scholarly journals Isolation and characterisation of porcine epidemic diarrhoea virus in Hungary – Short communication

2019 ◽  
Vol 67 (2) ◽  
pp. 307-313 ◽  
Author(s):  
Anna Valkó ◽  
Ervin Albert ◽  
Attila Cságola ◽  
Tünde Varga ◽  
Krisztián Kiss ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Alignment ◽  
Short Communication ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea virus (PEDV) is an emerging enteropathogen, causing great economic losses in the pig industry. After many years of quiescence, PEDV was detected in Hungary in 2016 with a recombination in its S gene. In order to determine the extent of this change, an attempt was made to isolate the recombinant PEDV. This study was extended with a variety of samples collected from three separate farms with newly identified PEDV in 2018. The recombinant PEDV from 2016 was isolated successfully along with three viruses from 2018, and one isolate from the new cases was used for whole genome determination. Whole genome sequence alignment revealed the highest identity with recombinant Hungarian and Slovenian PEDV within the low-pathogenic European viruses. This suggests that these recombinant PEDV are circulating in this area and may spread to other parts of the continent.

scholarly journals Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258318
Author(s):  
Marta Antas ◽  
Monika Olech ◽  
Anna Szczotka-Bochniarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Economic Losses ◽  
High Morbidity ◽  
Antigenic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

scholarly journals Genome Sequence of Fusarium graminearum ITEM 124 (ATCC 56091), a Mycotoxigenic Plant Pathogen

2017 ◽  
Vol 5 (45) ◽  
Author(s):  
Antonio Zapparata ◽  
Daniele Da Lio ◽  
Stefania Somma ◽  
Isabel Vicente Muñoz ◽  
Luca Malfatti ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Fusarium Graminearum ◽  
Crop Yield ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
Head Blight ◽  
Content Type ◽  
Yield And Quality

ABSTRACT Fusarium graminearum is among the main causal agents of Fusarium head blight (FHB), or scab, of wheat and other cereals, caused by a complex of Fusarium species, worldwide. Besides causing economic losses in terms of crop yield and quality, F. graminearum poses a severe threat to animal and human health. Here, we present the first draft whole-genome sequence of the mycotoxigenic Fusarium graminearum strain ITEM 124, also providing useful information for comparative genomics studies.

scholarly journals Improved whole genome sequence of Phytophthora capsici generated by long-read sequencing

2021 ◽  
Author(s):  
Jinxia Shi ◽  
Wenwu Ye ◽  
Dongfang Ma ◽  
Junliang Yin ◽  
Zhichao Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
Vegetable Crops ◽  
Long Read

The soil-borne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.

scholarly journals Short communication: Whole-genome sequence analysis of 4 fecal blaCMY-2-producing Escherichia coli isolates from Holstein dairy calves

2020 ◽  
Vol 103 (1) ◽  
pp. 877-883
Author(s):  
Babafela Awosile ◽  
Julian Reyes-Velez ◽  
Yesid Cuesta-Astroz ◽  
Juan Carlos Rodríguez-Lecompte ◽  
Matthew E. Saab ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genome Sequence ◽  
Short Communication ◽  
Dairy Calves ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis

scholarly journals Whole-genome sequence of Diaporthe citri isolate NFHF-8-4, the causal agent of citrus melanose

2021 ◽  
Author(s):  
Xiang-Yu Liu ◽  
Chingchai Chaisiri ◽  
Yang Lin ◽  
Wei-Xiao Yin ◽  
Chaoxi Luo
Keyword(s):  
Genome Sequence ◽  
Development Process ◽  
Resistance Mechanisms ◽  
Infection Process ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Jiangxi Province ◽  
Whole Genome ◽  
Infection Mechanisms ◽  
Citrus Varieties

Diaporthe species are the causal agents of melanose, stem-end rot and gummosis diseases of citrus. D. citri is the predominant species on different citrus varieties. These diseases exceedingly reduce quality and marketability of fresh fruits, especially melanose on fruits causes massive economic losses. The infection mechanisms of D. citri are still unclear and the genome sequence of D. citri has not been released. In order to systemically explore the interaction between citrus and D. citri, we sequenced the whole-genome of D. citri strain NFHF-8-4, which was isolated from a sample with melanose in Jiangxi Province. The NFHF-8-4 genome sequence will provide valuable information for studying the development process, infection process and resistance mechanisms to fungicides in D. citri.

scholarly journals Porcine epidemic diarrhoea virus with a recombinant S gene detected in Hungary, 2016

2017 ◽  
Vol 65 (2) ◽  
pp. 253-261 ◽  
Author(s):  
Anna Valkó ◽  
Imre Biksi ◽  
Attila Cságola ◽  
Tamás Tuboly ◽  
Krisztián Kiss ◽  
...  
Keyword(s):  
Present Report ◽  
Age Groups ◽  
Whole Genome Sequence ◽  
Enteric Disease ◽  
High Identity ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus ◽  
Pig Farm ◽  
Insight Into

Porcine epidemic diarrhoea virus (PEDV) can cause a severe enteric disease affecting pigs of all ages. In January 2016, diarrhoea with occasional vomiting was observed in a small pig farm in Hungary. All animals became affected, while mortality (of up to 30%) was only seen in piglets. Samples from different age groups and the carcass of a piglet were examined by various methods including pathology, bacteriology and molecular biology. PEDV was confirmed by PCR and its whole genome sequence was determined. The sequence PEDV HUN/5031/2016 showed high identity with recently reported European viruses. Differences were found mostly in the S gene, where recombination was detected with a newly identified and already recombinant swine enteric coronavirus (Se-CoV) from Italy. The present report describes the first porcine epidemic diarrhoea outbreak in Hungary after many years and gives an insight into the genetics of the Hungarian PEDV.

scholarly journals Short communication: Genomic prediction using imputed whole-genome sequence variants in Brown Swiss Cattle

2018 ◽  
Vol 101 (2) ◽  
pp. 1292-1296 ◽  
Author(s):  
Mirjam Frischknecht ◽  
Theodorus H.E. Meuwissen ◽  
Beat Bapst ◽  
Franz R. Seefried ◽  
Christine Flury ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Prediction ◽  
Short Communication ◽  
Whole Genome Sequence ◽  
Sequence Variants ◽  
Whole Genome ◽  
Brown Swiss ◽  
Brown Swiss Cattle
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