Reverse Transcription-polymerase Chain Reaction Sequencing Research Articles

WNT inhibitory factor 1 (WIF1) is a novel fusion partner of RUNX family transcription factor 1 (RUNX1) in acute myeloid leukemia with t(12;21)(q14;q22).

As a member of the core transcription factor family, RUNX1 plays an important role in stem cell differentiation. RUNX1 rearrangements are common in myeloid and lymphoid tumors [1]. (Blood 129(15):2070-2082, 2017). One of the most commonly detected abnormalities in acute myeloid leukemia (AML) is the translocation t(8;21)(q22;q22) (Blood Adv 4(1):229-238, 2020), resulting in a RUNX1::RUNX1T1 fusion. Occasionally, RUNX1 is translocated with other genes. This article describes an AML patient with a specific chromosomal translocation involving the RUNX1 gene and the identification of the RUNX1::WIF1 fusion. Chromosomal abnormalities were detected through karyotype analysis, break gene involved was identified via fluorescence in situ hybridization (FISH), and the novel fusion was identified through transcriptome sequencing and subsequently confirmed through reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing. A 79-year-old female patient diagnosed with AML was found to have a t(12;21)(q14;q12) translocation. FISH analysis provided evidence of RUNX1 gene rearrangement. Additionally, transcriptomic sequencing revealed a novel fusion known as RUNX1::WIF1, which consists of RUNX1 exon 2 and WIF1 exon 3. The novel fusion was further confirmed through RT-PCR and Sanger sequencing. We identified WIF1 as a novel fusion partner of RUNX1 in AML. Additionally, this is the first report of a RUNX1 fusion gene with the break point in intron 2, resulting in an out-of-frame fusion. Further research is needed to investigate the impact of this novel fusion on the establishment and progression of the disease.

Identification and characterization of a novel intronic splicing mutation in CSF1R-related leukoencephalopathy.

Colony stimulating factor 1 receptor (CSF1R)-related leukoencephalopathy is a rapidly progressing neurodegenerative disease caused by CSF1R gene mutations. This study aimed to identify and investigate the effect of a novel intronic mutation (c.1754-3C>G) of CSF1R on splicing. A novel intronic mutation was identified using whole-exome sequencing. To investigate the impact of this mutation, we employed various bioinformatics tools to analyze the transcription of the CSF1R gene and the three-dimensional structure of its encoded protein. Furthermore, reverse transcription polymerase chain reaction (RT-PCR) was performed to validate the findings. A novel mutation (c.1754-3C>G) in CSF1R was identified, which results in exon 13 skipping due to the disruption of the 3' splice site consensus sequence NYAG/G. This exon skipping event was further validated in the peripheral blood of the mutation carrier through RT-PCR and Sanger sequencing. Protein structure prediction indicated a disruption in the tyrosine kinase domain, with the truncated protein showing significant structural alterations. Our findings underscore the importance of intronic mis-splicing mutations in the diagnosis and management of CSF1R-related leukoencephalopathy.

First Report of Pitaya Virus X Infecting Lophocereus schottii f. mieckleyanus (Thin-Stemmed Totem Pole Cactus) in the United States.

Lophocereus is a genus of three species of columnar cacti native to Arizona and Mexico (Lodi, 2015). These cacti produce several tall, ascending, columnar stems that branch at the base in a candelabra-like arrangement. The most common species, L. schottii is known as the senita cactus. Several unusual knobby-stemmed spineless forms of senita cactus have been found in nature in Baja California, Mexico, which are collectively known as totem pole cacti. The thin-stemmed totem pole cactus, L. schottii f. mieckleyanus is an important part of landscapes in southern Arizona. Cacti are clonally propagated which makes viral infections of economic importance in the ornamental/nursery industry. In February 2023, virus-like symptoms, such as mosaic and chlorotic spots were observed on the stems of L. schottii f. mieckleyanus grown in a nursery in Phoenix, AZ, USA. Total RNA was extracted from two symptomatic cacti (YPHC-61 A & B) following the protocol by Tzanetakis et al. (2007), and cDNA was synthesized using the Superscript IV Reverse Transcriptase (Invitrogen, Vilnius, Lithuania). Reverse transcription polymerase chain reaction (RT-PCR) performed with cactus virus X specific primers (Kim et al. 2016) targeting the coat protein (CP) gene failed to generate any amplicon, while potexvirus-replicase primers, Potex 2RC and Potex 5 (van der Vlugt and Berendsen 2002) targeting RNA-dependent RNA polymerase (RdRp) gene amplified an expected amplicon of ~580 bp from both the samples. One of the amplicons was Sanger sequenced and showed 90.7% nucleotide (nt) identity with pitaya virus X (PiVX) in the GenBank (MN982522). Sequence was submitted in the GenBank under the accession number OR425049. PiVX is a new species of the genus Potexvirus and is named after its origin from pitaya (Hylocereus spp.). Further, RT-PCR was conducted with PiVX-specific primers, CP 110F/CP 604R targeting CP gene (Bae and Park 2022) and RdRp gene (RdRp F 5' GCGTGGGCCCTGGAAAA-3'/RdRp R 5' CTAAGATTCATCAATTCACCTCTCC-3') (this study). Amplicons of ~500 and 1100 bp were obtained using primers, CP 110F/CP 604R and RdRp F/RdRp R, respectively. A BLAST search revealed 90.5% nt identity to PiVX CP sequences (OM802135 and OM802134) and 87.3% nt identity to RdRp sequences (MN982523 and LC654699) in the GenBank. Sequences of isolates YPHC-61A and YPHC-61B were submitted in the GenBank under accession numbers, OQ915350 and PP182358 (CP gene) and OQ915351 and PP209539 (RdRp gene). Phylogenetic analysis based on the combined sequence datasets of CP and RdRp genes also grouped YPHC-61A and YPHC-61B with PiVX isolates and separated from other potexviruses species. For a bioassay of the virus, sap extract from symptomatic cactus was mechanically inoculated onto indicator plant species, i.e., beans, alfalfa, and melon. Ten days post- inoculation, chlorotic lesions were observed on beans and alfalfa plants, while melon and mock-inoculated plants did not show any symptoms. Similarly, L. schottii f. mieckleyanus plants grafted with infected cactus showed chlorotic spots after 30 days post grafting. Mechanically inoculated beans, alfalfa, and cactus plants were found to be positive for PiVX based on RT-PCR and Sanger sequencing. PiVX has earlier been detected on Notocactus leninghausii f. cristatus (Park et al. 2018) and dragon fruit (Selenicereus undatus) plants in South Korea (Bae and Park 2022). To our knowledge, this is the first report of PiVX on L. schottii f. mieckleyanus in the United States and worldwide.

Genus Orthotospovirus in Costa Rica: A Central American case

The Orthotospovirus genus encompasses a range of economically significant and emerging plant viruses that affect a variety of crops globally. While the prevalence and characteristics of these phytopathogenic viruses are extensively documented in North and South America, their presence in Central America remains comparatively underexplored. This study focuses on Costa Rica, strategically positioned at the nexus of North and South America, to enhance our understanding of orthotospovirus in this region. We analyzed 295 plant samples using enzyme-linked immunosorbent assay (ELISA) to test for the presence of INSV, IYSV, TSWV, and the GRSV/TCSV serogroup. Additionally, a subset (20 samples) underwent further scrutiny through reverse transcription-polymerase chain reaction (RT-PCR) employing both universal and species-specific primers. Our ELISA results indicated the absence of TSWV and the GRSV/TCSV serogroup. However, the presence of INSV in Costa Rica was substantiated through ELISA, RT-PCR, and partial sequencing, revealing its prevalence in both open-field and greenhouse environments. Despite previous diagnostic reports suggesting the presence of TSWV in Costa Rica, our study did not detect this virus. RT-PCR analysis with degenerate primers also found no evidence of other orthotospovirus species in our samples. The identification of a dominant INSV haplotype, along with three additional variants, suggests the likelihood of at least two independent virus introductions into the region. These findings underscore the necessity for more comprehensive surveys and research on orthotospoviruses in Central America to better understand their epidemiology and impact on agriculture.

Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale inRwanda.

Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.

Isolation and identification of a new strain Micropterus salmoides rhabdovirus (MSRV) from largemouth bass Micropterus salmoides in China

As an important farmed fish worldwide, largemouth bass (Micropterus salmoides) is suffering a severely disease caused by rhabdovirus, which has resulted to a massive economic loss. In the present study, a new Micropterus salmoides rhabdovirus (MSRV) strain named MSRV-NY01 was isolated from largemouth bass juvenile from a fish farm in Nanyang, Henan province, China. Cell culture, histopathological examination, reverse transcription-polymerase chain reaction (RT-PCR), plaque purification, phylogenetic analysis, transmission electron micrograph (TEM) observation, experimental infection, real-time quantitative polymerase chain reaction (RT-qPCR) were used for virus isolation and identification. The diseased fish exhibited abnormal symptoms with anorexia, exophthalmia, bloated abdomen, spiral swimming, hemorrhage on body surfaces, and fluid accumulation in the abdominal cavity. Histopathological examination showed obvious hemorrhage, inflammatory cell infiltration, and widespread cell degeneration and necrosis were presented in the liver, spleen, intestine and stomach of diseased fish. Obvious cytopathic effects (CPE) were induced in epithelioma papillosum cyprini (EPC), grouper spleen (GS) and grouper fin (GF-1) cell lines after inoculation of mixed liver and kidney homogenates from disease fish. RT-PCR, DNA sequencing and phylogenetic tree analysis showed that the virus belongs to rhabdovirus with the highest similar to the MSRV-FJ985 strain. Through five sequential rounds of plaque purification assay, a MSRV plaque isolate was derived and was confirmed by RT-PCR and DNA sequencing. TEM observation showed that numerous virions with typical bullet shape (100–150 nm in length and 70–90 nm in diameter) were present in infected GS cells. Thus, this newly isolated virus from diseased Micropterus salmoides was tentatively named as MSRV-NY01. Regression infection experiment indicated that MSRV-NY01 was highly pathogenic to Micropterus salmoides juvenile and the cumulative mortality of fish injected with 5 × 104, 104, 2 × 103, 4 × 102, 2 × 102, 102 and 50 PFU of virus were 100%, 100%, 100%, 96.7%, 96.7%, 93.3% and 90%, respectively. Moreover, RT-qPCR showed that MSRV was present in all 9 tested tissues of infected fish, and the virus loads of the spleen and heart were significantly higher than that in other tissues tested. In conclusion, we isolated and identified a new MSRV strain from diseased largemouth bass, and our results will provide new material and information for the prevention and control strategy for MSRV.

Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient With Meningoencephalitis.

Cache Valley virus (CVV) is a mosquito-borne virus that is a rare cause of disease in humans. In the fall of 2020, a patient developed encephalitis 6 weeks following kidney transplantation and receipt of multiple blood transfusions. After ruling out more common etiologies, metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) was performed. We reviewed the medical histories of the index kidney recipient, organ donor, and recipients of other organs from the same donor and conducted a blood traceback investigation to evaluate blood transfusion as a possible source of infection in the kidney recipient. We tested patient specimens using reverse-transcription polymerase chain reaction (RT-PCR), the plaque reduction neutralization test, cell culture, and whole-genome sequencing. CVV was detected in CSF from the index patient by mNGS, and this result was confirmed by RT-PCR, viral culture, and additional whole-genome sequencing. The organ donor and other organ recipients had no evidence of infection with CVV by molecular or serologic testing. Neutralizing antibodies against CVV were detected in serum from a donor of red blood cells received by the index patient immediately prior to transplant. CVV neutralizing antibodies were also detected in serum from a patient who received the co-component plasma from the same blood donation. Our investigation demonstrates probable CVV transmission through blood transfusion. Clinicians should consider arboviral infections in unexplained meningoencephalitis after blood transfusion or organ transplantation. The use of mNGS might facilitate detection of rare, unexpected infections, particularly in immunocompromised patients.

First Report of Tomato Brown Rugose Fruit Virus Infecting the Tomato Crop in Saudi Arabia.

Tomato (Solanum lycopersicum L.) is the most economically important member of family Solanaceae and cultivated worldwide and one of the most important crops in Saudi Arabia. The aim of this study is screening of the most common viruses in Riyadh region and identified the presence of tomato brown rugose fruit virus (ToBRFV) in Saudi Arabia. In January 2021, unusual fruit and leaf symptoms were observed in several greenhouses cultivating tomatoes commercially in Riyadh Region, Saudi Arabia. Fruit symptoms showed irregular brown spots, deformation, and yellowing spots which render the fruits non-marketable, while the leaf symptoms included mottling, mosaic with dark green wrinkled and narrowing. These plants presented the symptoms similar to those described in other studies (Salem et al., 2015, Luria et al., 2017). A total 45 Symptomatic leaf samples were collected and tested serologically against suspected important tomato viruses including: tomato chlorosis virus, tomato spotted wilt virus, tomato yellow leaf curl virus, tomato chlorotic spot virus, tomato aspermy virus, tomato bushy stunt virus, tomato black ring virus, tomato ringspot virus, tomato mosaic virus, pepino mosaic virus and ToBRFV using Enzyme linked immunosorbent assay (ELISA) test (LOEWE®, Biochemica, Germany), according to the manufacturers' instructions. The obtained results showed that 84.4% (38/45) of symptomatic tomato samples were infected with at least one of the detected viruses. The obtained results showed that 55.5% (25/45) of symptomatic tomato samples were found positive to ToBRFV, three out of 25 samples (12%) were singly infected, however 22 out of 45 (48.8%) had mixed infection between ToBRFV and with at least one of tested viruses. A sample with a single infection of ToBRFV was mechanically inoculated into different host range including: Chenopodium amaranticolor, C. quinoa, C. album, C. glaucum, Nicotiana glutinosa, N. benthamiana, N. tabacum, N. occidentalis, Gomphrena globosa, Datura stramonium, Solanum lycopersicum, S. nigrum, petunia hybrida and symptoms were observed weekly and the systemic presence of the ToBRFV was confirmed by RT-PCR and partial nucleotide sequence. A Total RNA was extracted from DAS-ELISA positive samples using Thermo Scientific GeneJET Plant RNA Purification Mini Kit. Reverse transcription-Polymerase chain reaction (RT-PCR) was carried out using specific primers F-3666 (5´-ATGGTACGAACGGCGGCAG-3´) and R-4718 (5´-CAATCCTTGATGTG TTTAGCAC-3´) which amplified a fragment of 1052 bp of Open Reading Frame (ORF) encoding the RNA-dependent RNA polymerase (RdRp). (Luria et al. 2017). RT-PCR products were analyzed using 1.5 % agarose gel electrophoresis. RT-PCR products were sequenced in both directions by Macrogen Inc. Seoul, South Korea. Partial nucleotide sequences obtained from selected samples were submitted to GenBank and assigned the following accession numbers: MZ130501, MZ130502, and MZ130503. BLAST analysis of Saudi isolates of ToBRFV showed that the sequence shared nucleotide identities ranged between 98.99 % to 99.50 % among them and 98.87-99.87 % identity with ToBRFV isolates from Palestine (MK881101 and MN013187), Turkey (MK888980, MT118666, MN065184, and MT107885), United Kingdom (MN182533), Egypt (MN882030 and MN882031), Jordan (KT383474), USA (MT002973), Mexico (MK273183 and MK273190), Canada (MN549395) and Netherlands (MN882017, MN882018, MN882042, MN882023, MN882024, and MN882045). To our knowledge, this is the first report of occurrence of ToBRFV infecting tomato in Saudi Arabia which suggests its likely introduction by commercial seeds from countries reported this virus and spread in greenhouses through mechanical means. The author(s) declare no conflict of interest. Keywords: Tomato brown rugose fruit virus, tomato, ELISA, RT-PCR, Saudi Arabia

Gynura japonica: A new host of Apple stem grooving virus and Chrysanthemum virus B in China.

Gynura japonica (Thunb.) Juel [Asteraceae; syn: G. segetum (Lour.) Merr] is an important perennial medicinal herb used in China for topical treatment of trauma injuries (Lin et al. 2003). It grows naturally in the southern provinces of China and is also sometimes cultivated. During 2018-2020, wild G. japonica plants exhibiting chlorotic spots and mosaic symptoms were observed in Zhejiang province, China. To identify the possible causal agents of the disease, a single symptomatic leaf sample was collected in August 2019 and sent to Zhejiang Academy of Agricultural Sciences (Hangzhou, China) for next generation sequencing (NGS). Total RNAs extracted with TRIzol (Invitrogen, Carlsbad, USA) were subjected to high throughput sequencing on the Illumina NovaSeq 6000 platform with PE150bp and data analysis was performed by CLC Genomic Workbench 11 with default parameters (QIAGEN, Hilden, Germany). A total of 37,314,080 paired-end reads were obtained, and 11,785 contigs (961 to 10,964 bp) were generated and compared with sequences in GenBank using BLASTn or BLASTx. Of the total of 12 viral-related contigs obtained, one with a length of 6,442 nt mapped to the genomic RNA of ASGV (MN495979), seven contigs with lengths ranging from 1,034 to 2,901 nt mapped to Chrysanthemum virus B (CVB), and four mapped to broad bean wilt virus 2 (BBWV2), a virus which is known to infect G. procumbens (Kwak et al. 2017). To further confirm the presence of ASGV and CVB, primers were designed and the complete nucleotide sequences of both viruses were amplified from the original NGS sample using reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) according to the manufacturer's instructions (Tiosbio, Beijing, China). BLASTn analysis revealed that the complete 6,451 nt sequence of ASGV (GenBank accession No. MW259059) shared the highest identity (81.2%) with a Chinese isolate of ASGV from citrus (MN495979). The two isolates grouped with another Chinese isolate (from pear) in phylogenetic analysis. The predicted coat protein of the virus had the highest nt identity of 93.7% (96.2% amino acid sequence identity) with that of the Chinese ASGV isolate XY from apple (KX686100). The complete genomes of two distinct molecular variants of CVB (both 8,987 nt in length) were also obtained from this sample (GenBank accession Nos. MW269552, MW269553). They shared 86.8% nt identity with each other and had 81.1% and 82.1% identity to the only known complete sequence of CVB from chrysanthemum (AB245142). Ten additional wild G. japonica plants with mosaic symptoms were collected randomly during 2019-2020 from Hangzhou (n=6) and Ningbo (n=4) in Zhejiang province and tested by RT-PCR with specific primer pairs to detect BBWV2, ASGV and CVB. RT-PCR and subsequent sequencing revealed that these three viruses were present in all the samples tested, indicating that co-infection of G. japonica by ASGV, CVB and BBWV2 is common. CVB mainly infects chrysanthemum (Singh et al. 2012), while ASGV is known as a pathogen of various fruit trees especially in the family Rosaceae, although there are recent reports that it can also infect some plants in Gramineae, Asparagaceae and Nelumbonaceae (Bhardwaj et al. 2017; Chen et al. 2019; He et al. 2019). Our results provide the first report that Gynura is a natural host of CVB and ASGV. Further surveys and biological studies are underway to evaluate the importance of Gynura as a virus reservoir for epidemics among the various hosts.

A Presumed Synonymous Mutation of PKD2 Caused Autosomal Dominant Polycystic Kidney Disease in a Chinese Family.

Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by the pathogenic mutation of PKD1 or PKD2 gene and usually affects bilateral kidneys. Synonymous mutations are generally assumed to be neutral as they do not alter amino acids. Herein, we described an extremely rare ADPKD child caused by a heterozygous synonymous mutation of PKD2 gene accompanied by massive proteinuria and congenital solitary kidney. Clinical characteristics of the patients were summarized. Whole-exome sequencing was performed to screen the disease-causing gene mutation, and reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing were applied to analyze the impact of the identified mutation on gene transcription and splicing. Polycystic changes were found in the solitary kidney of a girl initially presented with nephrotic-range proteinuria. Thereafter her mother and 2 other family members were diagnosed to be ADPKD. Whole-exome sequencing of the proband identified a heterozygous synonymous mutation (c.1716G>A, p.Lys572=) located in the splicing site of exon 7 in PKD2 gene, which was co-segregated with the PKD phenotype in the family. RT-PCR and direct sequencing of amplified products revealed that this heterozygous synonymous mutation led to exon7 skipping in PKD2 gene. We reported an extremely rare child case of ADPKD2 in combination with solitary kidney and nephrotic-range proteinuria, and firstly confirmed the pathogenicity of a heterozygous synonymous mutation (c.1716G>A) in PKD2 gene. The results indicate that synonymous mutations should not be excluded from disease-causing if they are located in splicing site of an exon.

Primary clear cell sarcoma of the femur: a unique case with RT-PCR and direct sequencing confirmation of EWSR1/ATF1 fusion gene

BackgroundIt is very rare for clear cell sarcomas (CCS) to arise in the bone. During diagnosis, it is important to distinguish primary CCS of bone from bone metastasis of melanoma because this difference fundamentally changes the therapeutic options. Recently, characteristic fusion genes of CCS have been detected using reverse transcription polymerase chain reaction (RT-PCR) or direct sequencing which allowed to distinguish CCS from melanoma. However, there was no study applying these analyses with positive results. In this case, we describe the use of fusion gene analysis to diagnose a primary CCS of the bone.Case presentationA 36-year-old male presented with a four-months history of left knee pain. Magnetic resonance imaging showed a lesion in the left femoral medial epicondyle. Histological examination of the biopsy specimen revealed proliferating oval or rounded cells. These cells had clear cytoplasm arranged in fascicles or compact nests with frequent deposits of brown pigment. Furthermore, immunohistochemistry analysis revealed that tumor cells were positive for S-100 protein, HMB-45, Melan-A, and SOX10. It stained negative for CD34 and BRAF v600e. Conclusively, detection of the EWSR1/ATF1 fusion gene using RT-PCR and direct sequencing confirmed that the lesion was a primary CCS of the bone. Wide-margin resection and reconstruction with a tumor endoprosthesis were performed.ConclusionsHerein, we diagnosed a rare case of primary CCS of the bone by detecting EWSR1/ATF1 fusion gene using RT-PCR and direct sequencing. Since fluorescence-in situ hybridization (FISH) and RT-PCR could show false positive by mainly due to technical problems, it is better to perform direct sequencing to confidently diagnose the tumor as a primary CCS especially at very rare site such as bone.

FUS-NFATC2 or EWSR1-NFATC2 Fusions Are Present in a Large Proportion of Simple Bone Cysts

A simple bone cyst (SBC) is a benign bone lesion of unknown etiology. It can be differentiated from an aneurysmal bone cyst (ABC) by radiologic and histopathologic features, as well as by the absence of fusions of the USP6 gene characteristic of an ABC. In an attempt to differentiate between ABC and SBC in a recurrent bone cyst, we performed targeted RNA sequencing and found an EWSR1-NFATC2 fusion and no fusion of the USP6 gene. We subsequently analyzed additional 10 cysts, consistent with SBCs after radiologic-pathologic correlation, for the presence of an NFATC2 gene fusion, by targeted RNA sequencing, reverse-transcription polymerase chain reaction (RT-PCR) and Sanger sequencing, and fluorescent in situ hybridization. Targeted RNA sequencing showed a FUS-NFATC2 fusion in 4 of 11 SBCs and an EWSR1-NFATC2 fusion in 2 of 11 SBCs. No fusion was identified in 3 SBCs and the analysis was not successful in 2 SBCs because of the low quantity or poor quality of isolated RNA. All the 6 fusions detected by targeted RNA sequencing were confirmed by RT-PCR and Sanger sequencing, and 5 of the 6 fusions by fluorescent in situ hybridization. An additional FUS-NFATC2 fusion was identified by RT-PCR, Sanger sequencing, and fluorescent in situ hybridization in 1 of the 3 cases negative for fusions by targeted RNA sequencing. At least a large subset of SBCs represents cystic neoplasms characterized by FUS-NFATC2 or EWSR1-NFATC2 fusions, which also define a group of distinct, rare "Ewing-like" sarcomas that predominantly arise in long bones. Our results provide additional evidence of the existence of benign lesions with FUS-NFATC2 or EWSR1-NFATC2 fusions. Although they can recur locally in a nondestructive manner, their clinical course and possible relation to sarcoma with EWSR1-NFATC2 or FUS-NFATC2 fusion remains to be elucidated.

First report of bidens mosaic virus infecting Centella asiatica in Brazil.

Centella asiatica is a perennial, herbaceous creeper plant that belongs to the family Apiaceae. It has been known since prehistoric times and has been used for therapeutic and cosmetic purposes (James and Dubery 2009; Gohil et al. 2010), and is easily propagated vegetatively. In 2018, plants of C. asiatica exhibiting foliar symptoms of mosaic and malformation were found in the botanical garden of the Plantarum Institute (Nova Odessa municipality, São Paulo state - 22°46'45.8"S 47°18'47.5"W) and in an experimental area at ESALQ/USP (Piracicaba municipality, São Paulo state - 22°42'26.0"S 47°37'48.6"W). In both locations the plants were grown in beds of approximately 4 m2 and all of them were symptomatic. Initially, leaf extract from symptomatic C. asiatica plants was examined by transmission electron microscopy (TEM) after being negatively stained with 1% uranyl acetate. Potyvirus-like flexuous filamentous particles were observed in leaf samples from both locations. TEM of thin sections of symptomatic leaf tissues revealed the presence of cylindrical inclusions, characteristic of infection by potyviruses, in the cytoplasm of epidermal, parenchymal, and vascular cells. Total RNA was extracted from symptomatic leaves collected in the Plantarum Institute (3 samples), and at Escola Superior de Agricultura Luiz de Queiroz (1 sample) using the Purelink viral RNA/DNA kit (Thermo Fisher Scientific, Waltham, USA). Reverse Transcription -Polymerase Chain Reaction (RT-PCR) was performed using the degenerate primers CIFor (5'-GGIVVIGTIGGIWSIGGIAARTCIAC-3') and CIRev (5'-ACICCRTTYTCDATDATRTTIGTIGC-3'), which amplify a fragment of approximately 700 bp within the the cylindrical inclusion protein gene of potyviruses (Ha et al. 2008). Amplicons of the expected size were obtained for all four samples analysed. One amplicon per location was purified using the Wizard® SV Gel and PCR Clean-Up System kit (Promega), and directly sequenced in both directions at Macrogen Inc (Seoul, South Korea). The nucleotide sequences obtained from the symptomatic C. asiatica plants collected in the Plantarum Institute (GenBank Acc. No. MT668627), and at ESALQ/USP (GenBank Acc. No. MT668626) showed 97.1% and 96.2% identity, respectively, with the nucleotide sequence of a Brazilian isolate of bidens mosaic virus (BiMV), family Potyviridae, genus Potyvirus (GenBank Acc. No. KF649336). To confirm the infection of C. asiatica plants with BiMV, the previously extracted RNAs were analyzed by RT-PCR using the specific primers 8331 (5'-CGTGGGGCTATCCTGAATTG-3') and 9046 (5'-CCACATCAGAGAAGTGTGCC-3'), which amplify a fragment of 715 bp corresponding to the BiMV coat protein gene (Suzuki et al. 2009). The expected size amplicons were obtained for all four samples of symptomatic plants of C. asiatica. The nucleotide sequences of two amplicons (GenBank Acc. Nos. MT668628, and MT668629), representing plants from each location, showed 94.6% to 95.6% identities with corresponding nucleotide sequences of the coat protein gene of BiMV from Brazil (GenBank Acc. Nos. KF649336, AY960150, and AY960151). A leaf extract of a symptomatic C. asiatica plant was mechanically inoculated to healthy plants of Apium graveolens, Bidens pilosa, C. asiatica, Chenopodium amaranticolor, C. quinoa, Coriander sativum, Nicotiana benthamiana, N. tabacum and Petroselinum crispum. C. asiatica became systemically infected, reproducing the original symptoms of leaf mosaic and malformation. N. benthamiana was infected and developed severe mosaic symptoms, whereas C. amaranticolor and C. quinoa reacted only with necrotic and chlorotic local lesions, respectively. Other assayed plants were not infected. Potyvirus-like particles were observed by TEM in the infected plants and BiMV infection was confirmed by RT-PCR. Transmission assays of the BiMV isolate by aphids Myzus persicae and Aphys gossypii to healthy C. asiatica plants were also performed. Virus-free aphids of the two species, reared on Capsicum annuum and Gossypium hirsutum respectively, were fasted for 30 min and then placed, separately, on symptomatic leaves of C. asiatica for an acquisition access period (AAP) of 10 min. After that, groups of six insects were transferred, separately, to four healthy C. asiatica plants for an inoculation access period (IAP) of 24 h. After inoculation the insects were killed manually. Approximately 30 days later, one plant inoculated with each species of aphid exhibited symptoms and infection was confirmed by RT-PCR and nucleotide sequencing of the amplicons. BiMV was absent in control, non-inoculated plants in both mechacial and aphid transmission assays. Infection of spontaneously growing C. asiatica plants by potyvirus, determined by TEM, was previously reported in Curitiba and Colombo, state of Paraná, Brazil by Lima Neto and Souza (1981), but the virus was not fully characterized and identified. In addition to BiMV, plants of C. asiatica are also suscptible to infection with cucumber mosaic virus (CMV), as reported by Cardin and Moury (2010) in Madagascar. This is the first identification of BiMV naturally infecting C. asiatica. Additional works on effects of BiMV infection of C. asiatica on commercial production and pharmaceutical properties are required.

Molecular characterization of foot-and-mouth disease viruses collected from Northern and Central Ethiopia during the 2018 outbreak

Background and Aim:Foot-and-mouth disease (FMD) is endemic in several developing countries and affects poor farmers through loss of production, death of diseased animals, and loss of animal byproducts. Forty-three samples were collected from 12 sites of five geographical located areas from suspected FMD virus (FMDV)-infected cattle during 2018. This study aimed to isolate and characterize the FMDVs using reverse transcription-polymerase chain reaction (RT-PCR) and gene sequencing.Materials and Methods:Forty-three FMDV-suspected clinical samples cultured on BHK-21 cell were examined, followed by virus serotype identification using RT-PCR and gene sequencing.Results:Twenty-nine (67.44%) samples were cultured on BHK-21 cell, of which 14 (32.56%) were not isolated; the 43 samples were analyzed using FMDV screening primers and serotype-specific primers. The contribution of the disease-causing serotype was serotype O of 8 (18.60%) samples, serotype A of 20 (46.51%) samples, and mixed infection (O and A) of 1 (2.33%) sample. Serotypes O and A were further characterized by phylogenetic analysis, which grouped them under East Africa 3 and Africa topotypes of genotype IV, respectively. Interestingly, serotype A was isolated for the 1st time from Keyet sub-woreda and Mulo woreda of Ethiopia, and mixed serotypes (O and A) were identified from the purchased animal.Conclusion:Molecular test result, sequencing, and phylogenetic tree reconstruction analysis revealed that the 2018 FMD outbreak in Ethiopia was caused by FMDV serotypes O and A. FMDV serotype A was the predominant strain circulating in most study areas of the country. Infections in one sample with mixed serotypes of O and A were also reported. The authors recommend a vaccine matching study of those field isolated viruses with the vaccine strain.

Full genome sequence of a chrysanthemum-infecting tomato spotted wilt virus isolate from Zimbabwe obtained by next-generation sequencing.

Tomato spotted wilt virus (TSWV) is an economically important pathogen of many crops worldwide. However, prior to this study, only one complete genome sequence of an African TSWV isolate was available in public databases. This limits genetic diversity and evolutionary studies of the pathogen on the continent. TSWV was detected in symptomatic Zimbabwean chrysanthemum plants using late-ral flow kits. The presence of the pathogen was subsequently confirmed by double antibody sandwich enzyme-linked immunosorbent assay and reverse transcription-polymerase chain reaction (RT-PCR). Total RNAs for RT-PCR and next-generation sequencing (NGS) were extracted using an RNA extraction kit. NGS performed on an Illumina HiSeq platform was used to recover the full TSWV genome and analyzed by different software packages. The tripartite genome of the Zimbabwe TSWV isolate consisted of L, M and S RNAs of 8914, 4824 and 2968 nucleotides, respectively. This isolate shared highest protein and nucleotide sequence identities with the isolate LK-1 from neighboring South Africa. The Zimbabwe TSWV isolate was found to be a non-recombinant and non-resistance-breaking. This study provides the first full genome of TSWV from Zimbabwe. It also adds useful information towards understanding the evolution of the pathogen. Keywords: Africa; tospovirus; phylogenetic analysis; recombination; virus identification.

First Report of Tomato Brown Rugose Fruit Virus Infecting Greenhouse Tomato in the United States

Tomato (Solanum lycopersicum L.), an important vegetable widely grown in the world, is susceptible to a number of emerging viruses. In September 2018, a severe disease outbreak, including mosaic, mottling, and plant stunting was observed on grafted tomato plants in a greenhouse (∼8 acres) in southern California, U.S.A. Initial screening of one symptomatic sample was positive for pepino mosaic virus (PepMV) and tomato mosaic virus (ToMV) using enzyme-linked immunosorbent assay (ELISA). Two types of particles, including flexuous potexvirus-like and rigid tobamovirus-like, were observed under an electron microscope. However, reverse transcription polymerase chain reaction (RT-PCR) tests using primers that are specific to ToMV and tomato mottle mosaic virus (ToMMV) (Sui et al. 2017) were negative. We suspected an involvement of tomato brown rugose fruit virus (ToBRFV) (Luria et al. 2017; Salem et al. 2016). A new set of primers specific to ToBRFV was designed and validated to have no cross-reaction to ToMV and ToMMV. Using this primer set, ToBRFV-F (5503), 5′-GAAGTCCCGATGTCTGTAAGG-3′, and ToBRFV-R (6344), 5′-GTGCCTACGGATGTGTATGA-3′, an expected PCR product (842 bp) was amplified and sequenced from this first sample but not from a healthy control. In a follow-up survey, 20 additional symptomatic samples were tested and shown to be all positive for PepMV using ELISA or qRT-PCR (Ling et al. 2007), and 14 of the same 20 samples were also positive for ToBRFV using RT-PCR. Sanger sequencing of seven amplicons generated a consensus 799-bp sequence after primer trimming, designated as isolate ToBRFV-US (accession no. MK109002). A BLASTn search of the NCBI database revealed 99.6% sequence identity to two other ToBRFV isolates from Jordan (KT383474; Salem et al. 2016) and Israel (KX619418; Luria et al. 2017). In pathogenicity assays, four tomato ‘Moneymaker’ seedlings (susceptible to tobamoviruses) were mechanically inoculated with an inoculum prepared from the first positive sample, and similar symptoms were visible. The target pathogen, ToBRFV, was confirmed on the inoculated plants using RT-PCR and amplicon sequencing. In a separate survey in October 2018, a disease outbreak was also observed on tomato in a greenhouse facility in Baja California, Mexico. An extensive crop health screen using ELISA tests to a panel of 19 common tomato viruses, as well as appropriate RT-PCR tests, were conducted on 14 collected samples. A mixed infection of multiple viruses was identified. In addition to common infection by PepMV, seven of 14 samples were also positive for tomato spotted wilt virus. Weak positives were observed for tobacco mosaic virus or ToMV when tested by ELISA. However, when using genus-specific primers for tobamoviruses (Tob-Uni1 and Tob-Uni2) (Letschert et al. 2002), amplicon sequencing revealed the presence of ToBRFV in both Californian and Mexican samples, with no mixed infection by any other tobamoviruses. Using the ToBRFV-specific primers, amplicon sequences from 14 Mexican samples resulted in a consensus sequence, designated as isolate ToBRFV-MX (accession no. MK109003). The two sequences of ToBRFV-US and ToBRFV-MX isolates were similar (99.6% sequence identity). Identification of the first ToBRFV outbreaks in the United States and Mexico, as well as its ability to break the Tm-2² resistance (Luria et al. 2017), raises a serious concern for the tomato industry. How ToBRFV was introduced to the United States and/or Mexico has not been determined. Eradication efforts are underway in both countries to contain and control these disease outbreaks.

APP processing and metabolism in corneal fibroblasts and epithelium as a potential biomarker for Alzheimer's disease

Alzheimer's disease (AD) primarily affects the brain and is the most common form of dementia worldwide. Despite more than a century of research, there are still no early biomarkers for AD. It has been reported that AD affects the eye, which is more accessible for imaging than the brain; however, links with the cornea have not been evaluated. To investigate whether the cornea could be used to identify possible diagnostic indicators of AD, we analyzed the proteolytic processing and isoforms of amyloid precursor protein (APP) and evaluated the expression of AD-related genes and proteins in corneal fibroblasts from wild-type (WT) corneas and corneas from patients with granular corneal dystrophy type 2 (GCD2), which is related to amyloid formation in the cornea. Reverse transcription polymerase chain reaction (RT-PCR) analysis was used to assess the expression of AD-related genes, i.e., APP, ADAM10, BACE1, BACE2, PSEN1, NCSTN, IDE, and NEP. RT-PCR and DNA sequencing analysis demonstrated that isoforms of APP770 and APP751, but not APP695, were expressed in corneal fibroblasts. Moreover, the mRNA ratio of APP770/APP751 isoforms was approximately 4:1. Western blot analysis also demonstrated the expression of a disintegrin and metalloprotease domain-containing protein 10 (ADAM10), beta-site APP-cleaving enzyme 1 (BACE1), nicastrin, insulin degradation enzyme, and neprilysin in corneal fibroblasts. Among these targets, the levels of immature ADAM10 and BACE1 protein were significantly increased in GCD2 cells. The expression levels of APP, ADAM10, BACE1, and transforming growth factor-beta-induced protein (TGFBIp) were also detected by western blot in human corneal epithelium. We also investigated the effects of inhibition of the autophagy-lysosomal and ubiquitin-proteasomal proteolytic systems (UPS) on APP processing and metabolism. These pathway inhibitors accumulated APP, α-carboxy-terminal fragments (CTFs), β-CTFs, and the C-terminal APP intracellular domain (AICD) in corneal fibroblasts. Analysis of microRNAs (miRNAs) revealed that miR-9 and miR-181a negatively coregulated BACE1 and TGFBIp, which was directly associated with the pathogenesis of AD and GCD2, respectively. Immunohistochemical analysis indicated that APP and BACE1 were distributed in corneal stroma cells, epithelial cells, and the retinal layer in mice. Collectively, we propose that the cornea, which is the transparent outermost layer of the eye and thus offers easy accessibility, could be used as a potential biomarker for AD diagnosis and progression.

All the Tested Human Somatic Cells Express Both Oct4A and Its Pseudogenes but Express Oct4A at Much Lower Levels Compared with Its Pseudogenes and Human Embryonic Stem Cells.

Oct4 pseudogenes and isoforms seriously confuse the detection of the pluripotency-associated Oct4A expression in somatic cells, which in many cases was not accurately determined. This confusion has recently been discussed, but the wrong conclusions have continuously been made. Most studies failed to detect the expression of Oct4 pseudogenes and isoforms in somatic cells but detected only Oct4A, for which the detection signals incorrectly came from its pseudogenes and isoforms. Some studies detected the expression of only Oct4 pseudogenes in somatic cells but failed to detect Oct4A. The other studies failed to detect the expression of any Oct4 genes. Oct4A is more homologous to its pseudogenes than its isoforms, and it is much more difficult to distinguish Oct4A from its pseudogenes, so this study focused on them. In this study, the strict experimental procedures were followed. Three pairs of Oct4A-specific polymerase chain reaction (PCR) primers were carefully designed and tested by sequencing reverse transcription-polymerase chain reaction (RT-PCR) clones, which showed that only one of them was truly specific to Oct4A. RT-PCR was also performed with the primers amplifying both Oct4A and its pseudogenes, and several hundreds of PCR clones from each cell type were sequenced to reliably distinguish the low-abundant Oct4A from its high-abundant pseudogenes. Western blot, immunocytochemistry, and flow cytometric analyses were performed with three Oct4 antibodies to confirm the results of Oct4 mRNA expression. This study undoubtedly made the correct conclusions about Oct4 expression in human somatic cells and showed that all the tested human somatic cells expressed both Oct4A and its pseudogenes but expressed Oct4A at much lower levels compared with its pseudogenes.

The RT-PCR identification and sequence analysis of Apple chlorotic leaf spot virus from apple cultivars in Jiaodong Peninsula, China

A set of specific primer pairs was utilized to detect Apple chlorotic leaf spot virus (ACLSV) from seven different apple cultivars in Jiaodong Peninsula via reverse transcription polymerase chain reaction (RT-PCR), and the sequence of ACLSV genome was analysed. The results indicate that: (1) High-purity total RNA could be successfully isolated using plant RNA rapid extraction kit. The ratios of A260/A280 varied between 1.8 and 2.1. The fragmentation in agarose gel was good and the 28S and 16S bands were clear, which suggested that the extracted RNA had better quality and could be used for RT-PCR. (2) The amplified products by RT-PCR were approximately 220 bp, which showed the tested samples were infected by ACLSV in this study. (3) Sequencing analysis showed that the lengths of the target fragments were 217 bp, and the sequence identity rate ranged from 85.7% to 99.1% at the nucleotide level aligned with the corresponding sequences of other ACLSV strains in National Center for Biotechnology Information.

A Pipeline with Multiplex Reverse Transcription Polymerase Chain Reaction and Microarray for Screening of Chromosomal Translocations in Leukemia

Chromosome rearrangements and fusion genes present major portion of leukemogenesis and contribute to leukemic subtypes. It is practical and helpful to detect the fusion genes in clinic diagnosis of leukemia. Present application of reverse transcription polymerase chain reaction (RT-PCR) method to detect the fusion gene transcripts is effective, but time- and labor-consuming. To set up a simple and rapid system, we established a method that combined multiplex RT-PCR and microarray. We selected 15 clinically most frequently observed chromosomal rearrangements generating more than 50 fusion gene variants. Chimeric reverse primers and chimeric PCR primers containing both gene-specific and universal sequences were applied in the procedure of multiplex RT-PCR, and then the PCR products hybridized with a designed microarray. With this approach, among 200 clinic samples, 63 samples were detected to have gene rearrangements. All the detected fusion genes positive and negative were validated with RT-PCR and Sanger sequencing. Our data suggested that the RT-PCR-microarray pipeline could screen 15 partner gene pairs simultaneously at the same accuracy of the fusion gene detection with regular RT-PCR. The pipeline showed effectiveness in multiple fusion genes screening in clinic samples.