepG2.RL1 cells. NCC is a potential antiviral agent against wild-type HBV and clinical lamivudine-resistant HBV and deserves evaluation for the treatment of HBV infection.

Asunto(s)

Humanos , Femenino , Persona de Mediana Edad , Antivirales/farmacología , Replicación Viral/efectos de los fármacos , Virus de la Hepatitis B/efectos de los fármacos , Lamivudine/farmacología , Citidina/análogos & derivados , ADN Viral/química , Pruebas de Sensibilidad Microbiana , Línea Celular , Virus de la Hepatitis B/aislamiento & purificación , Virus de la Hepatitis B/fisiología , Hepatocitos/virología , Farmacorresistencia Viral/efectos de los fármacos , Mutación

RESUMEN

The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.

Asunto(s)

ADN Viral/química , ADN Viral/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Papillomaviridae/clasificación , Papillomaviridae/genética , Infecciones por Papillomavirus/virología , Virología/métodos , Humanos , Infecciones por Papillomavirus/epidemiología

RESUMEN

A human adenovirus (HAdV) species D, was isolated from a hospitalised child with severe lower respiratory infection. It was initially detected in the nasopharyngeal aspirate of the child followed by conventional PCR amplification of the hexon, penton base, and fibre genes. Sanger DNA sequencing and phylogenetic analyses showed characteristics of a recombinant genome not described before. Next Generation Sequencing analysis was performed to reconstruct its complete DNA genome after viral isolation in adenocarcinoma human cell line (A549). A complete genomic sequence of 35.2 kb in length, with a G+C content of 57 % was obtained, related to HAdV-D29 (96 % identity). Imputed serology analysis demonstrated its novel type with a nucleotide sequence identity of 95.3 % (hexon loop 1) and 96 % (hexon loop 2) to HAdV-D9. The penton base gene showed a novel sequence, distantly related to HAdV-D44. The E3 and E4 regions evolved significantly from their ancestors. The fibre gene was almost identical to the knob region of HAdV-D15 but showed an unrelated shaft sequence. In conclusion the genomics of this novel HAdV, designated the HAdV-D83 [P83H9F15] prototype and bearing a new penton base gene, supports the importance of viral evolution to understand modified tissue tropism, enhanced transmission, or altered virulence.

Asunto(s)

Adenovirus Humanos/clasificación , Adenovirus Humanos/aislamiento & purificación , Células A549 , Infecciones por Adenoviridae/virología , Adenovirus Humanos/genética , Composición de Base , ADN Viral/química , ADN Viral/genética , Genoma Viral , Humanos , Lactante , Masculino , Nasofaringe/virología , Filogenia , Reacción en Cadena de la Polimerasa , Infecciones del Sistema Respiratorio/virología , Análisis de Secuencia de ADN , Homología de Secuencia , Infecciones Tumorales por Virus/virología , Proteínas Estructurales Virales/genética , Cultivo de Virus

RESUMEN

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and ß-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

Asunto(s)

Papillomavirus Humano 16/metabolismo , Proteínas Intrínsecamente Desordenadas/química , Modelos Moleculares , Proteínas E7 de Papillomavirus/química , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Secuencia de Bases , Secuencia Conservada , ADN Viral/química , ADN Viral/metabolismo , Eliminación de Gen , Concentración de Iones de Hidrógeno , Proteínas Intrínsecamente Desordenadas/genética , Proteínas Intrínsecamente Desordenadas/metabolismo , Leucina/química , Mutagénesis Sitio-Dirigida , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/metabolismo , Fragmentos de Péptidos/química , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/metabolismo , Mutación Puntual , Conformación Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Pliegue de Proteína , Estabilidad Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Alineación de Secuencia

RESUMEN

BACKGROUND: In Africa and Asia, sugarcane is the host of at least seven different virus species in the genus Mastrevirus of the family Geminiviridae. However, with the exception of Sugarcane white streak virus in Barbados, no other sugarcane-infecting mastrevirus has been reported in the New World. Conservation and exchange of sugarcane germplasm using stalk cuttings facilitates the spread of sugarcane-infecting viruses. METHODS: A virion-associated nucleic acids (VANA)-based metagenomics approach was used to detect mastrevirus sequences in 717 sugarcane samples from Florida (USA), Guadeloupe (French West Indies), and Réunion (Mascarene Islands). Contig assembly was performed using CAP3 and sequence searches using BLASTn and BLASTx. Mastrevirus full genomes were enriched from total DNA by rolling circle amplification, cloned and sequenced. Nucleotide and amino acid sequence identities were determined using SDT v1.2. Phylogenetic analyses were conducted using MEGA6 and PHYML3. RESULTS: We identified a new sugarcane-infecting mastrevirus in six plants sampled from germplasm collections in Florida and Guadeloupe. Full genome sequences were determined and analyzed for three virus isolates from Florida, and three from Guadeloupe. These six genomes share >88% genome-wide pairwise identity with one another and between 89 and 97% identity with a recently identified mastrevirus (KR150789) from a sugarcane plant sampled in China. Sequences similar to these were also identified in sugarcane plants in Réunion. CONCLUSIONS: As these virus isolates share <64% genome-wide identity with all other known mastreviruses, we propose classifying them within a new mastrevirus species named Sugarcane striate virus. This is the first report of sugarcane striate virus (SCStV) in the Western Hemisphere, a virus that most likely originated in Asia. The distribution, vector, and impact of SCStV on sugarcane production remains to be determined.

Asunto(s)

Geminiviridae/clasificación , Geminiviridae/aislamiento & purificación , Saccharum/virología , Clonación Molecular , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , ADN Viral/aislamiento & purificación , Florida , Guadalupe , Filogenia , Reunión , Análisis de Secuencia de ADN , Homología de Secuencia , Secuenciación Completa del Genoma

RESUMEN

We present the first longitudinal study reporting the natural history of human papillomavirus (HPV) infection in sun-exposed skin of healthy individuals living in a geographical area in which solar UV radiation is influenced by the ozone content of the atmosphere. During three climatic seasons, skin swab samples were obtained from 78 healthy individuals and the prevalence of cutaneous HPVs was assessed with broad-spectrum FAP and CUT primers and determined at 54, 45 and 47 % in spring, summer and winter, respectively. Frequencies of mixed HPV infections were significantly higher in spring with respect to summer and winter (P=0.02). Seventy-one different HPV types/putative types were identified. While 62 volunteers were HPV-infected in at least one season, 23 had persistent infections. ß-PVs (ß-1) were the most prevalent and persistent. Age was associated with both the infection status (P=0.01) and the type of HPV infection (no infection, indeterminate/transient, persistent P=0.02). The molecular/phylogenetic analysis of the newly identified ß-PV, officially designated as HPV209, showed that the virus has a typical genomic organization of cutaneous HPVs with five early (E6, E7, E1, E2 and E4) and two late genes (L2 and L1), which clusters to the species ß-2. This provides useful data on cutaneous HPV infections in high UV-exposed regions.

Asunto(s)

Betapapillomavirus/clasificación , Betapapillomavirus/aislamiento & purificación , Infecciones por Papillomavirus/epidemiología , Infecciones por Papillomavirus/virología , Piel/efectos de la radiación , Piel/virología , Adulto , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , Femenino , Genotipo , Voluntarios Sanos , Humanos , Estudios Longitudinales , Masculino , Persona de Mediana Edad , Filogenia , Prevalencia , Estaciones del Año , Análisis de Secuencia de ADN , Luz Solar , Rayos Ultravioleta

RESUMEN

Concurrent detection of hepatitis B surface antigen (HBsAg) and anti-HBs antibody or hepatitis B surface E antigen (HBeAg) and anti-HBe antibody in patients with chronic hepatitis B (CHB) infection is well established. However, the clinical implications of these proteins remain largely unknown. In this study, demographic, clinical, and laboratory data from 124,865 patients with chronic CHB infection were analyzed. Viral genotypes were determined by nested polymerase chain reaction. A chemiluminescent assay was applied to measure HBsAg, HBsAb, HBeAg, HBeAb, and HBcAb in sera. Among 124,865 patients with CHB infection, 324 (0.3%) were concurrently positive for HBsAg and anti-HBs, and 206 (0.2%) were concurrently positive for HBeAg and anti-HBe. The HBeAg+/anti-HBe+ group was composed of younger patients (P < 0.05). Subgenotype B2 was prevalent in HBV patients concurrently positive for HBeAg and anti-HBe, while HBV patients positive for both HBsAg and anti-HBs exhibited the C2 subgenotype. Among 530 concurrent patients, 126 (39%) HBsAg+/anti-HBs+ patients were in the low-replication phase, and 62 (19%) were in the reactivation phase; 87 (42%) HBeAg+/anti-HBe+, and 19 (6%) HBsAg+/anti-HBs+ patients were in the immune clearance phase. In this large-scale analysis, the clinical and viral characteristics of HBV infections with concurrent HBs Ag/antibody or HBe Ag/antibody presentations have been examined, and the results may contribute to the diagnosis and treatment of CHB patients.

Asunto(s)

Anticuerpos contra la Hepatitis B/sangre , Antígenos de Superficie de la Hepatitis B/sangre , Antígenos e de la Hepatitis B/sangre , Virus de la Hepatitis B/fisiología , Hepatitis B Crónica/sangre , Hepatitis B Crónica/virología , Adulto , ADN Viral/química , ADN Viral/genética , Femenino , Genotipo , Anticuerpos contra la Hepatitis B/inmunología , Antígenos de Superficie de la Hepatitis B/inmunología , Antígenos e de la Hepatitis B/inmunología , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/inmunología , Hepatitis B Crónica/inmunología , Interacciones Huésped-Patógeno/inmunología , Humanos , Masculino , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa , Análisis de Secuencia de ADN , Activación Viral/genética , Replicación Viral/genética , Adulto Joven

RESUMEN

The geminiviruses are a family of small, non-enveloped viruses with single-stranded, circular DNA genomes of 2500-5200 bases. Geminiviruses are transmitted by various types of insect (whiteflies, leafhoppers, treehoppers and aphids). Members of the genus Begomovirus are transmitted by whiteflies, those in the genera Becurtovirus, Curtovirus, Grablovirus, Mastrevirus and Turncurtovirus are transmitted by specific leafhoppers, the single member of the genus Topocuvirus is transmitted by a treehopper and one member of the genus Capulavirus is transmitted by an aphid. Geminiviruses are plant pathogens causing economically important diseases in most tropical and subtropical regions of the world. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Geminiviridae which is available at www.ictv.global/report/geminiviridae.

Asunto(s)

Geminiviridae/clasificación , Enfermedades de las Plantas/virología , Animales , Microscopía por Crioelectrón , ADN de Cadena Simple/química , ADN de Cadena Simple/genética , ADN Viral/química , ADN Viral/genética , Geminiviridae/genética , Geminiviridae/fisiología , Geminiviridae/ultraestructura , Orden Génico , Genoma Viral , Insectos/virología , Virión/química , Virión/genética , Virión/ultraestructura , Replicación Viral , Zea mays/virología

RESUMEN

Lonomia obliqua (Lepidoptera: Saturniidae) is a species of medical importance due to the severity of reactions caused by accidental contact with the caterpillar bristles. Several natural pathogens have been identified in L. obliqua, and among them the baculovirus Lonomia obliqua multiple nucleopolyhedrovirus (LoobMNPV). The complete genome of LoobMNPV was sequenced and shown to have 120,022 bp long with 134 putative open reading frames (ORFs). Phylogenetic analysis of the LoobMNPV genome showed that it belongs to Alphabaculovirus group I (lepidopteran-infective NPV). A total of 12 unique ORFs were identified with no homologs in other sequenced baculovirus genomes. One of these, the predicted protein encoded by loob035, showed significant identity to an eukaryotic transcription terminator factor (TTF2) from the Lepidoptera Danaus plexippus, suggesting an independent acquisition through horizontal gene transfer. Homologs of cathepsin and chitinase genes, which are involved in host integument liquefaction and viral spread, were not found in this genome. As L. obliqua presents a gregarious behavior during the larvae stage the impact of this deletion might be neglectable.

Asunto(s)

Genoma Viral , Mariposas Nocturnas/virología , Nucleopoliedrovirus/genética , Animales , Secuencia de Bases , ADN Viral/química , ADN Viral/aislamiento & purificación , ADN Viral/metabolismo , Transferencia de Gen Horizontal , Proteínas de Insectos/clasificación , Proteínas de Insectos/genética , Larva/metabolismo , Larva/virología , Mariposas Nocturnas/crecimiento & desarrollo , Mariposas Nocturnas/metabolismo , Nucleopoliedrovirus/clasificación , Nucleopoliedrovirus/aislamiento & purificación , Sistemas de Lectura Abierta/genética , Filogenia , Alineación de Secuencia , Análisis de Secuencia de ADN , Transactivadores/clasificación , Transactivadores/genética , Factores de Transcripción/clasificación , Factores de Transcripción/genética

RESUMEN

The genome of a novel group II alphabaculovirus, Perigonia lusca single nucleopolyhedrovirus (PeluSNPV), was sequenced and shown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids. An interesting feature of this novel genome was the presence of a putative nucleotide metabolism enzyme-encoding gene (pelu112). The pelu112 gene was predicted to encode a fusion of thymidylate kinase (tmk) and dUTP diphosphatase (dut). Phylogenetic analysis indicated that baculoviruses have independently acquired tmk and dut several times during their evolution. Two homologs of the tmk-dut fusion gene were separately introduced into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genome, which lacks tmk and dut. The recombinant baculoviruses produced viral DNA, virus progeny, and some viral proteins earlier during in vitro infection and the yields of viral occlusion bodies were increased 2.5-fold when compared to the parental virus. Interestingly, both enzymes appear to retain their active sites, based on separate modeling using previously solved crystal structures. We suggest that the retention of these tmk-dut fusion genes by certain baculoviruses could be related to accelerating virus replication and to protecting the virus genome from deleterious mutation.

Asunto(s)

Genoma Viral , Nucleopoliedrovirus/genética , Nucleósido-Fosfato Quinasa/metabolismo , Pirofosfatasas/metabolismo , Proteínas Virales/metabolismo , Animales , Secuencia de Bases , Sitios de Unión , ADN Viral/química , ADN Viral/aislamiento & purificación , ADN Viral/metabolismo , Vectores Genéticos/genética , Vectores Genéticos/metabolismo , Microscopía Confocal , Microscopía Electrónica de Rastreo , Nucleopoliedrovirus/clasificación , Nucleopoliedrovirus/fisiología , Nucleósido-Fosfato Quinasa/química , Nucleósido-Fosfato Quinasa/genética , Nucleótidos/biosíntesis , Nucleótidos/química , Sistemas de Lectura Abierta/genética , Filogenia , Estructura Terciaria de Proteína , Pirofosfatasas/química , Pirofosfatasas/genética , Alineación de Secuencia , Análisis de Secuencia de ADN , Células Sf9 , Spodoptera , Secuencias Repetidas en Tándem/genética , Proteínas Virales/genética , Replicación Viral

RESUMEN

The bacteriophage ΦAb-Sp7 was isolated from the cells of the Azospirillum brasilense Sp7. The morphology, size of the gram-negative colonies, and range of lytic activity against other strains and species of the genus Azospirillum was tested. The isolated phage DNA was examined using electrophoretic and restriction analysis, and the size of the genome were established. The electron microscopy. resuIts show that the phage (capsid) has a strand-like form. The electron microscopy study of the bacteriophage ΦAb-Sp7 adsorption on the A. brasilense Sp7 bacterial surface was performed.

Asunto(s)

Azospirillum brasilense/virología , Bacteriófagos/genética , ADN Viral/química , Genoma Viral , Adsorción , Azospirillum brasilense/química , Azospirillum brasilense/ultraestructura , Bacteriófagos/crecimiento & desarrollo , Bacteriófagos/ultraestructura , Cápside/ultraestructura , Enzimas de Restricción del ADN/química , Tamaño del Genoma , Lisogenia , Mapeo Restrictivo

RESUMEN

In 2003, Acanthamoeba polyphaga mimivirus (APMV) was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV), which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae.

Asunto(s)

Virus ADN/genética , Virus ADN/aislamiento & purificación , ADN Viral/química , ADN Viral/genética , Evolución Molecular , Genoma Viral , Filogenia , Brasil , Análisis por Conglomerados , Orden Génico , Sistemas de Lectura Abierta , Análisis de Secuencia de ADN , Homología de Secuencia , Sintenía

RESUMEN

Abstract Human adenovirus species F (HAdV-F) type 40 and 41 are commonly associated with acute diarrheal disease (ADD) across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV) detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p < 0.05), considering two conditions: the total of samples tested (377) and the total of negative samples for the remaining viruses tested (314). The overall prevalence of HAdV was 12.47% (47/377); and in 76.60% (36/47) of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients) in the two conditions tested: the total of samples tested (p = 0.598) and the total of negative samples for the remaining viruses tested (p = 0.614). There was a significant association in the occurrence of infection in children aged 0–12 months for the condition 1 (p = 0.030) as well as condition 2 (p = 0.019). The occurrence of infections due to HAdV did not coincide with a pattern of seasonal distribution. These data indicate the significant involvement of HAdV-F type 41 in the etiology of ADD in Minas Gerais, which demonstrates the importance of other viral agents in the development of the disease after the introduction of rotavirus vaccine immunization.

Asunto(s)

Niño , Preescolar , Humanos , Lactante , Recién Nacido , Vacunas contra el Adenovirus/administración & dosificación , Adenovirus Humanos/aislamiento & purificación , Diarrea/epidemiología , Diarrea/prevención & control , Infecciones por Rotavirus/epidemiología , Infecciones por Rotavirus/prevención & control , Vacunas contra el Adenovirus/inmunología , Adenovirus Humanos/clasificación , Adenovirus Humanos/genética , Brasil/epidemiología , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , ADN Viral/aislamiento & purificación , Heces/virología , Genotipo , Filogenia , Prevalencia , Análisis de Secuencia de ADN

RESUMEN

Human adenovirus species F (HAdV-F) type 40 and 41 are commonly associated with acute diarrheal disease (ADD) across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV) detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p<0.05), considering two conditions: the total of samples tested (377) and the total of negative samples for the remaining viruses tested (314). The overall prevalence of HAdV was 12.47% (47/377); and in 76.60% (36/47) of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients) in the two conditions tested: the total of samples tested (p=0.598) and the total of negative samples for the remaining viruses tested (p=0.614). There was a significant association in the occurrence of infection in children aged 0-12 months for the condition 1 (p=0.030) as well as condition 2 (p=0.019). The occurrence of infections due to HAdV did not coincide with a pattern of seasonal distribution. These data indicate the significant involvement of HAdV-F type 41 in the etiology of ADD in Minas Gerais, which demonstrates the importance of other viral agents in the development of the disease after the introduction of rotavirus vaccine immunization.

Asunto(s)

Vacunas contra el Adenovirus/administración & dosificación , Adenovirus Humanos/aislamiento & purificación , Diarrea/epidemiología , Diarrea/prevención & control , Infecciones por Rotavirus/epidemiología , Infecciones por Rotavirus/prevención & control , Vacunas contra el Adenovirus/inmunología , Adenovirus Humanos/clasificación , Adenovirus Humanos/genética , Brasil/epidemiología , Niño , Preescolar , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , ADN Viral/aislamiento & purificación , Heces/virología , Genotipo , Humanos , Lactante , Recién Nacido , Filogenia , Prevalencia , Análisis de Secuencia de ADN

RESUMEN

Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that cause serious infections in crop plants and are often also associated with non-cultivated plants. Here, we report the detection of two new begomoviruses in Pavonia sp. (Malvaceae). Sequence comparisons and phylogenetic analysis showed that these novel viruses are related to New World begomoviruses. The nucleotide sequences of the DNA-A of both viruses had the highest similarity to abutilon mosaic Bolivia virus (AbMBoV). Based on symptoms observed in the field and considering the host, we propose the names pavonia mosaic virus (PavMV) and pavonia yellow mosaic virus (PavYMV) for these two new begomoviruses.

Asunto(s)

Begomovirus/clasificación , Begomovirus/aislamiento & purificación , ADN Viral/química , ADN Viral/genética , Genoma Viral , Malvaceae/virología , Begomovirus/genética , Brasil , Análisis por Conglomerados , Datos de Secuencia Molecular , Filogenia , Enfermedades de las Plantas/virología , Plantas , Análisis de Secuencia de ADN , Homología de Secuencia

RESUMEN

Despite chronic hepatitis B virus (HBV) infection (CHB) being a leading cause of liver cirrhosis and cancer, HBV evolution during CHB is not fully understood. Recent studies have indicated that virus diversity progressively increases along the course of CHB and that some virus mutations correlate with severe liver conditions such as chronic hepatitis, cirrhosis and hepatocellular carcinoma. Using ultradeep sequencing (UDS) data from an intrafamilial case, we detected such mutations at low frequencies among three immunotolerant patients and at high frequencies in an inactive carrier. Furthermore, our analyses indicated that the HBV population from the seroconverter patient underwent many genetic changes in response to virus clearance. Together, these data indicate a potential use of UDS for developing non-invasive biomarkers for monitoring disease changes over time or in response to specific therapies. In addition, our analyses revealed that virus clearance seemed not to require the virus effective population size to decline. A detailed genetic analysis of the viral lineages arising during and after the clearance suggested that mutations at or close to critical elements of the core promoter (enhancer II, epsilon encapsidation signal, TA2, TA3 and direct repeat 1-hormone response element) might be responsible for a sustained replication. This hypothesis requires the decline in virus load to be explained by constant clearance of virus-producing hepatocytes, consistent with the sustained progress towards serious liver conditions experienced by many CHB patients.

Asunto(s)

Evolución Molecular , Variación Genética , Virus de la Hepatitis B/clasificación , Virus de la Hepatitis B/genética , Hepatitis B Crónica/virología , Secuenciación de Nucleótidos de Alto Rendimiento , Niño , Análisis por Conglomerados , ADN Viral/química , ADN Viral/genética , Salud de la Familia , Femenino , Virus de la Hepatitis B/aislamiento & purificación , Humanos , Lactante , Masculino , Datos de Secuencia Molecular , Filogenia , Análisis de Secuencia de ADN , Homología de Secuencia

RESUMEN

For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.

Asunto(s)

ADN Viral/química , Dieta , Retroviridae/genética , Animales , Heces/virología , Fósiles , Humanos , Metagenómica , Análisis de Secuencia de ADN