scholarly journals The evolution of African swine fever virus in Sardinia (1978 to 2014) as revealed by whole genome sequencing and comparative analysis

2020 ◽  
Author(s):  
Claudia Torresi ◽  
Mariangela Fiori ◽  
Luigi Bertolotti ◽  
Matteo Floris ◽  
Barbara Colitti ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome

scholarly journals A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 846 ◽  
Author(s):  
Jan Forth ◽  
Leonie Forth ◽  
Jacqueline King ◽  
Oxana Groza ◽  
Alexandra Hübner ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
High Quality

African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170–194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing. Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.

scholarly journals Comparative Analysis of Whole-Genome Sequence of African Swine Fever Virus Belgium 2018/1

2019 ◽  
Vol 25 (6) ◽  
pp. 1249-1252 ◽  
Author(s):  
Jan H. Forth ◽  
Marylène Tignon ◽  
Ann Brigitte Cay ◽  
Leonie F. Forth ◽  
Dirk Höper ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome Sequence ◽  
Whole Genome

scholarly journals A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing

2021 ◽  
Vol 8 ◽  
Author(s):  
ChiHai Ji ◽  
JingZhe Jiang ◽  
YingFang Wei ◽  
ZhiYuan Wang ◽  
YongJie Chen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
African Swine Fever Virus ◽  
Gene Prediction ◽  
African Swine Fever ◽  
Epidemiological Studies ◽  
Virus Genome ◽  
Fever Virus ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing

In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.

scholarly journals Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

2018 ◽  
Vol 12 (6) ◽  
pp. e0006566 ◽  
Author(s):  
Elizabeth M. Batty ◽  
Suwittra Chaemchuen ◽  
Stuart Blacksell ◽  
Allen L. Richards ◽  
Daniel Paris ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Orientia Tsutsugamushi ◽  
Human Pathogen ◽  
Long Read

scholarly journals A Simple Method for Sample Preparation to Facilitate Efficient Whole-Genome Sequencing of African Swine Fever Virus

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1129 ◽  
Author(s):  
Ferenc Olasz ◽  
István Mészáros ◽  
Szilvia Marton ◽  
Győző L. Kaján ◽  
Vivien Tamás ◽  
...  
Keyword(s):  
Sample Preparation ◽  
African Swine Fever Virus ◽  
Animal Health ◽  
African Swine Fever ◽  
Fever Virus ◽  
Whole Genome ◽  
Swine Industry ◽  
Viral Dna ◽  
Simple Method ◽  
Generation Sequencing

In the recent years, African swine fever has become the biggest animal health threat to the swine industry. To facilitate quick genetic analysis of its causative agent, the African swine fever virus (ASFV), we developed a simple and efficient method for next generation sequencing of the viral DNA. Execution of the protocol does not demand complicated virus purification steps, enrichment of the virus by ultracentrifugation or of the viral DNA by ASFV-specific PCRs, and minimizes the use of Sanger sequencing. Efficient DNA-se treatment, monitoring of sample preparation by qPCR, and whole genome amplification are the key elements of the method. Through detailed description of sequencing of the first Hungarian ASFV isolate (ASFV_HU_2018), we specify the sensitive steps and supply key reference numbers to assist reproducibility and to facilitate the successful use of the method for other ASFV researchers.

Isolation and whole-genome sequencing of a Crimean-Congo hemorrhagic fever virus strain, Greece

2018 ◽  
Vol 9 (4) ◽  
pp. 788-791 ◽  
Author(s):  
Anna Papa ◽  
Elpida Papadopoulou ◽  
Katerina Tsioka ◽  
Anastasia Kontana ◽  
Styliani Pappa ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Virus Strain ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Whole Genome ◽  
Crimean Congo Hemorrhagic Fever ◽  
Hemorrhagic Fever Virus

scholarly journals Newly emerged African swine fever virus strain Belgium/Etalle/wb/2018: Complete genomic sequence and comparative analysis with reference p72 genotype II strains

2019 ◽  
Vol 66 (6) ◽  
pp. 2566-2591 ◽  
Author(s):  
Gautier Gilliaux ◽  
Mutien Garigliany ◽  
Alain Licoppe ◽  
Julien Paternostre ◽  
Christophe Lesenfants ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Virus Strain ◽  
Genomic Sequence ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Complete Genomic Sequence ◽  
Genotype Ii ◽  
Complete Genomic

Whole genome sequencing of lamb rotavirus and comparative analysis with other mammalian rotaviruses

Virus Genes ◽  
2009 ◽  
Vol 38 (2) ◽  
pp. 302-310 ◽  
Author(s):  
Yanjun Chen ◽  
Weiwen Zhu ◽  
Shuo Sui ◽  
Yuxin Yin ◽  
Songnian Hu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome
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