Universal primers for rapid detection of hytrosaviruses

Hytrosaviridae is a proposed virus family encompassing viruses that cause salivary gland hypertrophy (SGH) syndrome in infected insects and reduce the fertility in their dipteran insect hosts. They contain a large, double stranded DNA genome of 120-190 kbp. To date, these viruses have been detected only in adult Diptera. These include hytrosaviruses detected in various tsetse fly species (Glossina spp.), the narcissus bulb fly Merodon equestris and the house fly Musca domestica. The limited number of hytrosaviruses reported to date may be a reflection of the frequent absence of external symptoms in infected adult flies and the fact that the virus does not cause rapid mortality. Based on the complete genome sequence of Glossinia pallidipes (GpSGHV) and Musca domestica (MdSGHV) salivary gland hypertrophy viruses, a PCR based methodology was developed to detect the viruses in these species. To be able to detect hytrosaviruses in other Diptera, five degenerate primer pairs were designed and tested on GpSGHV and MdSGHV DNA using gradient PCR with annealing temperatures from 37 to 61 °C. Two pairs of primers were selected from p74, two pairs from PIF-1 and one pair from ODV-e66 homologous proteins. Four primer pairs generated a virus specific PCR product on both MdSGHV and GpSGHV at all tested annealing temperatures, while the ODV-e66 based primers did not generate a virus specific product with annealing temperatures higher that 47 °C. No non-specific PCR product was found when using genomic DNA of infected flies as template DNA. These results offer new sets of primers that could be used to detect hytrosaviruses in other insects.     

A high level of mixed Trypanosoma brucei infections in tsetse flies detected by three hypervariable minisatellites.

The issue of whether genetic exchange occurs at a significant frequency in natural populations of Trypanosoma brucei is controversial and one of the arguments against a high frequency has been the apparent lack of host infections with mixtures of trypanosome genotypes. Three minisatellite markers (MS42, CRAM, 292) within the coding regions of three genes have been identified and PCR based methods developed for detecting variation at these loci using crude lysates of infected blood as templates. Initial PCR analysis, using primers flanking the repeats, of DNA from two cloned stocks of the parasite has shown that two DNA fragments of different size were amplified from each stock. Analysis of the inheritance of these fragments into the F1 progeny of crosses demonstrated that the different size fragments were alleles that segregated in a Mendelian manner. The alleles at each of the three loci segregated independently consistent with their localisation on three different chromosomes. Analysis of a series of cloned isolates from tsetse flies showed that these loci were highly variable giving heterozygosities of 94% and the identification of 12 distinct alleles in a sample of 17 cloned isolates. In order to determine whether isolates are heterogeneous in terms of trypanosome genotype, the allelic variation at these three loci was examined in uncloned samples from tsetse flies isolated in Kiboko, Kenya and Lugala, Uganda. A significant proportion of the isolates (36% in Lugala and 47% in Kiboko) contained more than two alleles at one or more of the loci thus demonstrating that a high proportion of tsetse flies were infected with more than one genotype of trypanosomes. This was established, unequivocally, for two isolates by generating a series of cloned trypanosome lines from each and determining the genotype of each clone; one isolate (927) contained seven different genotypes with a high proportion of the possible combinations of alleles at each locus. These results indicate the possibility of frequent genetic exchange in the field, they imply that a significant proportion of mammalian hosts must contain mixtures of different trypanosome genotypes and they demonstrate the advantages of using minisatellite markers for the analysis of the population structure of T. brucei.     

Detection of H-1 parvovirus and Kilham rat virus by PCR.

H-1 virus and Kilham rat virus (KRV) are autonomous parvoviruses which generally cause subclinical infections in rats and can cause persistent infections in cell cultures. In this study, primer sets specific for either H-1 or KRV were designed on the basis of DNA sequence comparisons of the rodent parvoviruses. The specificities of the H-1 and KRV-specific primer sets were determined by testing viral preparations of seven different parvoviruses and nine other viruses known to infect rodents. The H-1-specific PCR assay amplified the expected 254-bp product only in the presence of H-1 viral DNA and was able to detect as little as 100 fg of H-1 viral DNA. The KRV-specific PCR assay generated the expected 281-bp product only when KRV viral DNA was used as the template and was able to detect as little as 10 pg of KRV viral DNA. Each assay was able to detect its respective virus in tissues from rats experimentally infected with H-1 or KRV. In contrast, no product was amplified by either assay with tissues from mock-infected rats. Our findings indicate that these PCR assays provide rapid, specific, and sensitive methods for the detection of H-1 or KRV infection in rats and cell culture systems.     

Quantitation of encapsidated recombinant adeno-associated virus DNA in crude cell lysates and tissue culture medium by quantitative, real-time PCR

Recombinant AAV vectors are produced by transient transfection of mammalian cells. The virus is usually purified from a combination of lysed cells and spent culture medium by HPLC. We have developed a quantitative, real-time PCR assay for quantifying encapsidated single-stranded viral DNA (i.e. DNA-containing virions) in cell lysates and the spent culture medium. This requires extensive DNaseI digestion to reduce the amount of AAV replicative DNA, as well as plasmid and cellular DNA, to negligible amounts. To demonstrate the utility of this assay, we produced recombinant AAV in HeLa cells and five different types of 293 cells. We used primers to the EGFP transgene to detect the production of a recombinant AAV. We assayed the cell lysates and media by both our quantitative PCR assay and a functional transduction assay. The quantitative PCR assay data correlated well with the transduction assay data. Because this assay only requires standard PCR primers and SYBR Green I dye to detect the amplification of the PCR template, it will readily adapt to any target DNA sequence within the recombinant AAV genome. The recombinant AAV vector does not need to express a reporter gene, such as EGFP or beta-galactosidase in order to assay the amount of virus produced.     

Real-time RT-PCR (TaqMan) assays for the detection of viruses associated with Rugose wood complex of grapevine

Real-time TaqMan RT-PCR (TaqMan RT-PCR) assays were developed to detect the viruses associated with Rugose wood complex of grapevines. The viruses detected were Rupestris stem pitting-associated virus in the genus Foveavirus, Grapevine virus A, Grapevine virus B and Grapevine virus D in the genus Vitivirus. The coat protein was found to be the most conserved gene within the viral species, therefore, the primers and probes for TaqMan RT-PCR assays were designed from the multiple alignment of the coat protein sequence of various isolates of each virus. Comparisons were also made between the conventional one step RT-PCR and TaqMan RT-PCR for the detection of these viruses using four-fold serial dilutions of both purified RNA and crude extract prepared from grapevine tissue. Results showed that TaqMan RT-PCR was more sensitive and could detect viruses at 32- and 256-fold higher dilutions for purified RNA and crude extract, respectively, compared to RT-PCR. The use of an internal control (18S rRNA) allowed comparison of sample preparation protocols and amplification efficiencies between samples.     

Identification of a double-stranded RNA virus by using polymerase chain reaction and magnetic separation of the synthesized DNA segments.

A double-nested polymerase chain reaction assay (PCR), followed by magnetic separation of the PCR-synthesized DNA segments, was developed to detect a double-stranded RNA virus, infectious pancreatic necrosis virus from salmonid fish. Viral RNA was extracted from cell cultures and used for cDNA synthesis. The cDNA produced was used as a template in a double PCR. The sensitivity of this double PCR was approximately 0.8 pg of template double-stranded RNA. The DNA segment produced from the first PCR was also used as a template in a second PCR with a set of two 5'-labeled primers, one with biotin and the other with 32P. The PCR segment that was then synthesized was separated from the solution by using streptavidin-coated, superparamagnetic beads. The levels of radioactivity measured in the magnetically separated fractions were significantly higher in the positive samples than they were in the negative samples.     

猴空泡病毒40核酸序列检测法的优化研究

目的 对通常使用的猴空泡病毒40(Simian vacuolating virus 40,SV40)核酸序列检测法进行优化,寻找敏感性高、特异性强、适用面广的SV40核酸序列检测引物.方法 以21个SV40毒株完全基因组为基础数据,用Primer Premier 5.00软件重新设计两对SV40 DNA检测引物,用Oligo 6.71软件和DNAMAN 6.0.40软件对引物参数进行分析,将分析结果与通常使用的检测引物进行比较.用不同稀释度SV40核酸序列作模板,比较4对引物检测的敏感性.分别用无菌水、Vero细胞DNA、SV40 DNA作模板检测4对引物的特异性.结果 对于21个SV40病毒株,优化引物对VP1和T的序列是保守的;对于接受号为J02400、NC_001669、AF316139和AF316141的4个病毒株,通常使用的引物对GCVP1和GCT的序列是保守的;用同一稀释度的SV40 DNA作模板,引物对VP1和T的扩增效率明显高于引物对GCVP1和GCT;在特异性检测比较中,引物对VP1和T没有出现非特异性扩增条带,引物对GCVP1和GCT在100 bp处出现非特异性扩增条带.结论 优化的SV40核酸序列检测法具有敏感性高、特异性强、检测面广、引物及其PCR产物序列保守等特点.     

Development of a rapid and sensitive polymerase chain reaction assay for detection of bovine herpesvirus type 1 in bovine semen.

We developed a polymerase chain reaction (PCR) assay to detect bovine herpesvirus type 1 (BHV-1) in bovine semen. Since bovine semen contains components that inhibit PCR amplification, a protocol was developed to purify BHV-1 DNA from bovine semen. To identify failures of PCR amplification, we used an internal control template that was coamplified by the same PCR primers. When separated fractions of BHV-1-contaminated semen were analyzed by the PCR, we found that more than 90% of the BHV-1 DNA was present in a pooled fraction consisting of seminal fluid, nonsperm cells, and virus adsorbed to spermatozoa. By using this fraction, three to five molecules of BHV-1 DNA in 50 microliters of bovine semen could be detected. A pilot study to compare this PCR assay with the routinely used virus isolation method showed that this PCR assay is 2- to 100-fold more sensitive. In addition, the results of the PCR assay are available in 1 day, whereas the virus isolation method takes 7 days. Therefore, the PCR assay may be a good alternative to the virus isolation method.     

Detection of genital papillomavirus types by polymerase chain reaction using common primers.

We describe the detection of eight genital human papillomavirus (HPV) types, including HPV16 and HPV18, by PCR amplification of a 323 base-pair region of the genome within the L1 open reading frame (ORF). The primer sequences are: TGYAAATATCCWGATTWTWT and GTATCWACMACAGTAACAAA. The method will detect purified HPV16 DNA down to a concentration of as little as a single molecule in 100 microliters. The method is also applicable to purified DNA and crude lysates from tumour biopsies. Typing of the PCR product can be achieved with specific oligonucleotide probes.     

Reverse restriction fragment length polymorphism (RRFLP): A novel technique for genotyping infectious laryngotracheitis virus (ILTV) live attenuated vaccines

A novel technique, the reverse restriction fragment length polymorphism (RRFLP) assay, was developed as a means of detecting specific informative polymorphic sites in the infectious laryngotracheitis virus (ILTV) genome. During the RRFLP procedure, DNA is digested with restriction enzymes targeting an informative polymorphic site and then used as template in a real-time polymerase chain reaction (PCR) with primers flanking the informative region. The analysis of the ΔC_t values obtained from digested and undigested template DNA provides the genotype of the DNA. In this study, the RRFLP assay was applied as a method to differentiate between the two types of infectious laryngotracheitis virus attenuated live vaccines. Sequence analysis of ILTV vaccines revealed an informative polymorphic site in the 5′-non-coding region of the infected cell protein (ICP4) gene. Unique AvaI and AlwI restriction enzyme sites were identified in the tissue culture origin and chicken embryo origin attenuated vaccines, respectively. These two informative polymorphic sites were used in a RRFLP assay to genotype rapidly and reproducibly ILTV attenuated live vaccines.     

口服鼠疫F1-V重组融合基因DNA活菌疫苗的构建及免疫原性研究

目的 构建携带鼠疫耶尔森菌F1-V融合基因的重组减毒沙门菌苗,口服免疫Balb/c小鼠检测其免疫原性,为口服鼠疫活载体DNA疫苗研究打下基础.方法 将F1-V融合基因克隆到真核表达载体asd-pVAX1,进一步依次将重组质粒转化减毒沙门菌X3730、X4550得到重组沙门菌X4550(asd-pVAX1/F1-V),提取重组质粒转染COS-7细胞并做免疫组化和Western-blot检测F1-V融合蛋白在细胞中的表达.以1×109CFU/只的剂量3次口服免疫Balb/c小鼠,ELISA方法检测血清中抗体水平.结果 构建的重组减毒沙门菌转染COS-7细胞后,免疫组化和Western-blot试验证明F1-V融合蛋白在细胞中得到了瞬时表达,ELISA检测到免疫小鼠血清有特异性抗体IgG产生.结论 构建的重组沙门菌能运送DNA疫苗到体内并成功释放质粒刺激机体产生特异性免疫应答,为口服鼠疫活载体DNA疫苗的黏膜免疫研究打下了基础.     

Recombinant DNA probes reveal simultaneous infection of tsetse flies with different trypanosome species

The utility of recombinant DNA probes in the detection of natural trypanosome infection of tsetse flies has been assessed in Lambwe Valley, near the shores of Lake Victoria, Kenya. The tsetse flies were surveyed during two different seasons in 1988. Three different probes used each contained highly repetitive DNA sequences specific for a species or subspecies of trypanosomes of the Nanomonas subgenus. A fourth probe contained repetitive sequences common to trypanosome species of the Trypanozoon subgenus. Mixed mature or immature infections were detected in a variety of combinations in different individual tsetse flies. Such infections were detected in both the guts and mouthparts of some tsetse flies. Simultaneous natural infection of tsetse with the savannah type Trypanosoma congolense and Kilifi type T. congolense, T. congolense and Trypanosoma brucei or T. congolense and Trypanosoma simiae were demonstrated.

The probes have thus been used to demonstrate the presence in Lambwe Valley, south-western Kenya, of a type of T. congolense first observed among trypanosome isolates obtained from sentinel cattle exposed to natural infection on a ranch at Kilifi on the Kenya coast. This type of T. congolense appears not to be confined to the coastal region nor to any particular species of tsetse flies and may contribute significantly to livestock morbidity in other areas of eastern Africa. In the Kilifi area, T. congolense was found primarily in Glossina austeni; in Lambwe valley, it was found in Glossina pallidipes.     

Hytrosaviridae: a proposal for classification and nomenclature of a new insect virus family

Salivary gland hypertrophy viruses (SGHVs) have been identified from different dipteran species, such as the tsetse fly Glossina pallidipes (GpSGHV), the housefly Musca domestica (MdSGHV) and the narcissus bulbfly Merodon equestris (MeSGHV). These viruses share the following characteristics: (i) they produce non-occluded, enveloped, rod-shaped virions that measure 500–1,000 nm in length and 50–100 nm in diameter; (ii) they possess a large circular double-stranded DNA (dsDNA) genome ranging in size from 120 to 190 kbp and having G + C ratios ranging from 28 to 44%; (iii) they cause overt salivary gland hypertrophy (SGH) symptoms in dipteran adults and partial to complete sterility. The available information on the complete genome sequence of GpSGHV and MdSGHV indicates significant co-linearity between the two viral genomes, whereas no co-linearity was observed with baculoviruses, ascoviruses, entomopoxviruses, iridoviruses and nudiviruses, other large invertebrate DNA viruses. The DNA polymerases encoded by the SGHVs are of the type B and closely related, but they are phylogenetically distant from DNA polymerases encoded by other large dsDNA viruses. The great majority of SGHV ORFs could not be assigned by sequence comparison. Phylogenetic analysis of conserved genes clustered both SGHVs, but distantly from the nudiviruses and baculoviruses. On the basis of the available morphological, (patho)biological, genomic and phylogenetic data, we propose that the two viruses are members of a new virus family named Hytrosaviridae. This proposed family currently comprises two unassigned species, G. pallidipes salivary gland hypertrophy virus and M. domestica salivary gland hypertrophy virus, and a tentative unassigned species, M. equestris salivary gland hypertrophy virus. Here, we present the characteristics and the justification for establishing this new virus family.     

A capripoxvirus detection PCR and antibody ELISA based on the major antigen P32, the homolog of the vaccinia virus H3L gene.

Sheeppoxvirus (SPV), goatpoxvirus (GPV) and lumpy skin disease virus (LSDV) of cattle belong to the Capripoxvirus genus of the Poxviridae family and can cause significant economic losses in countries where they are endemic. Capripox diagnosis by classical virological methods dependent on live capripox virus is not suitable in countries such as Australia where the virus is exotic and live virus is not available. To develop diagnostic tests based on recombinant material, we cloned and sequenced a 3.7 kb viral DNA fragment of SPV that contained open reading frames homologous to the vaccinia virus J6R, H1L, H2R, H3L and H4L genes. A capripoxvirus specific PCR assay was developed that differentiated between SPV and LSDV on the basis of unique restriction sites in the corresponding PCR fragments. The vaccinia virus H3L homolog was identified as the capripoxvirus P32 antigen. The P32 proteins of SPV and LSDV were expressed in Escherichia coli as a fusion protein with a poly-histidine tag and affinity purified on metal binding resin. The full-length P32 protein contained a transmembrane region close to the carboxy terminus and was membrane associated but could be solubilised in detergent and used as trapping antigen in an antibody detection ELISA. The ELISA was specific for capripoxvirus as only sera from sheep infected with capripoxvirus but not orf or vaccinia virus reacted with the capripoxvirus P32 antigen.     

Detection and heterogeneity of herpesviruses causing Pacheco's disease in parrots

Pacheco's disease (PD) is a common, often fatal, disease of parrots. We cloned a virus isolate from a parrot that had characteristic lesions of PD. Three viral clones were partially sequenced, demonstrating that this virus was an alphaherpesvirus most closely related to the gallid herpesvirus 1. Five primer sets were developed from these sequences. The primer sets were used with PCR to screen tissues or tissue culture media suspected to contain viruses from 54 outbreaks of PD. The primer sets amplified DNA from all but one sample. Ten amplification patterns were detected, indicating that PD is caused by a genetically heterogeneous population of viruses. A single genetic variant (psittacid herpesvirus variant 1) amplified with all primer sets and was the most common virus variant (62.7%). A single primer set (23F) amplified DNA from all of the positive samples, suggesting that PCR could be used as a rapid postmortem assay for these viruses. PCR was found to be significantly more sensitive than tissue culture for the detection of psittacid herpesviruses.     

Identification of Francisella tularensis by both culture and real-time TaqMan PCR methods from environmental water specimens in outbreak areas where tularemia cases were not previously reported

Tularemia is an endemic disease in Turkey. In this study, we aimed to detect Francisella tularensis by two methods from natural water supplies thought to cause tularemia epidemiologically. A total of 154 water specimens from three different outbreaks caused by drinking water were collected. Water specimens were cultured on antibiotic-added cysteine heart agar base with blood and incubated at 37°C in a humidified atmosphere containing 5% CO(2) for 4-10?days. The suspected colonies were confirmed by F. tularensis antiserum (BD) and the real-time TaqMan polymerase chain reaction (PCR) method. DNA was isolated from samples obtained from filters. The primer and probe sets targeting the ISFtu2 genome were used. A total of four F. tularensis isolates were obtained from 154 water samples. At the same time, the presence of F. tularensis DNA from 17 water specimens was shown by the real-time TaqMan PCR method. Although the DNA presence of F. tularensis has been detected from water sources by the PCR method in Turkey up to now, there has been no isolation directly from water specimens by culture. In this study, the determination of F. tularensis from water sources has been exhibited as the first data by both culture and real-time TaqMan PCR methods.     

Nested polymerase chain reaction for detection of human immunodeficiency virus type 1 DNA in clinical specimens.

A highly sensitive two-step polymerase chain reaction (PCR) method was evaluated for detection of human immunodeficiency virus type 1 (HIV-1) DNA in clinical specimens. The product resulting from the first amplification reaction is used as the template for the second PCR with an internal (nested) primer pair. Even when starting from a single copy of HIV-1 DNA, the double PCR product was readily detected by direct visualization in ethidium bromide-stained agarose gels. Amplification of minute amounts of HIV-1 DNA was successful in a considerable excess of HIV-1 negative DNA than reported previously. All of 85 HIV-1-infected individuals were PCR-positive with at least two of the three sets of primers used, 252 of 255 amplifications allowing unambiguous visualization of a unique DNA fragment of the expected size. The two-step amplification protocol is simple and rapid and fulfills the requirements of sensitivity and specificity for use in a clinical laboratory.     

Development of the polymerase chain reaction for the detection of bluetongue virus in tissue samples

Total genomic dsRNA, extracted from purified core particles of bluetongue virus serotype 1 from South Africa (BTV1SA), was used as template to optimise a polymerase chain reaction (PCR) for the detection of bluetongue virus RNA. Pairs of oligonucleotides complementary to the 3' termini of eight of the ten genome segments were tested. Those representing the 5' termini of genome segment 7 gave the best amplification results producing a single DNA band with the same mobility during agarose gel electrophoresis as genome segment 7. It was confirmed by cloning and sequence analysis, that this PCR-amplified DNA contained both terminal regions of genome segment 7 and therefore represented full length cDNA. Using these segment 7 oligonucleotides it was not only possible to detect routinely as few as 6 molecules of segment 7 dsRNA per sample, but also to detect purified dsRNAs from isolates of other BTV serotypes (1 Australia (AUS), 2, 3, 4, 10, 16 and 20). However, with the exception of Tilligery virus, isolates from other Orbivirus serogroups tested all gave negative results (African horse sickness, epizootic haemorrhagic disease, Palyam, Warrego and Eubenangee). The PCR was also used to analyse red blood cells (RBC) and buffy coat samples from cattle infected with BTV4. Positive results were obtained from samples taken 7 days post-infection (p.i.) (containing 1.6 x 10(3) TCID50 of virus/ml of whole blood) and from the RBC sample only, taken 14 days p.i. (16 TCID50/ml). However, at 28 days p.i. (less than 1.6 TCID50/ml) BTV RNA was not detected using the PCR in either sample.     

The humoral defense system in tsetse: differences in response due to age, sex and antigen types

Inoculation of live Escherichia coli into tsetse flies, Glossina morsitans morsitans, stimulated a higher antibacterial immune response in females than in males. It increased with age in females from emergence to approximately 2 weeks and thereafter declined. In males, there was also a significant decrease in immune response with aging. Inoculation of killed bacteria failed to stimulate antibacterial activity but stimulated a lysozyme response which was weaker than that stimulated by live bacteria. No antibacterial activity was present in the hemolymph of larvae from immunized pregnant tsetse. Inoculation of live Trypanosoma brucei brucei and T. congolense failed to induce production of antibacterial activity and lysozyme. Furthermore, tsetse inoculated with or naturally infected with T. b. brucei and T. congolense failed to show any evidence of immunosuppression when challenged with live E. coli. Various species of live bacteria stimulated different levels of antibacterial factors, with Enterobacter cloacae stimulating the highest level of antibacterial activity and E. coli the highest level of lysozyme. Saline in which certain species of bacteria and T. b. brucei were incubated inactivated tsetse immune hemolymph.     

Detection of Rickettsia tsutsugamushi in Experimentally infected mice by PCR.

We developed a rapid procedure for the detection of Rickettsia tsutsugamushi DNA by the PCR technique. The primer pair used for the PCR was designed from the DNA sequence of the gene encoding a 120-kDa antigen, which was proven to be group specific by immunoblot analysis with mouse hyperimmune sera against various rickettsial strains. This PCR method was able to detect up to 10 ag of plasmid DNA (pKT12). Specific PCR products were obtained with DNAs from R. tsutsugamushi Kato, Karp, Gilliam, TA716, TA1817, and Boryong, but not with DNAs from other rickettsiae, such as R. prowazekii, R. typhi, R. akari, and strain TT118. In a study with experimentally infected mice, the PCR method could detect rickettsial DNA from 2 days after inoculation (DAI), whereas serum antibody against R. tsutsugamushi could be detected from 6 to 8 DAI by an immunofluorescence test. Although clinical manifestations subsided after 14 DAI, rickettsial DNA in blood samples could be detected by PCR for up to 64 DAI. These results suggest that this PCR method can be applied to the early diagnosis of scrub typhus and can also be used to detect the residual rickettsiae after clinical symptoms subside.