Dataset Information

Molecular characterization of strawberry vein banding virus from China and the development of loop‑mediated isothermal amplification assays for their detection.

ABSTRACT: Strawberry vein banding virus (SVBV) is one of the serious viral pathogens infecting strawberry worldwide. To understand the molecular characterization of SVBV from China, complete genome sequences of sixteen SVBV isolates were cloned and sequenced. Sequence comparison showed they shared high nucleotide sequence identity (93.6-99.5%) with isolates from China and Japan (96.6-98.4%), while relatively low identity with the isolates from Canada (91.9-93.7%) and USA (85.5-85.9%). Phylogenetic analyses based on the complete genome sequence or coat protein (CP) gene showed the SVBV isolates clustered into three clades correlated with geographic distribution. Recombination analyses identified 13 recombinants and 21 recombinant events, indicating frequent and multiple recombinations in SVBV evolution. Furthermore, a sensitive loop-mediated isothermal amplification (LAMP) method was developed for rapid detection of SVBV isolates, which could be especially suitable for seedling propagation, virus-free culture and routine diagnostics in field investigation. This study offers new understanding of the molecular evolution and may help to improve the management of SVBV.

SUBMITTER: Ren J

PROVIDER: S-EPMC8940885 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Molecular characterization of strawberry vein banding virus from China and the development of loop‑mediated isothermal amplification assays for their detection.

Ren Junda J Zhang Jiaxing J Wang Qiushi Q Zhou Yu Y Wang Jingxuan J Ran Ce C Shang Qiaoxia Q

Scientific reports 20220322 1

Strawberry vein banding virus (SVBV) is one of the serious viral pathogens infecting strawberry worldwide. To understand the molecular characterization of SVBV from China, complete genome sequences of sixteen SVBV isolates were cloned and sequenced. Sequence comparison showed they shared high nucleotide sequence identity (93.6-99.5%) with isolates from China and Japan (96.6-98.4%), while relatively low identity with the isolates from Canada (91.9-93.7%) and USA (85.5-85.9%). Phylogenetic analyse ...[more]

PMID: 35318413

Similar Datasets

Project description:BackgroundThe bacterium Vibrio cholerae causes diarrheal illness and can acquire genetic material leading to multiple drug resistance (MDR). Rapid detection of resistance-conferring mobile genetic elements helps avoid the prescription of ineffective antibiotics for specific strains. Colorimetric loop-mediated isothermal amplification (LAMP) assays provide a rapid and cost-effective means for detection at point-of-care since they do not require specialized equipment, require limited expertise to perform, and can take less than 30 min to perform in resource limited regions. LAMP output is a color change that can be viewed by eye, but it can be difficult to design primer sets, determine target specificity, and interpret subjective color changes.MethodsWe developed an algorithm for the in silico design and evaluation of LAMP assays within the open-source PCR Signature Erosion Tool (PSET) and a computer vision application for the quantitative analysis of colorimetric outputs. First, Primer3 calculates LAMP primer sequence candidates with settings based on GC-content optimization. Next, PSET aligns the primer sequences of each assay against large sequence databases to calculate sufficient sequence similarity, coverage, and primer arrangement to the intended taxa, ultimately generating a confusion matrix. Finally, we tested assay candidates in the laboratory against synthetic constructs.ResultsAs an example, we generated new LAMP assays targeting drug resistance in V. cholerae and evaluated existing ones from the literature based on in silico target specificity and in vitro testing. Improvements in the design and testing of LAMP assays, with heightened target specificity and a simple analysis platform, increase utility for in-field applications. Overall, 9 of the 16 tested LAMP assays had positive signal through visual and computer vision-based detection methods developed here. Here we show LAMP assays tested on synthetic AMR gene targets for aph(6), varG, floR, qnrVC5, and almG, which allow for resistance to aminoglycosides, penicillins, carbapenems, phenicols, fluoroquinolones, and polymyxins respectively.

Dataset Information

Molecular characterization of strawberry vein banding virus from China and the development of loop‑mediated isothermal amplification assays for their detection.

Publications

Molecular characterization of strawberry vein banding virus from China and the development of loop‑mediated isothermal amplification assays for their detection.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets