Differentiation of Capripox Viruses by Nanopore Sequencing

Eltom, Kamal H.; Christina, Althoff, Anna,; Hansen, Søren Gustenhoff; Böhlken-Fascher, Susanne; Yousif, Ausama; El-Sheikh, Hussein A.; ElWakeel, Ahmed A.; El‐Gamal, Mahmoud A.; Mossa, Hadeer M.; Aboul-Soud, Emad; Wolff, J. W.; Korthase, Christian; Hoffmann, Bernd; Adam, Nabawia Mohamed; Abdelaziz, Sanaa; Shalaby, Mohamed A.; Wahed, Ahmed Abd El

doi:10.3390/vaccines9040351

Cited by 6 publications

(4 citation statements)

References 35 publications

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“…The ease of replication of this database makes it more widely used. The advantages of this technology are that it is suitable for complex clinical environments, short detection time, and strong portability ( Eltom et al, 2021 ). Lesions caused by LSDV in other species can also be used as a differential diagnosis method, for example, the isolation of the virus into embryonated chicken eggs (ECEs) can cause characteristic pitting lesions on the chorioallantoic membrane ( El-Ansary et al, 2022 ).…”

Section: Research Advances On the Diagnostic Methods Of Lsdmentioning

confidence: 99%

Understanding the research advances on lumpy skin disease: A comprehensive literature review of experimental evidence

et al. 2022

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Lumpy skin disease is caused by lumpy skin disease virus (LSDV), which can induce cattle with high fever and extensive nodules on the mucosa or the scarfskin, seriously influencing the cattle industry development and international import and export trade. Since 2013, the disease has spread rapidly and widely throughout the Russia and Asia. In the past few decades, progress has been made in the study of LSDV. It is mainly transmitted by blood-sucking insects, and various modes of transmission with distinct seasonality. Figuring out how the virus spreads will help eradicate LSDV at its source. In the event of an outbreak, selecting the most effective vaccine to block and eliminate the threat posed by LSDV in a timely manner is the main choice for farmers and authorities. At present, a variety of vaccines for LSDV have been developed. The available vaccine products vary in quality, protection rate, safety and side effects. Early detection of LSDV can help reduce the cost of disease. In addition, because LSDV has a huge genome, it is currently also used as a vaccine carrier, forming a new complex with other viral genes through homologous recombination. The vaccine prepared based on this can have a certain preventive effect on many kinds of diseases. Clinical detection of disease including nucleic acid and antigen level. Each method varies in convenience, accuracy, cost, time and complexity of equipment. This article reviews our current understanding of the mode of transmission of LSDV and advances in vaccine types and detection methods, providing a background for further research into various aspects of LSDV in the future.

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Section: Research Advances On the Diagnostic Methods Of Lsdmentioning

confidence: 99%

Understanding the research advances on lumpy skin disease: A comprehensive literature review of experimental evidence

et al. 2022

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“…Animal virus infections can spread rapidly and have severe socioeconomic consequences. Nanopore sequencing has been used to identify various animal viruses, including differentiating between three Capripox Viruses in outbreaks in the Middle East and Africa, 277 identifying African horse sickness in an outbreak in Thailand, 278 and tracking Enzootic Bovine Leukosis caused by Bovine leukemia virus transmission in US pastures 279 . It has also been used to reveal the complex transcriptional landscape of porcine reproductive and respiratory syndrome virus 280 …”

Section: Applications Of Nanopore Sequencing In Other Microbial Detec...mentioning

confidence: 99%

Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third‐generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID‐19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus‐2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID‐19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID‐19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

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“…These limitations can now be addressed by long-read sequencing approaches of which Oxford Nanopore Technologies (ONT) is one example. Indeed, ONT has already demonstrated its ability to sequence and assemble several types of viruses from RNA [36][37][38][39][40][41][42] as well as DNA [43][44][45][46] matrices. Nanopore sequencing has also been successfully tested on Herpesviruses like the Human Herpes Virus Type 1 (HHV-1) [47], the Human cytomegalovirus (HCMV) [48], the Equine herpesvirus 1 (EHV-1) [49] and the koi herpesvirus (KHV) [50].…”

Section: Impact Statementmentioning

confidence: 99%

Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly

et al. 2022

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Whole-genome sequencing is widely used to better understand the transmission dynamics, the evolution and the emergence of new variants of viral pathogens. This can bring crucial information to stakeholders for disease management. Unfortunately, aquatic virus genomes are usually difficult to characterize because most of these viruses cannot be easily propagated in vitro. Developing methodologies for routine genome sequencing of aquatic viruses is timely given the ongoing threat of disease emergence. This is particularly true for pathogenic viruses infecting species of commercial interest that are widely exchanged between production basins or countries. For example, the ostreid herpesvirus type 1 (OsHV-1) is a Herpesvirus widely associated with mass mortality events of juvenile Pacific oyster Crassostrea gigas. Genomes of Herpesviruses are large and complex with long direct and inverted terminal repeats. In addition, OsHV-1 is unculturable. It therefore accumulates several features that make its genome sequencing and assembly challenging. To overcome these difficulties, we developed a tangential flow filtration (TFF) method to enrich OsHV-1 infective particles from infected host tissues. This virus purification allowed us to extract high molecular weight and high-quality viral DNA that was subjected to Illumina short-read and Nanopore long-read sequencing. Dedicated bioinformatic pipelines were developed to assemble complete OsHV-1 genomes with reads from both sequencing technologies. Nanopore sequencing allowed characterization of new structural variations and major viral isomers while having 99,98 % of nucleotide identity with the Illumina assembled genome. Our study shows that TFF-based purification method, coupled with Nanopore sequencing, is a promising approach to enable in field sequencing of unculturable aquatic DNA virus.

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Differentiation of Capripox Viruses by Nanopore Sequencing

Cited by 6 publications

References 35 publications

Understanding the research advances on lumpy skin disease: A comprehensive literature review of experimental evidence

Understanding the research advances on lumpy skin disease: A comprehensive literature review of experimental evidence

Nanopore sequencing technology and its applications

Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly

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