Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 3.747
Filtrar
1.
Recurso de Internet en Inglés | LIS - Localizador de Información en Salud, LIS-ES-PROF | ID: lis-LISBR1.1-46975

RESUMEN

La National Library of Medicine, a través de su base de datos de secuencias GenBank®, proporciona a la comunidad biomédica acceso gratuito a las secuencias del genoma del SARS-CoV-2. Se publican los datos asociados a este brote y los datos de las secuencias.


Asunto(s)
Betacoronavirus , Infecciones por Coronavirus , Genoma , Secuenciación Completa del Genoma , Neumonía Viral
2.
J Korean Med Sci ; 35(7): e84, 2020 Feb 24.
Artículo en Inglés | MEDLINE | ID: mdl-32080990

RESUMEN

Novel coronavirus (SARS-CoV-2) is found to cause a large outbreak started from Wuhan since December 2019 in China and SARS-CoV-2 infections have been reported with epidemiological linkage to China in 25 countries until now. We isolated SARS-CoV-2 from the oropharyngeal sample obtained from the patient with the first laboratory-confirmed SARS-CoV-2 infection in Korea. Cytopathic effects of SARS-CoV-2 in the Vero cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.


Asunto(s)
Betacoronavirus , Infecciones por Coronavirus , Orofaringe/virología , Neumonía Viral , Secuenciación Completa del Genoma , Adulto , Betacoronavirus/genética , Betacoronavirus/aislamiento & purificación , Infecciones por Coronavirus/diagnóstico , Femenino , Humanos , Microscopía Electrónica de Transmisión , Filogenia , Neumonía Viral/diagnóstico , República de Corea
3.
Nature ; 579(7798): 265-269, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32015508

RESUMEN

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1-3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here 'WH-Human 1' coronavirus (and has also been referred to as '2019-nCoV'). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.


Asunto(s)
Betacoronavirus/clasificación , Enfermedades Transmisibles Emergentes/complicaciones , Enfermedades Transmisibles Emergentes/virología , Infecciones por Coronavirus/complicaciones , Infecciones por Coronavirus/virología , Neumonía Viral/complicaciones , Neumonía Viral/virología , Síndrome Respiratorio Agudo Grave/etiología , Síndrome Respiratorio Agudo Grave/virología , Adulto , Betacoronavirus/genética , China , Enfermedades Transmisibles Emergentes/diagnóstico por imagen , Enfermedades Transmisibles Emergentes/patología , Infecciones por Coronavirus/diagnóstico por imagen , Infecciones por Coronavirus/patología , Genoma Viral/genética , Humanos , Pulmón/diagnóstico por imagen , Masculino , Filogenia , Neumonía Viral/diagnóstico por imagen , Neumonía Viral/patología , ARN Viral/genética , Recombinación Genética/genética , Síndrome Respiratorio Agudo Grave/diagnóstico por imagen , Síndrome Respiratorio Agudo Grave/patología , Tomografía Computarizada por Rayos X , Secuenciación Completa del Genoma
4.
N Engl J Med ; 382(7): 632-643, 2020 02 13.
Artículo en Inglés | MEDLINE | ID: mdl-32053299

RESUMEN

BACKGROUND: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.


Asunto(s)
Brotes de Enfermedades , Enfermedades Transmitidas por los Alimentos/epidemiología , Listeria monocytogenes/aislamiento & purificación , Listeriosis/epidemiología , Productos de la Carne/microbiología , Adolescente , Adulto , Anciano , Técnicas de Tipificación Bacteriana , Estudios de Casos y Controles , Femenino , Enfermedades Transmitidas por los Alimentos/etiología , Enfermedades Transmitidas por los Alimentos/mortalidad , Infecciones por VIH/complicaciones , VIH-1 , Humanos , Recién Nacido , Listeria monocytogenes/genética , Listeriosis/etiología , Listeriosis/mortalidad , Masculino , Productos de la Carne/efectos adversos , Persona de Mediana Edad , Embarazo , Complicaciones Infecciosas del Embarazo/epidemiología , Recall y Retirada del Producto , Distribución por Sexo , Sudáfrica/epidemiología , Secuenciación Completa del Genoma , Adulto Joven
5.
J Zoo Wildl Med ; 50(4): 803-812, 2020 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-31926510

RESUMEN

Avipoxvirus infections have been reported in both free-ranging and domestic birds worldwide. Fowlpox and canarypox viruses belong to the genus Avipoxvirus among the virus family Poxviridae. They cause cutaneous lesions with proliferative growths on the unfeathered parts of the skin and/or diphtheritic lesions generally associated with necrosis in the upper respiratory and digestive tracts. In this study, a poxvirus has been identified in wild-caught snow buntings (Plectrophenax nivalis) housed in an outdoor aviary in the region of Rimouski, Quebec. During the falls and winters of 2015 and 2016, eight snow buntings affected by this infection were examined. Macroscopic and microscopic lesions observed were characteristic of an avipoxvirus infection. Electron microscopy imaging of an ultrathin section of the histopathological lesions of two birds confirmed the presence of the poxvirus. Afterward, the presence of the poxvirus was confirmed in three birds by a specific polymerase chain reaction assay that amplified a segment of the gene encoding the fowlpox virus 4b core protein. A 576-nucleotide amplicon was obtained from one of them and sequenced. The analyses revealed a 99% homology to other previously described avipoxviruses. Using high-throughput sequencing, almost the entire viral genome of this avipoxvirus was revealed and found to possess a 359,853-nucleotide sequence in length. Bioinformatic analyses revealed that the virus was genetically related to canarypox virus. To our knowledge, this is the first confirmed case and full description of a poxviral infection in this species. This episode suggests a high susceptibility of this northern species of passerine to avipoxviruses circulating in southeastern Canada during the summer months. Even if the source of the viral infections remains undetermined, transmission by local biological vectors is suspected. Management of poxviral infections in snow buntings housed outdoors in southeastern Canada could rely on the control of biting insects.


Asunto(s)
Avipoxvirus/genética , Enfermedades de las Aves/virología , Genoma Viral , Passeriformes , Infecciones por Poxviridae/veterinaria , Secuenciación Completa del Genoma , Animales , Enfermedades de las Aves/patología , Femenino , Masculino , Filogenia , Infecciones por Poxviridae/virología
6.
J Med Microbiol ; 69(1): 82-86, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31904319

RESUMEN

In recent years, Serratia marcescens has emerged as an important agent of hospital-acquired infections, such as pneumonia, urinary tract infection, septicaemia and meningitis, particularly in vulnerable patients. Compared to Klebsiella pneumoniae and Escherichia coli, S. marcescens is less commonly associated with bla KPC genes, yet few cases of plasmid transmission at the gastrointestinal level from K. pneumoniae carbapenemase (KPC)-producing Enterobacterales to S. marcescens have been described. Here we report a case of in vivo acquisition, during a 3-month period of hospitalization in the intensive care unit, of a bla KPC-3 gene carried by a pKpQIL-IT plasmid, and its probable transmission at the bronchial level among different species of Enterobacterales, including K. pneumoniae and S. marcescens. By using whole genome sequence analyses we were able provide insight into the dynamics of carbapenem-resistance determinants acquisition in the lower respiratory tract, a novel anatomical region for such plasmid transmission events, that usually involve the gastrointestinal tract. The co-presence at the same time of both wild-type and resistant Enterobacterales could have been the critical factor leading to the spread of plasmids harbouring carbapenem-resistance genes, of particular importance during surveillance screenings. The possibility of such an event may have significant consequences in terms of antimicrobial treatment, with a potential limitation of therapeutic options, thereby further complicating the clinical management of high-risk critically ill patients.


Asunto(s)
Proteínas Bacterianas/genética , Transferencia de Gen Horizontal , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/genética , Plásmidos , Serratia marcescens/enzimología , Serratia marcescens/genética , beta-Lactamasas/genética , Adulto , Infección Hospitalaria/microbiología , Humanos , Unidades de Cuidados Intensivos , Infecciones por Klebsiella/microbiología , Masculino , Infecciones del Sistema Respiratorio/microbiología , Infecciones por Serratia/microbiología , Secuenciación Completa del Genoma
7.
Int J Infect Dis ; 92: 247-252, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31982619

RESUMEN

OBJECTIVES: The aim of this study was to describe the emergence in Nepal of clinical isolates of Klebsiella pneumoniae harboring both blaNDM-5 and blaOXA-181/-232. METHODS: Six clinical isolates of K. pneumoniae highly resistant to carbapenems and aminoglycosides were obtained from inpatients in Nepal. Their whole genomes were sequenced by a next generation sequencer. RESULTS: The minimum inhibitory concentrations of meropenem, amikacin and ciprofloxacin were ≥128 µg/ml, >1024 µg/ml and ≥256 µg/ml, respectively. All six isolates co-harbored blaNDM-5, blaOXA-181 or -232 and rmtB. Of them, 1 also harbored rmtF. The blaNDM-5, blaOXA-232 and rmtB in all six isolates were located on plasmids. Of the six isolates tested, one isolate harbored two copies of blaOXA-181 and rmtF on the chromosome. CONCLUSIONS: This is the first report of clinical isolates of K. pneumoniae co-harboring blaNDM-5, blaOXA-181 or -232 and rmtB in Nepal. These strains were highly carbapenem- and aminoglycoside-resistant, and belonged to ST147 or ST395. Of them, ST147 isolate harbored two copies of blaOXA-181 on the chromosome.


Asunto(s)
Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Carbapenémicos/farmacología , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/aislamiento & purificación , Amicacina/farmacología , Amicacina/uso terapéutico , Aminoglicósidos/farmacología , Aminoglicósidos/uso terapéutico , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Carbapenémicos/uso terapéutico , Genoma Bacteriano , Humanos , Infecciones por Klebsiella/tratamiento farmacológico , Klebsiella pneumoniae/genética , Pruebas de Sensibilidad Microbiana , Nepal , Plásmidos/genética , Secuenciación Completa del Genoma , beta-Lactamasas/genética
8.
Arch Virol ; 165(3): 753-756, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31965314

RESUMEN

The genome sequence of a novel Meiothermus bacteriophage, named MMP7, which was isolated from Tengchong hot spring in Yunnan Province of China and belongs to the family Myoviridae, was sequenced in this study. To the best of our knowledge, this is the first reported genome sequence of a Meiothermus phage, which has a circular DNA genome of 32,864 bp and a GC content of 64%. The MMP7 genome contains 53 putative protein-encoding genes but no rRNA or tRNA genes, and it exhibits low overall sequence similarity and no significant homology to phage genomes whose sequences are publicly available, suggesting that MMP7 is a novel phage. Consistent with current taxonomic results, whole-genome-based phylogenetic analysis revealed that Meiothermus phage MMP7 has close evolutionary relationship to Thermus phages. Together, our results could be helpful for discovering new thermostable antimicrobial agents and understanding the evolution and genetic diversity of Meiothermus phages in extreme environments.


Asunto(s)
Bacterias/virología , Genoma Viral , Myoviridae/genética , ADN Viral , Filogenia , Análisis de Secuencia de ADN , Secuenciación Completa del Genoma
9.
Gene ; 731: 144340, 2020 Mar 20.
Artículo en Inglés | MEDLINE | ID: mdl-31923575

RESUMEN

As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.


Asunto(s)
Brassicaceae/clasificación , Brassicaceae/genética , Genoma del Cloroplasto/genética , Planta de la Mostaza/genética , Sinapis/genética , Cloroplastos/genética , Evolución Molecular , Secuenciación de Nucleótidos de Alto Rendimiento , Planta de la Mostaza/clasificación , Planta de la Mostaza/citología , Filogenia , Raphanus/clasificación , Raphanus/citología , Raphanus/genética , Análisis de Secuencia de ADN/métodos , Sinapis/clasificación , Sinapis/citología , Secuenciación Completa del Genoma
10.
BMC Infect Dis ; 20(1): 17, 2020 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-31910804

RESUMEN

BACKGROUND: Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent. METHODS: We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection. RESULTS: There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections. CONCLUSIONS: Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.


Asunto(s)
Antituberculosos/uso terapéutico , Farmacorresistencia Bacteriana Múltiple/genética , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/genética , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Secuenciación Completa del Genoma/métodos , Adolescente , Adulto , Anciano , Antituberculosos/efectos adversos , Femenino , Humanos , Incidencia , Estudios Longitudinales , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Moldavia , Mycobacterium tuberculosis/aislamiento & purificación , Filogenia , Polimorfismo de Nucleótido Simple/genética , Recurrencia , Estudios Retrospectivos , Adulto Joven
11.
Arch Virol ; 165(3): 765-769, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31894416

RESUMEN

Mycoviruses from Metarhizium anisopliae have been extensively studied, but their sequences have yet to be deposited in the NCBI database. In the present study, we characterized a new partitivirus obtained from the entomogenous fungus Metarhizium brunneum, named "Metarhizium brunneum partitivirus 1" (MbPV1). The complete genome of MbPV1, determined by metagenomic sequencing, RT-PCR, and RACE, comprised two dsRNA segments of 1,829 bp and 1,720 bp, respectively. Both dsRNAs contained a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (61.4% and 44.4% identity, respectively) to those of Colletotrichum eremochloae partitivirus 1 (CePV1), which were obtained from the NCBI database. A phylogenetic tree based on the RdRp sequence showed that MbPV1 clustered with members of the proposed genus "Epsilonpartitivirus", belonging to family Partitiviridae. Here, we propose that MbPV1 is a member of a new species of the proposed genus "Epsilonpartitivirus". This is the first sequence data report of a new mycovirus from a member of the genus Metarhizium.


Asunto(s)
Metarhizium/virología , Virus , Secuencia de Aminoácidos , Proteínas de la Cápside/genética , China , Genoma Viral/genética , Sistemas de Lectura Abierta/genética , ARN Replicasa/genética , ARN Viral/genética , Análisis de Secuencia de ARN , Virus/clasificación , Virus/genética , Virus/aislamiento & purificación , Secuenciación Completa del Genoma
12.
Euro Surveill ; 25(3)2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31992391

RESUMEN

From September to October 2019, seven patients colonised or infected with a ceftazidime-avibactam (CZA)-resistant Klebsiella pneumoniae carbapenemase (KPC)-2-producing K. pneumoniae were detected in two intensive care units of a Greek general hospital. The outbreak strain was sequence type (ST)147 and co-produced KPC-2 and the novel plasmid-borne Vietnamese extended-spectrum ß-lactamase (VEB)-25 harbouring a K234R substitution associated with CZA resistance. Epidemiological investigations revealed that the resistance was probably acquired by horizontal transmission independently from previous CZA exposure.


Asunto(s)
Antibacterianos/farmacología , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/genética , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Anciano , Anciano de 80 o más Años , Compuestos de Azabiciclo , Ceftazidima , Brotes de Enfermedades , Combinación de Medicamentos , Farmacorresistencia Bacteriana , Femenino , Genoma Bacteriano , Grecia , Humanos , Unidades de Cuidados Intensivos , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/aislamiento & purificación , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Mutación/genética , Secuenciación Completa del Genoma
13.
Lancet ; 395(10223): 514-523, 2020 02 15.
Artículo en Inglés | MEDLINE | ID: mdl-31986261

RESUMEN

BACKGROUND: An ongoing outbreak of pneumonia associated with a novel coronavirus was reported in Wuhan city, Hubei province, China. Affected patients were geographically linked with a local wet market as a potential source. No data on person-to-person or nosocomial transmission have been published to date. METHODS: In this study, we report the epidemiological, clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after returning to Shenzhen, Guangdong province, China, after a visit to Wuhan, and an additional family member who did not travel to Wuhan. Phylogenetic analysis of genetic sequences from these patients were done. FINDINGS: From Jan 10, 2020, we enrolled a family of six patients who travelled to Wuhan from Shenzhen between Dec 29, 2019 and Jan 4, 2020. Of six family members who travelled to Wuhan, five were identified as infected with the novel coronavirus. Additionally, one family member, who did not travel to Wuhan, became infected with the virus after several days of contact with four of the family members. None of the family members had contacts with Wuhan markets or animals, although two had visited a Wuhan hospital. Five family members (aged 36-66 years) presented with fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3-6 days after exposure. They presented to our hospital (The University of Hong Kong-Shenzhen Hospital, Shenzhen) 6-10 days after symptom onset. They and one asymptomatic child (aged 10 years) had radiological ground-glass lung opacities. Older patients (aged >60 years) had more systemic symptoms, extensive radiological ground-glass lung changes, lymphopenia, thrombocytopenia, and increased C-reactive protein and lactate dehydrogenase levels. The nasopharyngeal or throat swabs of these six patients were negative for known respiratory microbes by point-of-care multiplex RT-PCR, but five patients (four adults and the child) were RT-PCR positive for genes encoding the internal RNA-dependent RNA polymerase and surface Spike protein of this novel coronavirus, which were confirmed by Sanger sequencing. Phylogenetic analysis of these five patients' RT-PCR amplicons and two full genomes by next-generation sequencing showed that this is a novel coronavirus, which is closest to the bat severe acute respiatory syndrome (SARS)-related coronaviruses found in Chinese horseshoe bats. INTERPRETATION: Our findings are consistent with person-to-person transmission of this novel coronavirus in hospital and family settings, and the reports of infected travellers in other geographical regions. FUNDING: The Shaw Foundation Hong Kong, Michael Seak-Kan Tong, Respiratory Viral Research Foundation Limited, Hui Ming, Hui Hoy and Chow Sin Lan Charity Fund Limited, Marina Man-Wai Lee, the Hong Kong Hainan Commercial Association South China Microbiology Research Fund, Sanming Project of Medicine (Shenzhen), and High Level-Hospital Program (Guangdong Health Commission).


Asunto(s)
Infecciones por Coronavirus/transmisión , Neumonía Viral/transmisión , Adulto , Anciano , Betacoronavirus/clasificación , Betacoronavirus/genética , China/epidemiología , Infecciones por Coronavirus/diagnóstico , Infecciones por Coronavirus/epidemiología , Salud de la Familia , Genoma Viral , Humanos , Persona de Mediana Edad , Filogenia , Neumonía Viral/diagnóstico , Neumonía Viral/epidemiología , Radiografía Torácica , Tomografía Computarizada por Rayos X , Secuenciación Completa del Genoma/métodos
14.
Arch Virol ; 165(3): 757-760, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31912293

RESUMEN

Echovirus 21 (E21) belongs to the species Enterovirus B, whose members are frequently associated with acute flaccid paralysis. E21 strain 553/YN/CHN/2013 was isolated from a healthy child in Yunnan, China, in 2013. This is the first report of the complete genome sequence of E21 in China. This strain shared 81.7% nucleotide sequence identity and 96.8% amino acid sequence identity with the E21 prototype strain Farina. Although strain 553/YN/CHN/2013 belongs to the E21 serotype, the only similarity to the E21 strain was in the VP1 region, as other genomic regions, including VP2-VP4, were more similar to other EV-B members. Recombination analysis showed evidence of recombination events between E21 and other EV-B viruses. E21 strain 553/YN/CHN/2013 failed to infect suckling mice via intracerebral injection. Surveillance of E21 is very important to help forecast the potential of emerging E21 outbreaks and related diseases.


Asunto(s)
Enterovirus Humano B/genética , Enterovirus Humano B/aislamiento & purificación , Infecciones por Enterovirus/virología , Genoma Viral/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Proteínas de la Cápside/genética , Línea Celular , Niño , China , Enterovirus Humano B/clasificación , Humanos , Ratones , Recombinación Genética , Análisis de Secuencia de ARN , Secuenciación Completa del Genoma
15.
Gene ; 732: 144355, 2020 Mar 30.
Artículo en Inglés | MEDLINE | ID: mdl-31935501

RESUMEN

Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.


Asunto(s)
Curcuma/clasificación , Genoma del Cloroplasto , Secuenciación Completa del Genoma/métodos , Cloroplastos/genética , Curcuma/citología , Curcuma/genética , Evolución Molecular , Tamaño del Genoma , Repeticiones de Microsatélite , Filogenia
16.
Arch Virol ; 165(1): 223-226, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31655850

RESUMEN

Analysis of a loquat tree with leaf curl symptoms by deep sequencing revealed a novel virus with a single-stranded RNA genome, for which the name "loquat virus A" (LoVA) was proposed. The complete genome sequence comprised 7553 nucleotides (nt) and an additional poly(A) tail at the 3' terminus. Sequence comparisons of LoVA showed moderate similarity to cherry virus A (CVA), currant virus A (CuVA), and mume virus A (MuVA), which are members of the genus Capillovirus in the family Betaflexiviridae. Phylogenetic analysis of the full-genome nt sequence and replicase-like protein supported the placement of LoVA within the genus Capillovirus. However, it has a distinct genome organization, differing from recognized capilloviruses, as it contains three open reading frames (ORFs), with the coat protein (CP) expressed separately from the replication-associated protein (RP) rather than being encoded in the same ORF. This indicates that LoVA is a novel member of the genus Capillovirus in the family Betaflexiviridae with a distinct genomic organization.


Asunto(s)
Eriobotrya/virología , Flexiviridae/genética , Secuenciación Completa del Genoma/métodos , Composición de Base , Flexiviridae/clasificación , Tamaño del Genoma , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Sistemas de Lectura Abierta , Filogenia
17.
Arch Virol ; 165(1): 193-199, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31701223

RESUMEN

BACKGROUD: The presence of PCV3 genome has been detected in pigs affected by different clinical and pathological conditions as well as in healthy animals. Its presence has been reported in many countries of North and South America, Asia and Europe. However, there is no evidence of the presence and genetic characteristics of PCV3 in many European countries and especially the countries of the Balkan Peninsula. PURPOSE: The major objective of this study was to investigate the presence and obtain further genetic characterization of PCV-3 in the pig populations in Serbia. METHODS: To demonstrate the presence of PCV-3 DNA a conventional PCR assay was performed. The samples where no PCR product was observed (n=32), were further tested with a real-time PCR assay. The six PCR samples that were strongly positive for PCV-3 were subjected to amplification and sequencing of their entire cap genes and complete viral genome. RESULTS: We report on the first identification, genetic diversity and potential association in pathogenesis of some systemic and respiratory swine diseases of PCV-3 in Serbia. CONCLUSION: The results imply that PCV-3 circulates widely in the pig population and has a high similarity with previously reported isolates. Detected PCV-3 can be associated with some swine systemic and respiratory diseases but these associations are strongly influenced by the clinical or pathological condition of the animals. Our findings demonstrate that there are certain PCV-3 loads in pigs suffering from active PRRSV infection, Glässer's disease, APP pleuropneumonia, pneumonic pasteurellosis and PRDC; however, the significance of this viral load, as well as the mechanism by which PCV-3 may act as a secondary agent in aggravating the severity during co-infections of these pathogens, requires further research.


Asunto(s)
Circovirus/clasificación , Enfermedades Pulmonares/veterinaria , Enfermedades de los Porcinos/virología , Secuenciación Completa del Genoma/métodos , Animales , Circovirus/aislamiento & purificación , Circovirus/patogenicidad , Granjas , Variación Genética , Enfermedades Pulmonares/virología , Filogenia , Serbia , Porcinos , Carga Viral
18.
Arch Virol ; 165(1): 241-244, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31701224

RESUMEN

A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named "rose virus A" (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.


Asunto(s)
Carlavirus/genética , Rosa/virología , Secuenciación Completa del Genoma/métodos , Carlavirus/clasificación , Tamaño del Genoma , Genoma Viral , Secuenciación de Nucleótidos de Alto Rendimiento , Sistemas de Lectura Abierta , Filogenia
19.
Arch Virol ; 165(1): 233-236, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31676997

RESUMEN

The Siphoviridae phage PMBT6 was identified by transmission electron microscopy in the supernatant of Bifidobacterium thermophilum MBT94004 bioreactor fermentation culture, where it occurred at a moderately high titer. Genome analysis of the bacterial DNA confirmed the presence of this prophage within the genome of the lysogenic host. Under laboratory conditions, the prophage could not be induced by mitomycin C, ultraviolet C irradiation or hydrogen peroxide, suggesting that the prophage was released by spontaneous induction under (yet unknown) bioreactor conditions. Genome sequencing of the virion resulted in a linear, double-stranded DNA molecule of 36,561 bp with a mol% G + C content of 61.7 and 61 predicted open reading frames with low similarity to other Bifidobacterium spp. genomes, confirming that PMBT6 represents a novel temperate phage for this genus.


Asunto(s)
Bacteriófagos/genética , Bifidobacterium/crecimiento & desarrollo , Secuenciación Completa del Genoma/métodos , Bacteriófagos/clasificación , Bacteriófagos/ultraestructura , Composición de Base , Bifidobacterium/virología , Reactores Biológicos/microbiología , Fermentación , Tamaño del Genoma , Genoma Viral , Microscopía Electrónica de Transmisión , Sistemas de Lectura Abierta , Profagos/clasificación , Profagos/genética
20.
Arch Virol ; 165(1): 127-135, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31741097

RESUMEN

In clinical virome research, whole-genome/transcriptome amplification is required when starting material is limited. An improved method, named "template-dependent multiple displacement amplification" (tdMDA), has recently been developed in our lab (Wang et al. in BioTechniques 63:21-25. https://doi.org/10.2144/000114566, 2017). In combination with Illumina sequencing and bioinformatics pipelines, its application in virome sequencing was explored using a serum sample from a patient with chronic hepatitis C virus (HCV) infection. In comparison to an amplification-free procedure, virome sequencing via tdMDA showed a 9.47-fold enrichment for HCV-mapped reads and, accordingly, an increase in HCV genome coverage from 28.5% to 70.1%. Eight serum samples from acute patients liver failure (ALF) with or without known etiology were then used for virome sequencing with an average depth at 94,913x. Both similarity-based (mapping, NCBI BLASTn, BLASTp, and profile hidden Markov model analysis) and similarity-independent methods (machine-learning algorithms) identified viruses from multiple families, including Herpesviridae, Picornaviridae, Myoviridae, and Anelloviridae. However, their commensal nature and cross-detection ruled out an etiological interpretation. Together with a lack of detection of novel viruses in a comprehensive analysis at a resolution of single reads, these data indicate that viral agents might be rare in ALF cases with indeterminate etiology.


Asunto(s)
Biología Computacional/métodos , Hepatitis C Crónica/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Fallo Hepático Agudo/virología , Suero/virología , Anelloviridae/aislamiento & purificación , Anelloviridae/fisiología , Perfilación de la Expresión Génica/métodos , Hepacivirus/genética , Hepacivirus/aislamiento & purificación , Hepatitis C Crónica/sangre , Herpesviridae/aislamiento & purificación , Herpesviridae/fisiología , Humanos , Fallo Hepático Agudo/sangre , Myoviridae/aislamiento & purificación , Myoviridae/fisiología , Picornaviridae/aislamiento & purificación , Picornaviridae/fisiología , Especificidad de la Especie , Simbiosis , Secuenciación Completa del Genoma/métodos
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA