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1.
Two TaqMan-based real-time One-Step RT-PCR assays were developed for the rapid and efficient detection of Raspberry bushy dwarf virus (RBDV) and Raspberry leaf mottle virus (RLMV), two of the most common raspberry viruses in North America and Europe. The primers and probes were designed from conserved fragments of the polymerase region of each virus and were effective for the detection of different isolates tested in this study. The RBDV assay amplified a 94 bp amplicon and was able to detect as few as 30 viral copies. Whereas the RLMV assay amplified a 180 bp amplicon and detected as few as 300 viral copies from plant and aphid RNA extracts. Both assays were significantly more sensitive than their corresponding conventional RT-PCR methods. The sensitivity of the RLMV assay was also tested on single aphids after a fixed acquisition access period (AAP). In addition, the assays revealed a novel synergistic interaction between the two viruses, where the concentration of RBDV was enhanced ∼400-fold when it occurred in combination with RLMV compared to its concentration in single infections. The significance of this finding and the importance of the development of real-time RT-PCR assays for the detection of RBDV and RLMV are discussed. 相似文献
2.
D. Tapalski R. S. Hendriksen H. Hasman P. Ahrens F. M. Aarestrup 《Clinical microbiology and infection》2007,13(10):1030-1033
This study describes the characterisation by pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA) typing and antimicrobial resistance profiles of 35 Salmonella enterica serovar Typhimurium isolates, mostly from infections in children who acquired an infection outside hospitals in the Gomel region of Belarus. Thirty-one isolates were highly similar according to PFGE and MLVA typing, were multidrug-resistant, including resistance to ceftiofur, and harboured the bla(CTX-M-5) gene. These results indicate that a common source may have been responsible for most of the infections. 相似文献
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Nidhi Bhatnagar Shantanu Prakash Vangala Ramakrishna Danish Nasar Khan Shakti Saumnam Shrivastava Vimala Venkatesh D. Himanshu Reddy Amita Jain 《Indian journal of medical microbiology》2022,40(1):91-95
PurposeHepatitis E virus (HEV) is responsible for >50% of acute viral hepatitis (AVH) in developing countries. It has 4 major genotypes and various subtypes which vary in geographical distribution, clinical manifestations and epidemiological patterns. This study was conducted to characterise HEV isolates from north India to study the effect of host and viral factors on HEV infection.MethodsSerum samples collected from 536 AVH patients admitted to Department of Medicine, King George's Medical University, Lucknow from July 2016 to June 2017 were screened for anti HEV IgM, anti HAV IgM, HBsAg and anti HCV antibodies using commercial ELISA kits. Samples either positive for anti HEV IgM antibodies (n ?= ?204) or negative for all 4 hepatotropic viruses (n ?= ?37) were enrolled and tested by real time PCR for HEV RNA. HEV RNA positive samples with high viral load were further subjected to nested PCR for amplification of capsid gene. Sequencing and phylogenetic analysis were performed. HEV strains isolated from this study were deposited to GenBank under accession numbers MG571274 to MG571283.ResultsAnti HEV IgM positivity was observed among 38% clinically suspected AVH cases. HEV RNA was detected in 31.8% seropositive HEV cases and additional 3 seronegative cases. Males outnumbered females and the most affected age group was of young adults. Maximum number of cases were seen during the months of June to September. Phylogenetic analysis showed that HEV strains in our study belonged to genotype 1a. Mortality in HEV infected pregnant females was 23.5% as compared to 2.4% in non-pregnant females. Adverse fetal outcome was recorded in 51% of HEV infected pregnancies.ConclusionsHEV genotype 1a is prevalent in our setting. HEV during pregnancy is associated with adverse maternal and fetal outcome. 相似文献
4.
Twenty-nine faecal specimens from Slovenian patients in which Cryptosporidium oocysts had been identified were studied. A fragment of the Cryptosporidium 18S rRNA gene and a fragment of the Cryptosporidium COWP gene were amplified by PCR and sequenced. Cryptosporidium parvum was identified in 26 of the 29 specimens, Cryptosporidium hominis in two, and Cryptosporidium cervine genotype in one. The fact that C. parvum, which is associated traditionally with animals, was identified in the majority of human faecal specimens suggests that cryptosporidiosis may have primarily a zoonotic origin in Slovenia. 相似文献
5.
Monecke S Nitschke H Slickers P Ehricht R Swanston W Manjunath M Roberts R Akpaka PE 《European journal of clinical microbiology & infectious diseases》2012,31(7):1497-1500
Eighty methicillin-resistant Staphylococcus aureus (MRSA) isolates from three hospitals in Trinidad and Tobago were collected and genotyped using microarray hybridisation. They were found to belong to three distinct MRSA strains. Of the 80 isolates, 76 were assigned to ST239-MRSA-III. They were largely homogeneous, although some variations affected the presence of the enterotoxin A gene, as well as of resistance markers (mercury resistance operon, aadD, tet(K), qacA). The mupA gene conferring mupirocin resistance was found in 7.3% of isolates. One isolate was identified as CC5-MRSA-II and three isolates belonged to the Panton-Valentine leukocidin (PVL)-positive ST8-MRSA-IV strain USA300. While community-acquired MRSA strains are rare in Trinidad and Tobago, the vast majority of MRSA cases can be attributed to healthcare-associated strains. Thus, infection control procedures within medical facilities need to be revised and enforced. This could substantially reduce the burden of MRSA to healthcare in Trinidad and Tobago. 相似文献
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Molecular characterisation of segments 1 to 6 of Rice black-streaked dwarf virus from China provides the complete genome 总被引:4,自引:0,他引:4
Summary. The nucleotide sequences of segments S1 to S6 of a Chinese isolate of Rice black-streaked dwarf virus (RBSDV) were determined. This provides the first complete sequence of a plant pathogenic member of the genus Fijivirus. The complete ten-segment genome has 29141 nucleotides, making it the largest reovirus genome so far reported. Each of the
segments S1–S6 is predicted to encode a single major protein. Protein comparisons indicated that S1 encoded an RNA dependent
RNA polymerase, with similarities to that encoded by S1 of Nilaparvata lugens reovirus (NLRV). S2 and S3 appeared to be homologous to S3 and S4 respectively of both Fiji disease virus (FDV) and NLRV. The protein encoded on S4 showed some similarity to that of NLRV S2. The proteins encoded on S5 and S6, though
similar in size to those of NLRV S5 and S6, had no detectable homologies to them or to any other known protein.
Received April 4, 2001 Accepted August 1, 2001 相似文献
8.
Relationships among three isolates of barley yellow dwarf virus 总被引:2,自引:0,他引:2
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Munné MS Vladimirsky S Otegui L Soto S Brajterman L Castro R Velasco MC Bonnano A Fernández E Remondegui C Passeggi C Rodríguez C Pizarro M Fabre A Moreiro R Quarleri J González JE 《Journal of medical virology》2007,79(7):887-894
Hepatitis A, a vaccine preventable disease, is now of transitional or intermediate endemicity in Argentina, as the epidemiologic pattern of the disease has shifted with improvements in living conditions in some parts of the country. Increase in the susceptibility of older children and adults has led to increasing disease incidence. Molecular epidemiology has played an important role in the understanding of HAV infection by identifying modes of spreading and by permitting the monitoring of changes in circulating virus brought about by prevention programs. South American isolates characterized are limited. Eighty-two sporadic and outbreak isolates from Argentina were sequenced in the VP1/2A region of HAV genome over a 9-year period. All the isolates belonged to subgenotype IA. All our sequences grouped into two big clusters. Apparently, at least two lineages have been co-circulating in the same place at the same time. Despite great genetic variability, few point amino acid changes could be deduced. Four sequences showed an Arg --> Lys substitution at 1-297 which characterized the genotype IB at the amino acid level. Many isolates carried a conservative amino acid substitution Leu --> Ile at position 42 of the 2A domain, previously described as a possible fingerprint of HAV sequences in Brazil. The other rare changes have been found before, except for a 1-277 Asn --> Ser substitution displayed in two isolates that has not been previously reported. Argentina recently implemented universal vaccination in 1-year-old children. Molecular tools would be useful in an active surveillance program. 相似文献
11.
An isolate (RPV) of barley yellow dwarf virus transmitted specifically by Rhopalosiphum padi and an isolate (PAV) transmitted nonspecifically by both R. padi and Macrosiphum avenae were purified by procedures previously found satisfactory for another isolate (MAV) transmitted specifically by M. avenae. As with MAV, infectivity of RPV and PAV samples removed from sucrose gradient columns was associated with a dense polyhedral particle about 30 nm in diameter in shadowed preparations. No differences in sedimentation rate (sedimentation coefficient 115–118 S) among the 3 virus isolates were detected in parallel sucrose gradient centrifugation tests. 相似文献
12.
A single major protein was identified in preparations of the MAV and RPV isolates of barley yellow dwarf virus in tests based on SDS gel electrophoresis. The molecular weight of each protein was measured in experiments using a series of gels of different acrylamide concentrations. Although the precision of these determinations was affected by some anomalous migration of the proteins, we estimate the molecular weight of the protein of the MAV isolate to be 23,500, and that of RPV to be 24,450. 相似文献
13.
D. F. Quito-Avila M. A. Ibarra R. Alvarez E. L. Peralta R. R. Martin 《Archives of virology》2014,159(9):2519-2521
Sequencing of the complete genome of a raspberry bushy dwarf virus isolate from Rubus glaucus in Ecuador revealed that its RNA-1 and RNA-2 were 5449 and 2231 nucleotides (nt) long, respectively, and phylogenetically closest to isolates from Sweden and Slovenia. In dsRNA analysis of infected plants, an additional band of 3 kbp was observed. Sequencing of this band revealed that it was 3279 nt long. BLAST searches revealed that this band contained a modified version of RNA-2, which consisted of RNA-2 (2231 nt) plus an additional 1048-nt fragment that was concatenated in a reverse-complement fashion to its 5’ terminus. 相似文献
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Argentini C Dettori S Villano U Guadagnino V Infantolino D Dentico P Coppola RC Rapicetta M 《Journal of medical virology》2000,62(1):84-90
The characteristics of genotype 4 subtype variability of HCV isolates circulating in Italy were studied. The viral isolates were identified from 736 HCV-RNA positive sera originated from seroepidemiological studies undertaken in 4 different regions of North, South Italy and Sardinia. 24 out of 28 genotype 4 isolates (86%) were classified by phylogenetic analysis of E1 genome region (915-1128) as belonging to subtype 4d (Neighbour Joining Method). Three isolates classified as subtype 4a were detected in haemophilic patients, possibly related to infections from blood products. One isolate classified as a new subtype derived from an Eritrean patient subjected to haemodialysis. Very high genome homogeneity (mean 4.3%) was shown by genetic comparisons (DNA dist programs Phylip Package) for all the 4d isolates relative to the studies performed in Veneto, Calabria and Sardinia and originated from subjects from the general population and outpatients (19 subtype 4d isolates out of 24). In the 3 studies different prevalence rates of HCV genotype 4 (3.1%, 1. 3%, 14% respectively) were found. In contrast a considerable degree of heterogeneity, both intragroup and with the other groups (mean 8. 2% and 8.7%, respectively) was observed among subtype 4d isolates identified in the patients of a haemodialysis centre in Apulia region. In conclusion the subtype 4d of genotype 4 was highly prevalent and endemic in Italy. An elevated level of viral heterogeneity was observed in one study carried out in a region of Southern Italy. This can be related to a longer period of past endemicity of this genotype and to a high level of exposure to reinfections in particular categories of patients such as haemodialysis patients. 相似文献
16.
Summary. The genetic structure of natural populations of Alaskan barley yellow dwarf virus (BYDV)-PAV, BYDV-PAS, and cereal yellow
dwarf virus (CYDV)-RPV from barley (Hordeum vulgare L.) and oats (Avena sativa L.) in Alaska were analyzed between 2002 and 2004. PCR products spanning the viral coat protein gene of 187 isolates were
cloned and sequenced. The majority (78%) were similar to BYDV-PAS, 19% were similar to CYDV-RPV, and only about 3% resembled
BYDV-PAV. The CYDV-RPV isolates clustered in three groups: 44, 17, and 39% resembled RPS-like CP from Mexico, resembled RPV-like
CP from New York, or formed a unique clade that was RPV/RPS recombinant CP, respectively. The patterns of genetic variation
of PAS and RPV varied little over time or with respect to host plant. The difference in spatial and temporal population genetic
structures of the PAS and RPV isolates suggests that these two viruses are influenced by different agroecological factors.
Sequence of PCR products spanning the carboxyl terminus of the polymerase gene, the intergenic region, and most of the coat
protein gene of RPV revealed two probable ancestral recombination events for some isolates. 相似文献
17.
We determined the entire RNA1, 2 and 3 sequences of two prunus necrotic ringspot virus (PNRSV) isolates, Chr3 from cherry
and Pch12 from peach, obtained from an orchard in the Niagara Fruit Belt, Canada. The RNA1, 2 and 3 of the two isolates share
nucleotide sequence identities of 98.6%, 98.4% and 94.5%, respectively. Their RNA1- and 2-encoded amino acid sequences are
about 98% identical to the corresponding sequences of a cherry isolate, CH57, the only other PNRSV isolate with complete RNA1
and 2 sequences available. Phylogenetic analysis of the coat protein and movement protein encoded by RNA3 of Pch12 and Chr3
and published PNRSV isolates indicated that Chr3 belongs to the PV96 group and Pch12 belongs to the PV32 group. 相似文献
18.
Gulube Z Chirara M Kew M Tanaka Y Mizokami M Kramvis A 《Journal of medical virology》2011,83(2):235-244
Hepatitis B virus (HBV) is endemic in Africa, being hyperendemic in sub-Saharan Africa. Genotypes A, D, and E circulate in Africa, showing a distinct geographical distribution. The aim of the present study was to determine the HBV genotype distribution in blood donors from different geographical locations in Zimbabwe. Using a restriction fragment polymorphism assay, sequencing of the basic core promoter/precore region and of the complete S open reading frame showed that 29 HBV isolates from geographically distinct regions belong to subgenotype A1. The complete genome of two of these Zimbabwean HBV isolates was sequenced. Forty-four percent of the Zimbabwean HBV isolates (11/23) were characterized by a G1862C missense mutation, which causes a Val to Leu amino acid substitution at position 17 of the precore region. The majority of Zimbabwean HBV isolates clustered with a number of South African HBV isolates, with which they shared characteristic amino acids in the preS1, preS2, and polymerase spacer regions. The wide distribution of subgenotype in Africa, as well as the high intragroup divergence and the geographical clustering of the African and Asian subgenotype A1 HBV isolates indicate that this subgenotype has a long period of endemicity in these regions. 相似文献
19.
Banana bunchy top disease is caused by a single-stranded circular DNA virus, banana bunchy top virus (BBTV), which is a member
of the genus Babuvirus (family Nanoviridae). We have cloned and sequenced five components (DNA-R, DNA-S, DNA-N, DNA-M and DNA-C) of a BBTV isolate originating from
Pakistan. In addition, the DNA-R and several other components of five further isolates, originating from geographically distinct
sites across the banana-growing area of Sindh province, Pakistan, were cloned and sequenced. Analysis of the sequences indicates
that BBTV present in Pakistan belongs to the “South Pacific” group of isolates and that the genetic diversity of the virus
in the country is very low. The virus shows the highest levels of sequence identity to BBTV isolates originating from Egypt,
India and Australia. The significance of these results with respect to the possible origin of the virus in Pakistan and the
prospects for obtaining genetically engineered resistance to the virus are discussed. 相似文献
20.
Isolates of potato virus Y (PVY) have been divided into several strains. We determined the genomic sequences of PVY isolates
AQ4 and FZ10 from tobacco in China. AQ4 and FZ10 had genome of 9700 and 9698 nucleotides, respectively. In phylogenetic analysis
of complete genome sequences, AQ4 was clustered with strain N-Wi, and FZ10 with NTN. AQ4 had two recombination sites within
the P1 and P3 genes, while FZ10 had three within the P1, P3 and NIa-Pro genes. When compared to typical NTN isolates, FZ10
lacked a recombination site within the CP gene and, thus, represents a novel recombination type of PVY. 相似文献