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1.
Washington; Organización Panamericana de la Salud; mar. 24, 2021. 9 p.
No convencional en Español | LILACS | ID: biblio-1151432

RESUMEN

A la fecha, 141 los países/territorios han detectado casos de infección por alguna de las tres variantes de preocupación (VOC) reconocidas actualmente por la Organización Mundial de la Salud (OMS). De ese total, 32 países/territorios corresponden a la Región de las Américas.


Asunto(s)
Neumonía Viral/genética , ADN Viral/genética , Infecciones por Coronavirus/genética , Pandemias/prevención & control , Monitoreo Epidemiológico , Betacoronavirus/inmunología , Mutación , Américas/epidemiología
2.
Zhonghua Gan Zang Bing Za Zhi ; 29(2): 126-132, 2021 Feb 20.
Artículo en Chino | MEDLINE | ID: mdl-33685080

RESUMEN

Objective: To study the use of preS1-tp fusion protein as a novel vector to mediate the entry of small interfering RNA (siRNA) targeting the carboxy-terminal nuclear localization signal (NLS) region of hepatitis B virus (HBV) core protein into HBV-infected hepatocytes, and to further explore the HBV replication inhibition and covalently closed circular DNA synthesis. Methods: HepG2.2.15 cells expressing the human sodium taurocholate co-transporting polypeptide were established on the basis of lentivirus infection system. siRNA against HBV NLS region was designed and synthesized. PreS1-tp fusion protein expression and purification was observed to test its ability to cell entry and DNA binding. NLS siRNA were delivered into HepG2.2.15- sodium taurocholate co-transporting polypeptide cells by preS1-tp fusion protein as a vector to observe the effects of NLS siRNA on HBV replication and covalently closed circular DNA levels. Analysis of variance was used for comparison between multiple groups, and the measurement data differences between groups were analyzed by t-test. Results: HepG2.2.15-sodium taurocholate co-transporting polypeptide cell line was successfully constructed. Screened synthetic HBV NLS siRNA had significantly inhibited HBV replication. The preS1-tp fusion protein was expressed and purified on a large-scale. The fusion protein as a vector for HBV NLS siRNA had targeted delivery. The result showed that the fusion protein had effectively targeted siRNA to Hepg2.2.15-sodium taurocholate co-transporting polypeptide cell, which not only had effectively inhibited the expression of HBV mRNA, HBsAg and HBeAg, but also had significantly reduced the levels of HBV DNA and covalently closed circular DNA. Conclusion: The preS1-tp fusion protein constructed in this study uses the dual functional characteristics of preS1 binding to hepatocyte HBV receptor, and tp binding to nucleic acids, and targets HBV NLS siRNA against HBV-infected cells and block rcDNA from being transported to nucleus. siRNA plays a role in inhibiting HBV replication and covalently close circular DNA synthesis, providing a new strategy for the treatment of chronic hepatitis B caused by HBV infection, and a new research perspective for the complete elimination of HBV from the body.


Asunto(s)
Virus de la Hepatitis B , Hepatitis B , ADN Circular/genética , ADN Viral/genética , Células Hep G2 , Antígenos de Superficie de la Hepatitis B/genética , Virus de la Hepatitis B/genética , Humanos , ARN Interferente Pequeño/genética , Replicación Viral
3.
Methods Mol Biol ; 2278: 71-85, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33649949

RESUMEN

Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.


Asunto(s)
Bacteriófagos/genética , Bifidobacterium/virología , Heces/microbiología , ADN Viral/genética , Microbioma Gastrointestinal , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Lactante
4.
Nat Commun ; 12(1): 1591, 2021 03 11.
Artículo en Inglés | MEDLINE | ID: mdl-33707452

RESUMEN

Hepatitis B virus (HBV) is a highly contagious pathogen that afflicts over a third of the world's population, resulting in close to a million deaths annually. The formation and persistence of the HBV covalently closed circular DNA (cccDNA) is the root cause of HBV chronicity. However, the detailed molecular mechanism of cccDNA formation from relaxed circular DNA (rcDNA) remains opaque. Here we show that the minus and plus-strand lesions of HBV rcDNA require different sets of human repair factors in biochemical repair systems. We demonstrate that the plus-strand repair resembles DNA lagging strand synthesis, and requires proliferating cell nuclear antigen (PCNA), the replication factor C (RFC) complex, DNA polymerase delta (POLδ), flap endonuclease 1 (FEN-1), and DNA ligase 1 (LIG1). Only FEN-1 and LIG1 are required for the repair of the minus strand. Our findings provide a detailed mechanistic view of how HBV rcDNA is repaired to form cccDNA in biochemical repair systems.


Asunto(s)
Reparación del ADN/genética , ADN Circular/genética , ADN Viral/genética , Virus de la Hepatitis B/genética , Hepatitis B Crónica/patología , Línea Celular Tumoral , ADN Ligasa (ATP)/metabolismo , ADN Polimerasa III/metabolismo , Replicación del ADN/genética , Endonucleasas de ADN Solapado/metabolismo , Células Hep G2 , Humanos , Antígeno Nuclear de Célula en Proliferación/metabolismo , Proteína de Replicación C/metabolismo , Replicación Viral/genética
5.
Pan Afr Med J ; 38: 40, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33777308

RESUMEN

Introduction: head and neck cancers have essentially been a disease of the elderly but recent studies are beginning to demonstrate their increasing incidence in young people with infections such as human papilloma virus (HPV). This study was carried out to determine the prevalence of high risk Human papilloma virus (hrHPV) related oropharyngeal carcinoma and its prevalent genotypes as well as their strength of association with HIV in adult Nigerian subjects. Methods: this was a cross-sectional study of 41 patients with oropharyngeal carcinomas seen over a 2-year period. Patients had incisional and/or excisional biopsy done under anesthesia. A portion of the specimen from which the DNA was extracted was placed in Digene HC2 DNA collection device while the 2nd portion for histopathological analysis was fixed using 10% Neutral Buffered Formalin (NBF) and embedded in paraffin blocks. Oropharyngeal cancer HPV genotyping was done using HPV genotypes 14 real-tm quant kit (SACACE, Italy). The data was analyzed using SPSS version 23. Results: prevalence of HPV was 17.1% with a male to female ratio of 2.7: 1. The identified genotypes were 16, 33, 35 and 52 with 28.6% of patients having more than one genotype. Most of the age groups studied were affected. Squamous cell carcinoma and ameloblastic carcinoma were the cancers associated with HPV. HPV was not identified in the HIV positive patients. Conclusion: high-risk human papilloma virus genotypes 16, 33, 35 and 52 are associated with oropharyngeal carcinoma in Nigeria but were not found in HIV patients. This finding provides a strong evidence for the use of the 9-valent prophylactic vaccine for the prevention of oropharyngeal cancer in Nigeria. Public awareness and HPV prevention strategies should reduce significantly the incidence of oropharyngeal carcinomas in our environment.


Asunto(s)
Neoplasias Orofaríngeas/virología , Papillomaviridae/genética , Infecciones por Papillomavirus/complicaciones , Adulto , Anciano , Ameloblastoma/epidemiología , Ameloblastoma/virología , Carcinoma de Células Escamosas/epidemiología , Carcinoma de Células Escamosas/virología , Estudios Transversales , ADN Viral/genética , Femenino , Genotipo , Infecciones por VIH/epidemiología , Neoplasias de Cabeza y Cuello/epidemiología , Neoplasias de Cabeza y Cuello/patología , Neoplasias de Cabeza y Cuello/virología , Humanos , Masculino , Persona de Mediana Edad , Nigeria , Neoplasias Orofaríngeas/epidemiología , Neoplasias Orofaríngeas/patología , Papillomaviridae/aislamiento & purificación , Infecciones por Papillomavirus/epidemiología , Infecciones por Papillomavirus/virología , Prevalencia , Adulto Joven
6.
Viruses ; 13(2)2021 02 04.
Artículo en Inglés | MEDLINE | ID: mdl-33557409

RESUMEN

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.


Asunto(s)
Carcinoma Hepatocelular/genética , Virus de la Hepatitis B/genética , Neoplasias Hepáticas/genética , Integración Viral , Carcinogénesis/genética , Carcinoma Hepatocelular/patología , Carcinoma Hepatocelular/virología , ADN Viral/genética , Frecuencia de los Genes , Genoma Humano/genética , Genoma Viral/genética , Virus de la Hepatitis B/fisiología , Hepatitis B Crónica/genética , Hepatitis B Crónica/patología , Hepatitis B Crónica/virología , Humanos , Neoplasias Hepáticas/patología , Neoplasias Hepáticas/virología , Programas Informáticos
7.
Viruses ; 13(2)2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33572209

RESUMEN

Porcine circovirus 3 (PCV-3) has been widely detected in healthy and diseased pigs; among different pathologic conditions, the strongest evidence of association comes from reproductive disease cases. However, simple viral detection does not imply the causality of the clinical conditions. Detection of PCV-3 within lesions may provide stronger evidence of causality. Thus, this study aimed to assess the frequency of PCV-3 detection in tissues from fetuses/stillborn piglets in cases of reproductive problems in domestic swine, as well as the histopathologic assessment of fetal tissues. Fetuses or stillborn piglets from 53 cases of reproductive failure were collected and analyzed by PCV-3 qPCR. The presence of porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV-2), and porcine parvovirus 1 (PPV1) was also checked. PCV-3 qPCR positive samples with a high viral load were tested by PCV-3 in situ hybridization (ISH), sequenced, and phylogenetically analyzed. PCV-3 DNA was detected in 18/53 (33.9%) reproductive failure cases and in 16 of them PCV-3 was the only pathogen found. PCV-2 DNA was found in 5/53 (9.4%), PRRSV RNA in 4/53 (7.5%) and PPV1 was not detected. Four out of the six PCV-3 qPCR-positive cases with Ct value <30 were positive when tested by ISH. In these samples, PCV-3 was detected within mild histopathologic lesions, such as arteritis and periarteritis in multiple tissues. The present work emphasizes the need to include PCV-3 as a potential causative agent of reproductive failure in swine.


Asunto(s)
Aborto Veterinario/virología , Infecciones por Circoviridae/veterinaria , Circovirus/aislamiento & purificación , Enfermedades de los Porcinos/virología , Feto Abortado/patología , Feto Abortado/virología , Aborto Veterinario/patología , Animales , Animales Domésticos , Infecciones por Circoviridae/patología , Infecciones por Circoviridae/virología , Circovirus/clasificación , Circovirus/genética , ADN Viral/genética , Femenino , Genoma Viral/genética , Filogenia , Embarazo , Mortinato/veterinaria , Porcinos , Enfermedades de los Porcinos/patología , Carga Viral , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación
8.
Viruses ; 13(2)2021 02 09.
Artículo en Inglés | MEDLINE | ID: mdl-33572446

RESUMEN

Analysis of pooled genomic short read sequence data revealed the presence of nudivirus-derived sequences from U.S. populations of both southern corn rootworm (SCR, Diabrotica undecimpunctata howardi Barber) and western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte). A near complete nudivirus genome sequence was assembled from sequence data for an SCR population with relatively high viral titers. A total of 147,179 bp was assembled from five contigs that collectively encode 109 putative open reading frames (ORFs) including 20 nudivirus core genes. In contrast, genome sequence recovery was incomplete for a second nudivirus from WCR, although sequences derived from this virus were present in three geographically dispersed populations. Only 48,989 bp were assembled with 48 putative ORFs including 13 core genes, representing about 20% of a typical nudivirus genome. Phylogenetic analysis indicated that both corn rootworm nudiviruses grouped with the third known nudivirus of beetles, Oryctes rhinoceros nudivirus in the genus Alphanudivirus. On the basis of phylogenetic and additional analyses, we propose further taxonomic separation of nudiviruses within Alphanudivirus and Betanudivirus into two subfamilies and five genera. Identification of nudivirus-derived sequences from two species of corn rootworm highlights the diversity of viruses associated with these agricultural insect pests.


Asunto(s)
Escarabajos/virología , Nudiviridae/genética , Animales , Escarabajos/clasificación , ADN Viral/genética , Genes Virales , Genoma Viral/genética , Genómica , Nudiviridae/clasificación , Sistemas de Lectura Abierta , Filogenia , /genética
9.
Viruses ; 13(2)2021 01 30.
Artículo en Inglés | MEDLINE | ID: mdl-33573130

RESUMEN

Human hepatitis B virus (HBV) can cause chronic, lifelong infection of the liver that may lead to persistent or episodic immune-mediated inflammation against virus-infected hepatocytes. This immune response results in elevated rates of killing of virus-infected hepatocytes, which may extend over many years or decades, lead to fibrosis and cirrhosis, and play a role in the high incidence of hepatocellular carcinoma (HCC) in HBV carriers. Immune-mediated inflammation appears to cause oxidative DNA damage to hepatocytes, which may also play a major role in hepatocarcinogenesis. An additional DNA damaging feature of chronic infections is random integration of HBV DNA into the chromosomal DNA of hepatocytes. While HBV DNA integration does not have a role in virus replication it may alter gene expression of the host cell. Indeed, most HCCs that arise in HBV carriers contain integrated HBV DNA and, in many, the integrant appears to have played a role in hepatocarcinogenesis. Clonal expansion of hepatocytes, which is a natural feature of liver biology, occurs because the hepatocyte population is self-renewing and therefore loses complexity due to random hepatocyte death and replacement by proliferation of surviving hepatocytes. This process may also represent a risk factor for the development of HCC. Interestingly, during chronic HBV infection, hepatocyte clones detected using integrated HBV DNA as lineage-specific markers, emerge that are larger than those expected to occur by random death and proliferation of hepatocytes. The emergence of these larger hepatocyte clones may reflect a survival advantage that could be explained by an ability to avoid the host immune response. While most of these larger hepatocyte clones are probably not preneoplastic, some may have already acquired preneoplastic changes. Thus, chronic inflammation in the HBV-infected liver may be responsible, at least in part, for both initiation of HCC via oxidative DNA damage and promotion of HCC via stimulation of hepatocyte proliferation through immune-mediated killing and compensatory division.


Asunto(s)
ADN Viral/genética , Virus de la Hepatitis B/fisiología , Hepatitis B Crónica/virología , Hepatocitos/virología , Animales , Virus de la Hepatitis B/genética , Hepatitis B Crónica/genética , Hepatitis B Crónica/inmunología , Hepatocitos/inmunología , Humanos , Hígado/inmunología , Hígado/virología , Integración Viral
10.
Microbiome ; 9(1): 51, 2021 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-33610182

RESUMEN

BACKGROUND: The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS: A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS: The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS: The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.


Asunto(s)
/aislamiento & purificación , Virus/aislamiento & purificación , Zoonosis/diagnóstico , Animales , ADN Viral/genética , Genoma Viral , Humanos , ARN Viral/genética , Virus/clasificación
11.
Artículo en Inglés | MEDLINE | ID: mdl-33533809

RESUMEN

The efficacy of direct-acting antivirals (DAAs) in the treatment of chronic hepatitis C (CHC) in liver transplant recipients is poorly understood, and several factors, including immunosuppression, drug interactions, elevated viraemia, and intolerance to ribavirin (RBV), can reduce cure rates. We conducted a real-life study on liver transplant recipients with CHC treated with a combination of sofosbuvir (SOF) and daclatasvir (DCV) or simeprevir (SIM), with or without RBV, followed-up for 12 to 24 weeks. The treatment effectiveness was assessed by determining the sustained virological response (SVR) rates at 12 or 24 weeks after the treatment cessation. Eighty-four patients were evaluated, with a mean age of 63.4 ± 7.4 years, HCV genotype 1 being the most prevalent (63.1%). Nineteen patients (22.7%) had mild fibrosis (METAVIR < F2) and 41 (48.8%) significant fibrosis (METAVIR ≥ F2). The average time between liver transplantation and the start of treatment was 4 years (2.1-6.6 years). The SOF + DCV regimen was used in 58 patients (69%). RBV in combination with DAAs was used in seven patients (8.3%). SVR was achieved in 82 patients (97.6%), and few relevant adverse events could be attributed to DAA therapy, including a patient who stopped treatment due to a headache. There was a significant reduction in ALT, AST, GGT and FA levels, or the APRI index after 4 weeks of treatment, which remained until 12/24 weeks post-treatment. DAA treatment of CHC in liver-transplanted patients achieved a high SVR rate and resulted in the normalization of serum levels of liver enzymes.


Asunto(s)
Antivirales/uso terapéutico , Hepacivirus/efectos de los fármacos , Hepatitis C Crónica/tratamiento farmacológico , Trasplante de Hígado/efectos adversos , Ribavirina/uso terapéutico , Anciano , Antivirales/efectos adversos , Brasil , ADN Viral/genética , Quimioterapia Combinada , Femenino , Genotipo , Hepacivirus/genética , Humanos , Cirrosis Hepática/cirugía , Masculino , Persona de Mediana Edad , Ribavirina/efectos adversos , Receptores de Trasplantes , Resultado del Tratamiento
13.
Anal Chem ; 93(9): 4208-4216, 2021 03 09.
Artículo en Inglés | MEDLINE | ID: mdl-33631072

RESUMEN

The gold standard of molecular pathogen detection is the quantitative polymerase chain reaction (qPCR). Modern qPCR instruments are capable of detecting 4-6 analytes in a single sample: one per optical detection channel. However, many clinical applications require multiplexing beyond this traditional single-well capacity, including the task of simultaneously testing for SARS-CoV-2 and other respiratory pathogens. This can be addressed by dividing a sample across multiple wells, or using technologies such as genomic sequencing and spatial arrays, but at the expense of significantly higher cost and lower throughput compared with single-well qPCR. These trade-offs represent unacceptable compromises in high-throughput screening scenarios such as SARS-CoV-2 testing. We demonstrate a novel method of detecting up to 20 targets per well with standard qPCR instrumentation: high-definition PCR (HDPCR). HDPCR combines TaqMan chemistry and familiar workflows with robust encoding to enable far higher levels of multiplexing on a traditional qPCR system without an increase in cost or reduction in throughput. We utilize HDPCR with a custom 20-Plex assay, an 8-Plex assay using unmodified predesigned single-plex assays from Integrated DNA Technologies and a 9-Plex pathogen panel inclusive of SARS-CoV-2 and other common respiratory viruses. All three assays were successful when tested on a variety of samples, with overall sample accuracies of 98.8, 98.3, and 100%, respectively. The HDPCR technology enables the large install base of qPCR instrumentation to perform mid-density multiplex diagnostics without modification to instrumentation or workflow, meeting the urgent need for increased diagnostic yield at an affordable price without sacrificing assay performance.


Asunto(s)
/métodos , /virología , Reacción en Cadena de la Polimerasa Multiplex/métodos , /aislamiento & purificación , ADN Viral/genética , Humanos , Sensibilidad y Especificidad
14.
Arch Virol ; 166(4): 1217-1225, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33550505

RESUMEN

In this study, we report the complete genome sequence of swinepox virus from a clinical sample from a naturally occurring infection in India. The sequencing was done on a Nanopore MinION sequencer from Oxford Nanopore Technologies. Two new annotations were added to the genome. Three of the genes were found to have frameshifts, which might be of importance in relation to infection. When compared to the only other reported whole genome sequence of swinepox virus, which was obtained from an isolate from America in 1999, our sequence is only 98.19% identical at the nucleotide level. The average amino acid sequence identity of the viral proteins, based on the common 149 annotations, is also 98.19%, demonstrating that these viruses are distinctly divergent. Owing to the fact that swinepox virus infects only swine, it could not have entered America until the introduction of swine in the 16th century from Europe. The swinepox viruses in both continents have continued to evolve independently. The sequence divergence identified here indicates a Eurasian-lineage virus that is geographically distinct from the American-lineage swinepox virus.


Asunto(s)
Genoma Viral/genética , Infecciones por Poxviridae/veterinaria , Suipoxvirus/genética , Enfermedades de los Porcinos/virología , Animales , ADN Viral/genética , Variación Genética , India , Infecciones por Poxviridae/virología , Análisis de Secuencia de ADN , Homología de Secuencia , Suipoxvirus/clasificación , Suipoxvirus/aislamiento & purificación , Porcinos , Proteínas Virales/genética
15.
Arch Virol ; 166(4): 1157-1161, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33550506

RESUMEN

Numerous raised plaques were observed on the feet of a red-billed gull (Chroicocephalus novaehollandiae scopulinus) that had been found dead. The plaques consisted of thickened epidermis with cell changes indicative of papillomavirus (PV) infection prominent within affected areas. Evidence suggesting progression to neoplasia was visible in one lesion. A DNA sequence that was most similar, but only 68.3% identical, to duck PV type 3 was amplified from the papillomas, suggesting a novel PV type. Lesions containing PV DNA have only previously been reported in three avian species. This is the first evidence that PVs could cause neoplasia in birds.


Asunto(s)
Enfermedades de las Aves/virología , Carcinoma in Situ/veterinaria , Charadriiformes/virología , Papiloma/veterinaria , Papillomaviridae/aislamiento & purificación , Infecciones por Papillomavirus/veterinaria , Animales , Enfermedades de las Aves/patología , Proteínas de la Cápside/genética , Carcinoma in Situ/patología , Carcinoma in Situ/virología , ADN Viral/genética , Pie/patología , Pie/virología , Papiloma/patología , Papiloma/virología , Papillomaviridae/clasificación , Papillomaviridae/genética , Infecciones por Papillomavirus/patología , Infecciones por Papillomavirus/virología , Filogenia
16.
Arch Virol ; 166(4): 1227-1230, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33554288

RESUMEN

A new badnavirus, aucuba ringspot virus (AuRV), was identified in plants of Aucuba japonica showing mild mosaic, vein banding, and yellow ringspot symptoms on the leaves. The complete nucleotide sequence of the AuRV genome was determined and found to be 9,092 nt in length, and the virus was found to have a genome organization typical of members of the genus Badnavirus. ORF3 was predicted to encode a polyprotein containing conserved movement protein, coat protein, aspartic protease, reverse transcriptase (RT), and RNase H domains. Phylogenetic analysis suggested that this virus is most closely related to codonopsis vein clearing virus but belongs to a distinct species, based on only 69.6% nucleotide sequence identity within the part of ORF 3 encoding the RT and RNase H domains. The vector of AuRV is unknown, but based on phylogenetic relationships, it is predicted to be a type of aphid.


Asunto(s)
Badnavirus/genética , Genoma Viral/genética , Magnoliopsida/virología , Enfermedades de las Plantas/virología , Badnavirus/clasificación , Badnavirus/aislamiento & purificación , Secuencia de Bases , ADN Viral/genética , Sistemas de Lectura Abierta , Filogenia , Hojas de la Planta/virología , Poliproteínas/genética , Análisis de Secuencia de ADN , Homología de Secuencia de Ácido Nucleico , Especificidad de la Especie , Proteínas Virales/genética
17.
Arch Virol ; 166(4): 1171-1175, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33559747

RESUMEN

Seven novel tailed lytic viruses (Ds3CZ, Ds5CZ, Ds9CZ, Ds16CZ, Ds20CZ, Ds23CZ, Ds25CZ) infecting the bacterium Dickeya solani were isolated in the Czech Republic. Genomes of these viruses are dsDNA, 149,364 to 155,285 bp in length, and the genome arrangement is very similar to that of the type virus Dickeya virus LIMEstone 1. All but the Ds25CZ virus should be regarded as strains of a single species. Most of the sequence differences are due to the presence or absence of homing endonuclease (HE) genes, with 23 HEs found in Ds3CZ, Ds5CZ, and Ds20CZ, 22 in Ds9CZ, 19 in Ds16CZ, 18 in Ds25CZ, and 15 in Ds23CZ.


Asunto(s)
Caudovirales/genética , Caudovirales/aislamiento & purificación , /virología , Caudovirales/clasificación , República Checa , ADN Viral/genética , Endonucleasas/genética , Variación Genética , Genoma Viral/genética , Filogenia , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Solanum tuberosum/microbiología , Solanum tuberosum/virología , Proteínas Virales/genética
18.
Arch Virol ; 166(4): 1093-1102, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33570666

RESUMEN

Porcine circovirus type 2 (PCV2) is the most ubiquitous viral pathogen of pigs and has persistently affected the global swine industry. Since first being identified in South Korea in 1999, the virus has undergone considerable genetic change and genotype shifts during the past two decades. These events have contributed to the coexistence of genotypes PCV2a, PCV2b, and PCV2d in Korean pig populations, which may promote viral recombination. The genotypic and phylogenetic characteristics of PCV2 strains circulating in pig herds on Jeju Island from 2019 to 2020 were the focus of this study. Genotype-specific PCR indicated that PCV2d is the dominant viral genotype and that coinfections with PCV2d and PCV2a (75%) or PCV2a and PCV2b (25%) are common in provincial pig herds. The complete genome sequences of 11 PCV2 strains, including three PCV2a, two PCV2b, and six PCV2d strains, were determined. A genomic comparison showed that all of the viruses had the highest nucleotide sequence identity to their corresponding genotypic reference strain. Notably, genetic and phylogenetic analysis revealed that one PCV2d strain, KNU-1931, exhibited nucleotide sequence variation in the ORF1 gene when compared to other PCV2d strains but showed a high degree of similarity to the PCV2b strains. Comprehensive recombination analysis suggested that KNU-1931 originated from natural recombination within ORF1 between PCV2b (the minor parent) and PCV2d (the major parent) strains. Our findings provide information about the frequency of genetic recombination between two different PCV2 genotypes circulating in the field domestically, illustrating the importance of continual intergenotypic recombination for viral fitness when multiple genotypes are present.


Asunto(s)
Infecciones por Circoviridae/veterinaria , Circovirus/genética , Recombinación Genética , Enfermedades de los Porcinos/virología , Animales , Infecciones por Circoviridae/epidemiología , Infecciones por Circoviridae/virología , Circovirus/clasificación , Circovirus/aislamiento & purificación , ADN Viral/genética , Variación Genética , Genoma Viral/genética , Genotipo , Islas/epidemiología , Hibridación de Ácido Nucleico , Filogenia , República de Corea/epidemiología , Análisis de Secuencia de ADN , Porcinos , Enfermedades de los Porcinos/epidemiología
19.
Arch Virol ; 166(4): 1263-1265, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33585960

RESUMEN

Xanthomonas oryzae pv. oryzae is a bacterial pathogen that gives rise to diseases in rice all over the world. A bacteriophage infecting this bacterium was isolated from rice fields in China. Here, we report the complete genome sequence of this phage, which has a linear dsDNA genome of 309,023 bp and a G + C content of 42.43%. It contains 401 open reading frames and encodes 28 tRNAs. It belongs to the family Myoviridae and has a broad host range, making it a possible candidate for phage therapy.


Asunto(s)
Bacteriófagos/genética , Genoma Viral/genética , Xanthomonas/virología , Bacteriófagos/clasificación , Bacteriófagos/aislamiento & purificación , Composición de Base , Secuencia de Bases , ADN Viral/genética , Especificidad del Huésped , Myoviridae/clasificación , Myoviridae/genética , Myoviridae/aislamiento & purificación , Sistemas de Lectura Abierta , Oryza/microbiología , Enfermedades de las Plantas/microbiología , ARN de Transferencia/genética , Análisis de Secuencia de ADN , Homología de Secuencia , Microbiología del Suelo
20.
Klin Lab Diagn ; 66(1): 59-64, 2021 Feb 10.
Artículo en Inglés | MEDLINE | ID: mdl-33567175

RESUMEN

A method for detecting HBV DNA in peripheral blood at low viral load using real-time PCR was developed and its significance in identifying HBsAg-negative viral hepatitis B was evaluated. When developing the method, blood plasma samples and liver tissue biopsy material were used from 128 patients living in St. Petersburg, in various regions of the Russian Federation, as well as in the Central Asia countries. We also used blood plasma samples from 96 pregnant women and 37 hemodialysis center patients living in Northwestern Federal District, 199 foreign citizens undergoing medical examination to obtain work permits at the Directorate for Migration in the Northwestern Federal District, 397 conditionally healthy people living in the Socialist Republic of Vietnam. HBV was detected by nested PCR. Analytical sensitivity was tested using the stepwise dilution method. According to the method developed by us, at the first stage, the HBV DNA is amplified using at the first stage oligonucleotides flanking the genome region 2932-3182 ... 1-1846 nt., and at the second stage two oligonucleotides pairs to the genome virus regions (gene S and gene X) and corresponding oligonucleotide fluorescently labeled probes complementary to the amplified fragments regions carrying fluorophores at the 5'-end, and non-fluorescent quenchers at the 3'-end. The channel corresponding to the FAM fluorophore detects the HBV DNA S-region amplification product, and the channel corresponding to the ROX fluorophore detects the HBV DNA X-region amplification product. The method sensitivity for DNA extraction from plasma with a 100 µl volume was 10 IU/ml. Obtaining a threshold cycle Ct for only one FAM or ROX fluorophore may indicate the HBV DNA presence in a sample at a load of less than 10 IU / ml, HBV detection in this case is possible with a repeated PCR study of the corresponding sample with HBV DNA extraction from an increased plasma volume (200-1000 µl). The developed method makes it possible to identify various HBV genovariants, both characteristic and rare in the Russian Federation, circulating in other world regions. The method can be used to detect HBV in risk groups, in the population, as well as in screening blood donors in order to ensure the blood transfusions safety.


Asunto(s)
Virus de la Hepatitis B , Hepatitis B , Donantes de Sangre , ADN Viral/genética , Femenino , Hepatitis B/diagnóstico , Hepatitis B/epidemiología , Antígenos de Superficie de la Hepatitis B/genética , Virus de la Hepatitis B/genética , Humanos , Plasma , Embarazo , Reacción en Cadena en Tiempo Real de la Polimerasa , Federación de Rusia , Carga Viral
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