Two-step Reverse Transcription Research Articles

Genetic analyses of the structural protein E2 bovine viral diarrhea virus isolated from dairy cattle in Yogyakarta, Indonesia

Background and Aim: Bovine viral diarrhea (BVD), a highly pathogenic ribonucleic acid (RNA) virus, causes devastating financial losses and reproductive deaths among dairy cattle in Yogyakarta and globally. This study aimed to identify point mutations within the E2 structural protein of the acquired BVD virus (BVDV) isolates using genetic analysis. Materials and Methods: The study period shows that we performed the research in 2023. We collected 118 serum samples from 2019 to 2023, among which only 10 BVDV positive were used and 108 were negative lacking the BVDV antigen. An anti-Erns monoclonal antibody-coated protein was used in indirect antigen capture enzyme-linked immunosorbent assay (I-ACE) to detect the BVD antigen present in positive BVDV serum specimens. In the initial step of the two-step reverse transcription polymerase chain reaction, the enzyme (superscript III reverse transcriptase) and the primer (random hexamer) were used to convert the RNA of the BVDV into complementary deoxyribonucleic acid (cDNA) during the process of reverse transcription. The final step involved the amplification of the E2 gene of the resultant BVDV cDNA through gene-specific primers (E2_fwd: 5′-TGGTGGCCTTATGAGAC-3′ and P7_rev: 5′-CCCATCATCACTATTTCACC-3′) and enzyme (platinum taq DNA polymerase high fidelity). For conducting Sanger sequencing, those 3 BVDV-1-positive isolates (about 2.6% of all isolates) were selected as a typical specimen for each site and year between 2019 and 2023 using a proportional computation. Therefore, only two BVDV isolates with complete genomes were chosen to perform their homological and genetic analysis based on the E2 gene by means of Blast and MEGA Version 11 in addition to the Bioedit 7.2.5 program. Results: By applying phylogenetic analysis relying on the E2 gene, a sum of 1011 nucleotides of the BVDV-1 isolates derived from each of the two BVDV-1 Indonesian isolates (n = 2) and its 23 reference BVDV strains were acquired from the National Center for Biotechnology Information (NCBI) database. The findings of the genetic analysis inside the phylogenetic tree revealed that the two BVDV Indonesian isolates were clustered into BVDV-1a subgenotype, while the reference BVDV strains were clustered into the five BVDV subgenotype, BVDV-1a (n = 6), BVDV-1b (n = 3), BVDV-1c (n = 11), BVDV-1m (n = 1), and BVDV-1n (n = 2). The branch exists in phylogenetic tree located before the division of our two BVDV isolates was divided into two branches with the same maximum bootstrap values of 99%, indicating a high degree of confidence, was seen. Next, we observed the branch near our study samples, which displayed the bootstrap value of 100, indicating that our 02 isolates were identical. In both isolates, V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/ Yogyakarta/2023 with GenBank accession numbers PP836388 and PP836389, respectively, conserved D7E residues were mutated as well as cysteine changed/altered into serine (S) was identified at amino acid position 201. Conclusion: We identified two isolates of BVDV belonging to the BVDV-1a subgenotype. Our findings indicate that the conserved D7E residues of isolates V11 BVDV1/Indonesia/Yogyakarta/2023 and V16 BVDV1/Indonesia/Yogyakarta/2023 were altered. The Indonesian BVDV isolates exhibited a cysteine to serine mutation at amino acid position 201, leads to vaccination failure, range of animal’s host will increase, and diagnostic kit will not be effective. Keywords: bovine viral diarrhea virus, cysteine mutation, E2 protein, serine, V11 bovine viral diarrhea virus1, V16 bovine viral diarrhea virus1.

Optimization of the 5-plex digital PCR workflow for simultaneous monitoring of SARS-CoV-2 and other pathogenic viruses in wastewater

Wastewater-based epidemiology is a valuable tool for monitoring pathogenic viruses in the environment, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). While quantitative polymerase chain reaction (qPCR) is widely used for pathogen surveillance in wastewater, it can be affected by inhibition and is limited to relative quantification. Digital PCR (dPCR) offers potential solutions to these limitations. In this study, a 5-plex dPCR workflow was optimized for the simultaneous detection of SARS-CoV-2, influenza A virus, enteroviruses (EnV), and noroviruses of genogroups I (NoV-GI) and GII (NoV-GII) in wastewater samples. Wastewater samples (n = 36) were collected from a wastewater treatment plant in Japan between August and October 2022. The optimization included the evaluation of singleplex and 5-plex dPCR assays, and two different concentration methods, extraction kits, and dPCR approaches. The performance of singleplex and 5-plex dPCR assays showed comparable linearity and reliability, with the 5-plex assays showing greater efficiency. The polyethylene glycol (PEG) precipitation method showed better performance over the centrifugation method, two-step reverse transcription (RT)-dPCR over the one-step RT-dPCR, and AllPrep PowerViral DNA/RNA Kit showed better performance than the QIAamp Viral RNA Mini Kit. The optimal workflow therefore included PEG precipitation, the AllPrep PowerViral DNA/RNA Kit, and two-step RT-dPCR. This workflow was selected to monitor the presence of SARS-CoV-2 and other pathogenic viruses in wastewater samples in a 5-plex dPCR approach, yielding promising results. SARS-CoV-2 RNA was detected in the majority of samples, with NoV-GI, NoV-GII, and EnV also being detected. The successful optimization and application of the 5-plex dPCR assay for pathogen surveillance in wastewater offers significant benefits, including enhanced community health assessment and more effective responses to public health threats.

A duplex droplet digital PCR assay for absolute quantification and characterization of long self-amplifying RNA

Self-amplifying messenger ribonucleic acid (saRNA) provides extended expression of genes of interest by encoding an alphavirus-derived RNA replicase and thus is 2–3 times larger than conventional messenger RNA. However, quality assessment of long RNA transcripts is challenging using standard techniques. Here, we utilized a multiplex droplet digital polymerase chain reaction (ddPCR) assay to assess the quality of saRNA produced from an in vitro transcription reaction and the replication kinetics in human cell lines. Using the one-step reverse transcription ddPCR, we show that an in vitro transcription generates 50–60% full-length saRNA transcripts. However, we note that the two-step reverse transcription ddPCR assay results in a 20% decrease from results obtained using the one-step and confirmed using capillary gel electrophoresis. Additionally, we provided three formulas that differ in the level of stringency and assumptions made to calculate the fraction of intact saRNA. Using ddPCR, we also showed that subgenomic transcripts of saRNA were 19-to-108-fold higher than genomic transcripts at different hours post-transfection of mammalian cells in copies. Therefore, we demonstrate that multiplex ddPCR is well suited for quality assessment of long RNA and replication kinetics of saRNA based on absolute quantification.

Production of Encapsidated RNA Particles as a Working Standard in Detecting Foodborne Viruses in Oysters

Monitoring foodborne viruses via nucleic acid amplification tests rely on stable RNA standards to obtain reliable testing. This study aimed to produce RNA-based standard reagents for hepatitis virus (HAV) or norovirus detections which relies on viral-like particle (VLP) technology. Using a plasmid packaging system, plasmids containing DNA encoding Qβcoat protein (CP) monomer and the VP1 gene of viruses were co-transformed into E. coli host cells. In cell lysates, expressed CP was characterized by western blot and the whole icosahedral formation of VLPs was proved by electron microscope analysis. Encapsidated RNAs were measured and assessed as a standard by a two-step reverse transcription recombinase polymerase amplification (RT-RPA). Our results showed that CP has a distinguished protein band with a molecular weight of 14.5 kDa but a few variabilities of particle size were visualized. When adjusting the pH of the lysate to lower than 6, a more intense protein band and substantial particles with homogenous particle size were observed. These VLPs were found to enclose HAV and norovirus RNA contents to 1.2×107 copies/ng and 1.9×107 copies/ng, respectively. When analyzed by RT-RPA, linear regression analysis confirmed the alternative application of RNAs enclosed in VLPs to naked RNA synthesized from in vitro transcription. Using the E. coli expression system to produce Qβ VLPs allows cost-effective production and, therefore, can be implemented in laboratories with basic equipment. These encapsidated RNAs may become an ideal “standard” for detecting foodborne viruses via a molecular test in food and clinical samples. Keywords: Molecular testing, Nanoparticles, Nucleic amplification, RNA standards, Viral-like particles

Development of a Reverse Transcription-Recombinase Polymerase Amplification Assay for Duplex Detection of Foodborne Viruses in Oysters

Abstract Viral contamination may occur at any stage of food processing. The study aim was to develop a two-step reverse transcription (RT)-recombinase polymerase amplification (RPA) assay and evaluate for in-field duplex detection of hepatitis A virus (HAV) and norovirus in oysters. The RNA expression plasmids were generated by amplifying a fragment of the VP1 gene of HAV and norovirus through PCR and cloning it into an expression vector. The RNAs were transcribed in vitro from the plasmids and further used for reverse transcription. The resulting single-stranded cDNAs were used as the purified or spiking templates to determine the sensitivities of simplex and duplex RT-RPA compared with RT-PCR, and RT-qPCR assays. The reproducibility and application of duplex RT-RPA in the field were also evaluated. Our results showed that simplex RT-RPA was at least 100 times more sensitive than RT-PCR and RT-qPCR and even more than duplex detection using purified targets. Unlike RT-PCR, the RT-RPA reaction was unaffected by inhibitors found in food, allowing simple sample preparation methods for detection within a fraction of the time. The duplex assay detected HAV, norovirus, or both in 12/30 (40%) oyster samples tested. Duplex RT-RPA proved to be a rapid, accurate, and reproducible method in a field test for detecting HAV and norovirus. Thus, duplex RT-RPA should be suitable for use in minimally equipped laboratories and field settings. If in-field RT-RPA services are provided to oyster farmers, the technique can minimize the risk of infection to consumers, thereby improving food safety. Keywords: Food safety, Hepatitis A virus, Direct extraction, Norovirus, Nucleic acid amplification

Role of circulating miRNA-130b-3p and TGF-β 1cytokine in patients with systemic lupus erythematosus

BackgroundMicroRNAs (miRNAs) a single-stranded “noncoding” RNAs that regulate gene expression post transcriptionally and they were shown to play a role in the pathophysiology of lupus. MiR-130b-3p, which targets ERBIN (Erbb2 Interacting Protein), has been demonstrated to aid the epithelial to mesenchymal transition (EMT) in renal tubular epithelial cells. MiR-130b-3p is also identified as negative regulator of transforming growth factor-b1 (TGF-β1)-induced signaling pathway. This study aimed to investigate whether MiR-130b-3p is involved in the pathogenesis of lupus and to explore the correlation between MiR-130b-3p with TGF-β 1cytokine in patients with SLE. MethodsThe study was conducted in a total of 70 individuals which include 35 SLE patients and 35 healthy controls, The serum level of MiR-130b-3p were determined by two-step reverse transcription polymerase chain reaction (RT-PCR) and TGF-β1 levels were estimated by ELISA. ResultsThe MiR-130b-3p gene expression was increased (1.6-fold change) among SLE patients compared to controls, the difference was not statistically significant (p < 0.05). There was also a statistically significant increase in TGF-B1 serum levels (p < 0.001) in SLE patients compared to controls, however, a non-statistically significant difference between the SLE disease activity severity, anti-dsDNA antibodies positivity, and renal affection with the MiR-130b-3p gene expression (p < 0.01) and TGF-β1 level (p < 0.01) in this study. ConclusionThe results of the current study indicates that the serum levels of MiR-130b-3p and TGF-β1 are associated with pathogenesis of SLE and might be used as biomarker for the diagnosis of early lupus nephritis in SLE.

First report of Cucurbit chlorotic yellows virus infecting cantaloupe (Cucumis melo L.) in Texas.

Texas is a major producer of cucurbits such as cantaloupe (Cucumis melo L.), but outbreaks of virus-like diseases often adversely affect yields. Little is known about the identity of the causal or associated viruses. During studies conducted in fall 2020 to explore the virome of cucurbit fields in Texas, a commercial cantaloupe field (~4.1 ha) in Cameron County was observed with virus-like symptoms of interveinal chlorotic mottle and foliar chlorosis and disease incidence was estimated at 100%. Virus-like symptoms including mosaic and leaf curl were also observed in six additional fields across five south and central Texas counties of Atascosa, Hidalgo, Fort Bend, Frio, and Wharton. Forty-six plants, which included 32 symptomatic and 14 non-symptomatic, were sampled from these fields for virus diagnosis and each sample was subjected to total nucleic acid extraction according to Dellaporta et. al. (1983). Initially, equal amounts of nucleic acids from 14 symptomatic plants (two/field) were pooled into one composite sample for preliminary diagnosis by high throughput sequencing (HTS). The cDNA library obtained from the composite sample with a TruSeq Stranded Total RNA with Ribo-Zero Plant Kit (Illumina) was sequenced on the Illumina NextSeq 500 platform, generating ~26.3 M single-end HTS reads (75 nucleotides [nt] each). Analyses of the reads according to Al Rwahnih et al. (2018) revealed several virus-like contigs; among them 23 contigs (206 to 741 nt) shared 98 to 100% nt identities to isolates of cucurbit chlorotic yellows virus (CCYV), genus Crinivirus, family Closteroviridae. Three pairs of CCYV-specific primers were designed from the HTS contigs with primers CCYV-v1330: 5'-AGTCCCTTACCCTGAGATGAA/CCYV-c2369: 5'-CGGAGCATTCGACAACTGAATA targeting ~1 kb fragment of the ORF1a (RNA1), primers CCYV-v4881: 5'-ATAAGGCGGCGACCTAATC/CCYV-c5736: 5'-GATCACTTGACCATCTCCTTCT targeting a ~0.9 kb fragment encompassing the coat protein (CP) cistron of CCYV (RNA2), and primers CCYV-v6362: 5'-CACCTCTTCCAGAACCAGTTAAA/CCYV-c7423: 5'-TGGGAACAACTTATTTCTCCTAGC targeting ~1 kb spanning partial minor coat protein (CPm) and p26 sequences (RNA2). Total nucleic acid extracts of each of the 46 samples from the seven fields were tested by two-step reverse transcription polymerase chain reaction using all three CCYV-specific primer pairs and they yielded amplicons of expected sizes from all five symptomatic cantaloupe samples from the Cameron County field and one additional symptomatic butternut squash sample from a field in Hidalgo County. The DNA bands from three randomly chosen cantaloupe samples were cloned and sequenced as previously described (Oke et al. 2020). In pairwise comparisons, the obtained 1,040 nt ORF1a (MW584332-334), 753 nt complete CP (MW584335-337), and 1,062 nt CPm/p26 (MW584338-340) gene specific sequences from the three samples shared 100% nt identity with each other, and 99-100% nt identities with corresponding RNA1 (AB523788) and RNA2 (AB523788) sequences of the exemplar isolate of CCYV. This is the first report of CCYV in Texas, thus expanding the current geographical range of the virus in the U.S. that includes California (Wintermantel et al. 2019) and Georgia (Kavalappara et al. 2021). The abundance of whiteflies of the Bemisia tabaci species complex in south Texas and other major U.S. cucurbit production areas presents additional challenges to virus disease management.

Breast Milk and Breastfeeding of Infants Born to SARS-CoV-2 Positive Mothers: A Prospective Observational Cohort Study

There are limited published data on the transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus from mothers to newborns through breastfeeding or from breast milk. The World Health Organization released guidelines encouraging mothers with suspected or confirmed COVID-19 to breastfeed as the benefits of breastfeeding outweighs the possible risk of transmission. The objective of this study was to determine if SARS-CoV-2 was present in the breast milk of lactating mothers who had a positive SARS-CoV-2 nasopharyngeal swab test prior to delivery, and the clinical outcomes for their newborns. This was a single-center, observational, prospective cohort study. Maternal-newborn dyads that delivered at New York University Langone Hospital Brooklyn with confirmed maternal SARS-CoV-2 positive screen test at the time of admission were recruited for the study. Breast milk samples were collected during postpartum hospitalization and tested for the presence of SARS-CoV-2 genes N1 and N2 by two-step reverse transcription polymerase chain reaction. Additionally, the clinical characteristics of the maternal newborn dyad, results of nasopharyngeal SARS-CoV-2 testing, and neonatal follow-up data were collected. A total of 19 mothers were included in the study and their infants who were all fed breast milk. Breast milk samples from 18 mothers tested negative for SARS-CoV-2, and 1 was positive for SARS-CoV-2 RNA. The infant who ingested the breast milk that tested positive had a negative nasopharyngeal test for SARS-CoV-2, and had a benign clinical course. There was no evidence of significant clinical infection during the hospital stay or from outpatient neonatal follow-up data for all the infants included in this study. In a small cohort of SARS-CoV-2 positive lactating mothers giving birth at our institution, most of their breast milk samples (95%) contained no detectable virus, and there was no evidence of COVID-19 infection in their breast milk-fed neonates. · Breast milk may rarely contain detectable SARS-CoV-2 RNA and was not detected in asymptomatic mothers.. · Breast milk with detectable SARS-CoV-2 RNA from a symptomatic mother had no clinical significance for her infant.. · Breast feeding with appropriate infection control instructions appears to be safe in mother with COVID infection..

A Rapid and Sensitive Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Indian Citrus Ringspot Virus.

Indian citrus ringspot virus (ICRSV) is a devastating pathogen that has a particularly deleterious effect on the 'Kinnow mandarin', a commercial citrus crop cultivated in the northwest of India. ICRSV belongs to the Mandarivirus genus within the family of Alphaflexiviridae and has a positive sense single-stranded RNA (ssRNA) genome consisting of six open reading frames (ORFs). Severe cases of ICRSV result in a significant reduction in both the yield and quality of crops. Consequently, there is an urgent need to develop methods to detect ICRSV in an accurate and timely manner. Current methods involve a two-step reverse transcription polymerase chain reaction (RT-PCR) that is time consuming. Here, we describe a novel, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the sensitive and rapid detection of ICRSV. To standardize the RT-LAMP assay, four different primers were designed and tested to target the coat protein gene of ICRSV. Amplification results were visualized by a color change after addition of SYBR Green I. The standardized RT-LAMP assay was highly specific and successfully detected all 35 ICRSV isolates tested from the Punjab and Haryana states of India. Furthermore, there was no cross-reaction with 17 isolates of five other citrus pathogens that are common in India. The ICRSV RT-LAMP assay developed in the present study is a simple, rapid, sensitive, specific technique. Moreover, the assay consists of only a single step and is more cost effective than existing methods. This is the first application of RT-LAMP for the detection of ICRSV. Our RT-LAMP assay is a powerful tool for the detection of ICRSV and will be particularly useful for large-scale indexing of field samples in diagnostic laboratories, in nurseries, and for quarantine applications.

GSF3, a polysaccharide from guava (Psidium guajava L.) seeds, inhibits MCF-7 breast cancer cell growth via increasing Bax/Bcl-2 ratio or Fas mRNA expression levels

Guava seed polysaccharide fraction 3 (GSF3) is an immunomodulatory polysaccharide from guava (Psidium guajava L.) seed polysaccharides. However, effects of GSF3 on the growth of breast cancer cells were not understood, yet. To clarify the GSF3 effects on breast cancer cell growth, GSF3 was subjected to treat MCF-7 cells using direct action or indirect immunotherapy using immune cells conditioned media, respectively. The viabilities of MCF-7 cells were measured using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Changes in pro-(Bax)/anti-apoptotic (Bcl-2) and Fas mRNA expression levels in the treated MCF-7 cells were measured using two-step reverse transcription quantitative polymerase chain reaction. Our results showed that GSF3 inhibited MCF-7 cell growth through either direct action or indirect immunotherapy. GSF3 direct action significantly (P < 0.05) decreased Bcl-2 mRNA expression amount but increased pro-(Bax)/anti-apoptotic (Bcl-2) mRNA expression ratios in the treated cells. The splenocytes conditioned media cultured with GSF3 increased Fas mRNA expression amounts in the treated MCF-7 cells. There was a significant negative correlation between Th2-polarized cytokines secreted by immune cells and Fas mRNA expression levels in the corresponding treated MCF-7 cells. Our findings suggested that GSF3 is a potent anti-cancerous polysaccharide by direct action or indirectly modulating immune cell cytokine secretion profiles.

Development of RT-PCR degenerate primers to overcome the high genetic diversity of grapevine virus T

Grapevine virus T (GVT) is a new member of the genus Foveavirus and has been reported to infect grapevines in several European countries. In 2018, GVT was detected for the first time in California in a domestic selection of wine grape, cv. Lambrusca di Alessandria, via high-throughput sequencing (HTS). To further investigate the presence of GVT in other grapevine plants, a two-step reverse transcription (RT)-PCR assay involving degenerate primers was developed. In order to cover the high genetic diversity of GVT, the sequences of available isolates were aligned to identify a conserved region in the coat protein gene that was a suitable target for the assay. The results of the RT-PCR assay showed that GVT was present in three additional grapevine selections among 416 plants integrating the Foundation Plant Services introduction pipeline; all were later confirmed by HTS. A complete and three near-complete genomes of the four GVT isolates were characterized and found to be divergent, sharing an overall 81 % pairwise identity in their nucleotide sequences. This suggested that the new RT-PCR assay was effective in detecting a broad range of GVT variants. The RT-PCR detection method developed in this study would be useful for routine virus testing.

Applying Next Generation Sequencing Technology to Hepatitis C genotyping in a routine diagnostic laboratory

Background To meet the target of Hepatitis C elimination in the UK, a rapid and high throughput method of genotyping is desirable. Current methods target the NS5B region with a nested PCR followed by Sanger sequencing. Drawbacks include insufficient information to guide second line treatment in the event of failure and poor sensitivity compared to assays targeting the 5’UTR. Method Previously tested HCV positive patient samples were selected and RNA extracted using an ultra-centrifugation manual extraction method. A two-step reverse transcription long range PCR generated amplicons which were quantified using the Qubit fluorometer and libraries prepared using the Nextera XT library preparation kit. Sequencing was performed using an Illumina Miseq and genomes were assembled using a Linex-based bioinformatics pipeline. Results A total of 150 samples were tested, with full HCV genomes obtained for genotypes 1–6 and the sensitivity of the assay corresponded to around 1000 IU ml−1. Where previous sequence data for resistance associated variants (RAVs) was available, mutations were consistent. Furthermore, the assay identified a 2 k/1b recombinant and allowed the typing of previously unassigned genotypes, demonstrating its utility in the diverse local population. Conclusion This study displayed the utility of a whole genome sequencing approach to HCV. A major benefit of whole genome analysis was the inclusion of regions targeted by antiviral therapy such as NS5A and NS3. This allowed the identification of RAVs in patients experiencing treatment failure. Its application to dried blood spots is currently being investigated as part of a wider screening programme.

First Report of Cucumber mosaic virus Infecting Siam Tulip (Curcuma alismatifolia) in Florida

Siam tulip (Curcuma alismatifolia) has become an important crop for breeding new varieties owing to its high economic value as a tropical ornamental. In September 2017, C. alismatifolia potted plants, originally from Alachua, FL, were submitted to the Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, for identification. The plants exhibited petal and bract necrosis. Initial serological testing for the presence of cucumber mosaic virus (CMV) using ELISA yielded positive results. To confirm pathogen identification, a two-step quantitative reverse transcription PCR, using primers targeting CMV-specific coat protein (amplicon of ∼450 bp), was performed. The PCR product, GenBank accession MG652768, had 99% nucleotide identity with CMV isolates in GenBank. Although all the tissues tested positive for CMV, it is unknown whether the necrotic symptoms were solely owing to CMV infection. CMV is known to infect a wide variety of plants in the ginger family, but to our knowledge, this is the first report of CMV in C. alismatifolia.

Rapid detection of foot-and-mouth disease virus using reverse transcription recombinase polymerase amplification combined with a lateral flow dipstick

Foot-and-mouth disease caused by foot-and-mouth disease virus (FMDV) is one of the most highly contagious diseases of domestic animals, and leads to enormous economic loss. Currently there are two main prevention and control strategies for the disease: eradication of the infected animals in FMDV free countries, and vaccination of the susceptible animals in countries with endemic FMDV infection. Early discovery and diagnosis of the source of infection is therefore integral to the containment of FMDV. In this study, a two-step reverse transcription recombinase polymerase amplification assay combined with lateral flow detection (RPA-LFD) was developed to detect FMDV. With incubation at 38 °C, a region of the 2B gene on the FMDV genome was successfully amplified within 20 min using specific primers and a probe. The amplified RPA product can be visualized on a lateral flow dipstick. The RPA-LFD assay was highly sensitive, detecting down to 10 copies of plasmid DNA. There was no cross-reactivity with other pathogens causing vesicular lesions. In addition, 143 clinical samples were used to compare RPA-LFD with real-time PCR, with 98.6% concordance between the assays. Therefore, the developed RPA-LFD assay provides a rapid, simple, highly promising approach to be used as point-of-care diagnostics in the field.

First Report of Maize yellow mosaic virus Infecting Sugarcane (Saccharum spp.) and Itch Grass (Rottboellia cochinchinensis) in Nigeria

HomePlant DiseaseVol. 101, No. 7First Report of Maize yellow mosaic virus Infecting Sugarcane (Saccharum spp.) and Itch Grass (Rottboellia cochinchinensis) in Nigeria PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Maize yellow mosaic virus Infecting Sugarcane (Saccharum spp.) and Itch Grass (Rottboellia cochinchinensis) in NigeriaA. Yahaya, M. Al Rwahnih, D. B. Dangora, L. Gregg, M. D. Alegbejo, P. Lava Kumar, and O. J. AlabiA. YahayaSearch for more papers by this author, M. Al RwahnihSearch for more papers by this author, D. B. DangoraSearch for more papers by this author, L. GreggSearch for more papers by this author, M. D. AlegbejoSearch for more papers by this author, P. Lava KumarSearch for more papers by this author, and O. J. AlabiSearch for more papers by this authorAffiliationsAuthors and Affiliations A. Yahaya , Department of Biological Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria M. Al Rwahnih , Department of Plant Pathology, University of California, Davis D. B. Dangora , Biological Sciences, Ahmadu Bello University, Zaria, Kaduna State, Nigeria L. Gregg , Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596 M. D. Alegbejo , Department of Crop Protection, Ahmadu Bello University, Zaria, Kaduna State, Nigeria P. Lava Kumar , International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria O. J. Alabi , Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596. Published Online:9 May 2017https://doi.org/10.1094/PDIS-03-17-0315-PDNAboutSectionsSupplemental ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat During routine surveys conducted from February to July 2015 in the northern guinea savannah region of Nigeria, sugarcane and itch grass (Rottboellia cochinchinensis) plants showing virus-like mosaic symptoms were encountered in farmers’ sugarcane fields in Kaduna State. Symptomatic leaf tissue samples from five randomly selected plants (sugarcane = 4; itch grass = 1) were dried and stored under CaCl2 at room temperature then shipped to Texas A&M AgriLife Research and Extension Center, Weslaco, TX, with USDA-APHIS-PPQ permit (P526P-14-04321) for further analysis. The MagMAX-96 viral RNA isolation kit (Thermo Fisher) was used to isolate total nucleic acid (TNA) from each sample and from a sample subset consisting of pooled leaf tissue materials from both plants. TNA aliquot from the pooled sample was subjected to ribosomal RNA depletion and cDNA library construction using a TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina), then sequenced on the Illumina NextSeq 500 platform. The raw high-throughput sequencing (HTS) reads were analyzed as previously described (Alabi et al. 2015), generating ∼43.5 million Illumina reads (76 nucleotides [nt] in length), of which 31,486 de novo assembled reads mapped to Maize yellow mosaic virus (MaYMV; genus Polerovirus; family Luteoviridae) along with reads mapped to Sugarcane mosaic virus (data not shown). Assembly of the sequence reads (CLC Genome Assembler, Qiagen) yielded 5,566 nt long near complete (∼99%) genome of MaYMV (KY684356) that was 95 to 97% identical and phylogenetically related to corresponding sequences of MaYMV isolates available in GenBank (KU291099–108). To further confirm the occurrence of this virus in source samples, TNA from individual samples were subjected to two-step reverse transcription (RT)-PCR using the Pol-G-F/Pol-G-R primer pair (Knierim et al. 2010). The expected ∼1,100 bp DNA band specific to a region encompassing partial P1-P2 fusion protein and coat protein genes of luteovirids was amplified from three of the five samples (sugarcane = 2; itch grass = 1). The DNA fragment from one sugarcane and the itch grass sample were cloned individually into the pCR2.1 TOPO-TA vector (Life Technologies, Carlsbad, CA) and two independent clones per amplicon sequenced bidirectionally. Pairwise comparisons of sequences from both samples revealed that they shared 99 to 100% nt identity with each other and 97 to 99% identity with the corresponding MaYMV sequences derived by HTS in this study (KY684356), and those retrieved from GenBank (KU291099–108). They also shared 86, 79, and 61% nt identities, respectively, with corresponding sequences of Barley virus G (KT962089), Maize yellow dwarf virus-RMV (KC921392), and Sugarcane yellow leaf virus (AF157029). MaYMV is a recently characterized tentative member of the genus Polerovirus reported from maize in China (Chen et al. 2016). Therefore, our results represent, to the best of our knowledge, the first report of MaYMV in sugarcane and itch grass worldwide and the first report of the virus in an African country. The occurrence of MaYMV in these perennial crop and pernicious weed host have implications for disease epidemiology since both plant species could serve as green bridges for virus perpetuation in cereal production systems.

Role of Th1/Th2 cells and related cytokines in autoimmune hepatitis.

Dysregulation of T cell response is thought to play an important role in the immunopathogenesis of autoimmune hepatitis. However, no consensus has yet been reached regarding the implications of a distinct T cell subset in the pathogenesis of this progressive liver disease. Therefore, T-bet and GATA-3 expression was examined in patients with autoimmune hepatitis (AIH) and in healthy controls. Moreover, the profile of Th1 (IFN-γ) and Th2 (IL-4) cytokine gene expression was analyzed. Levels of mRNA transcripts were measured in peripheral blood mononuclear cells (PBMCs) using a two-step reverse transcription quantitative real-time polymerase chain reaction with SYBR Green. T-bet and IFN-γ mRNA expression was significantly higher in AIH patients compared to healthy controls (p<0.05), whereas no differences were observed for either GATA-3 or IL-4 mRNA expression (p>0.05). Alterations in the Th1/Th2 cell balance may be responsible for both disease progression and the resulting complications.

Abstract 857: Diagnostic test system for sensitive, specific and reproducible detection of EML4-ALK RNA fusion transcripts in the blood of patients with NSCLC

Abstract Clinical testing for the detection of RNA fusions in tissue currently include FISH, IHC, PCR and NGS. However, approximately 30% of patients with advanced non-small cell lung cancer (NSCLC) are not candidates for tissue biopsies and in some cases where tissue is obtained, it is not always of sufficient quantity for molecular testing. For these reasons, the detection of nucleic acids in circulation has become increasingly relevant to clinical testing. In this study, we have focused on the development of an EML4-ALK diagnostic test system that includes the prospective collection of whole blood and the reproducible detection of mRNA fusion transcripts by a PCR-based technology. The focus was on the detection of EML4-ALK transcripts from donors with and without previously diagnosed NSCLC. Pre-analytic complexity was reduced by restricting the handling of samples to 72 hours from time of sample receipt to test result. Recovery methods for RNA extraction from donor plasma were then optimized to enrich for RNA recovered from both circulating-free, and RNA within blood vesicles, including platelets and exosomes. A two-step reverse transcription and Droplet Digital™ PCR (RT-ddPCR) method was evaluated in detection testing using a multiplexed EML4-ALK assay that includes variants 1, 2 and 3. Analytic assay specificity and sensitivity was examined for RT-ddPCR efficiency using a cell-line positive for EML4-ALK variant 1 and in vitro RNA designed to mimic variants 1, 2, and 3. Analytic sensitivity was determined to be 0.2% of fusion RNA spiked into a background of normal plasma. Precision studies were conducted with two different amounts of input RNA (high and low), over three consecutive days, three runs in one day and with two operators. The SD of detected fusion transcripts in this study did not exceed 25%. Finally, normal (n = 10) and FISH positive NSCLC donor (n = 9) plasma samples were processed for the recovery of RNA and tested for EML4-ALK fusions. All FISH positive cases were accurately detected by the RT-ddPCR test with EML4-ALK variant copies ranging from 13 to 150 copies. EML4-ALK fusion transcripts were not identified in normal donor plasma. We conclude that the developed test system is highly suited for a 72 hour test to result turnaround, reproducible and sensitive detection of diagnostic fusion RNA variants, including EML4-ALK in blood in the clinical laboratory. Citation Format: Hestia Mellert, Leisa Jackson, Dianna Maar, Dawne Shelton, Gary Pestano. Diagnostic test system for sensitive, specific and reproducible detection of EML4-ALK RNA fusion transcripts in the blood of patients with NSCLC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 857.

Rapid detection of Prunus necrotic ringspot virus using magnetic nanoparticle-assisted reverse transcription loop-mediated isothermal amplification

Prunus necrotic ringspot virus (PNRSV) has seriously reduced the yield of Prunus species worldwide. In this study, a highly efficient and specific two-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed to detect PNRSV. Total RNA was extracted from sweet cherry leaf samples using a commercial kit based on a magnetic nanoparticle technique. Transcripts were used as the templates for the assay. The results of this assay can be detected using agarose gel electrophoresis or by assessing in-tube fluorescence after adding SYBR Green I. The assay is highly specific for PNRSV, and it is more sensitive than reverse-transcription polymerase chain reaction (RT-PCR). Restriction enzyme digestion verified further the reliability of this RT-LAMP assay. To our knowledge, this is the first report of the application of RT-LAMP to PNRSV detection in Prunus species.

First Report of Hop stunt viroid Infecting Japanese Plum, Cherry Plum, and Peach in Greece.

Dapple plum and peach fruit is a widely distributed disorder of plum and peach resulting in significant economic losses (4). During a survey for the presence of Hop stunt viroid (HSVd) on stone fruit trees in Greece, samples from 30 European plums (Prunus domestica L., cvs. President, Tuleu Grass), 45 Japanese plums (Prunus salicina Lindl., cvs. Angeleno, Diamond, Santa Rosa), 12 cherry plums (Prunus domestica L. var. insititia (L.) Fiori & Paoletti of unknown cultivar), and 107 peaches (Prunus persica (L.) Batsch, cvs. Red Haven, Elberta, June Gold, Spring Crest, Lemonato) were collected in several orchards around Greece. Their fruit skin symptomatology indicated viroid infection (reddish dappling blotches and cracks in European and Japanese plum, green dappling in cherry plum, and light colored blotches and lines in peach). Samples were screened with tissue-print hybridization (TPH) for HSVd using a full length DIG-labelled riboprobe deriving from in vitro transcription of the positive control, a citrus isolate of HSVd (G. Vidalakis, CCPP, University of California, Riverside). In total, 44 out of the 194 trees surveyed were HSVd-positive with TPH. For a small number (40) of TPH-positive field samples, TNA phenol extraction from fruit skin, leaves, and bark and one-tube two-step reverse transcription (RT)-PCR assays followed, using a standardized protocol (3) with two different primer pairs, one new primer pair (this study) and a previously reported primer pair (2). RT-PCR analysis showed the presence of HSVd in peach and Japanese plum in prefectures Pella (Central Macedonia), Achaia, and Korinthia (Peloponnesus) and in cherry plum in Achaia (Peloponnesus). Six of 11 Japanese plums (cvs. Angeleno, Santa Rosa), 2 of 12 cherry plums, and 8 of 12 peaches (cvs. Spring Crest, Red Haven) examined were found HSVd-infected, but none of the five European plums were. Nucleotide sequence analyses of purified and cloned amplicons from peaches and Japanese and cherry plums revealed sizes of 297 to 308 nt and similarity to sequence variants of other HSVd isolates previously characterized: 95 to 97% identity with the Moroccan isolates apr.9, apr.10, apr.11, and apr.12 and the Spanish isolate apr.4 from apricot (1) (GenBank Accession Nos. AJ297825 to AJ297828 and Y09346, respectively). For confirmation of HSVd presence in field trees, 10 Japanese plums cv. Angeleno, 10 peaches cv. June Gold, and 10 peaches cv. Spring Crest, HSVd-negative (TPH), were bud- or chip-grafted from two of the aforementioned Japanese plums cv. Angeleno and two of the aforementioned peaches cv. Red Haven. Two years later, five Japanese plum trees (cv. Angeleno) and five peach trees (three cv. Spring Crest and two cv. June Gold) were found HSVd-positive with TPH; no fruits were observed to produce fruit symptoms as the grafted trees were kept in an insect-proof greenhouse (no bees for cross-pollination). To our knowledge, our investigation reports for the first time the occurrence of HSVd infecting Japanese plum, cherry plum, and peach in Greece, emphasizing the need for a certification program for the prevention of spreading stone fruit tree viroids in this country.

Expression of Vibrio salmonicida virulence genes and immune response parameters in experimentally challenged Atlantic salmon (Salmo salar L.)

The Gram-negative bacterium Vibrio salmonicida is the causative agent of cold-water vibriosis (CV), a hemorrhagic septicemia that primarily affects farmed Atlantic salmon (Salmo salar L.). The mechanisms of disease development, host specificity and adaptation, as well as the immunogenic properties of V. salmonicida are largely unknown. Therefore, to gain more knowledge on the pathogenesis of CV, 90 Atlantic salmon parr were injected intraperitoneally with 6 × 106 CFU of V. salmonicida LFI1238. Samples from blood and spleen tissue were taken at different time points throughout the challenge for gene expression analysis by two-step reverse transcription (RT) quantitative real-time polymerase chain reaction. Out of a panel of six housekeeping genes, accD, gapA, and 16S rDNA were found to be the most suitable references for expression analysis in Vibrio salmonicida. The bacterial proliferation during challenge was monitored based on the expression of the 16S rRNA encoding gene. Before day 4, the concentrations of V. salmonicida in blood and spleen tissue demonstrated a lag phase. From day 4, the bacterial proliferation was exponential. The expression profiles of eight genes encoding potential virulence factors of V. salmonicida were studied. Surprisingly, all tested virulence genes were generally highest expressed in broth cultures compared to the in vivo samples. We hypothesize that this general muting of gene expression in vivo may be a strategy for V. salmonicida to hide from the host immune system. To further investigate this hypothesis, the expression profiles of eight genes encoding innate immune factors were analyzed. The results demonstrated a strong and rapid, but short-lasting innate immune response against V. salmonicida. These results suggest that the bacterium possesses mechanisms that inhibit and/or resist the salmon innate immune system until the host becomes exhausted of fighting the on-going and eventually overwhelming infection.