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 Current status of porcine epidemic diarrhoea (PED) in European pigs

2019 ◽  
Vol 63 (4) ◽  
pp. 465-470
Author(s):  
Marta Antas ◽  
Grzegorz Woźniakowski
Keyword(s):  
Rna Virus ◽  
Acute Diarrhoea ◽  
Current Status ◽  
Economic Losses ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus ◽  
The Us ◽  
The Usa ◽  
Suckling Piglets ◽  
Farming Industry

Abstract Porcine epidemic diarrhoea (PED) is a highly contagious and devastating enteric disease of pigs caused by porcine epidemic diarrhoea virus (PEDV), an enveloped, single-stranded RNA virus belonging to the Alphacoronavirus genus of the Coronaviridae family. The disease is clinically similar to other forms of porcine gastroenteritis. Pigs are the only known host of the disease, and the occurrence of PED in wild boars is unknown. The virus causes acute diarrhoea, vomiting, dehydration, and high mortality in suckling piglets reaching 100%. Heavy economic losses in the pig-farming industry were sustained in the USA between 2013 and 2015 when PEDV spread very quickly and resulted in epidemics. The loss in the US pig industry has been estimated at almost seven million pigs. The purpose of this review is a description of the current status of porcine epidemic diarrhoea in European pigs and the risk presented by the introduction of PEDV to Poland in comparison to the epidemics in the USA.

scholarly journals Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 830 ◽  
Author(s):  
Yuliya Kleschenko ◽  
Danyil Grybchuk ◽  
Nadezhda S. Matveeva ◽  
Diego H. Macedo ◽  
Evgeny N. Ponirovsky ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cutaneous Leishmaniasis ◽  
Molecular Characterization ◽  
Leishmania Major ◽  
Geographical Origin ◽  
Rna Virus ◽  
Viral Sequences

Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.

Phylogenetic Analysis of the Spike (S) Gene of the New Variants of Porcine Epidemic Diarrhoea Virus in Taiwan

2015 ◽  
Vol 64 (1) ◽  
pp. 157-166 ◽  
Author(s):  
H.-Y. Chiou ◽  
Y.-L. Huang ◽  
M.-C. Deng ◽  
C.-Y. Chang ◽  
C.-R. Jeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

scholarly journals Molecular characterization of goose parvovirus in geese of Turkey

2021 ◽  
Vol 41 ◽  
Author(s):  
Oya Bulut ◽  
Irmak Dik ◽  
Hatice P. Aslim ◽  
Cagri Avci ◽  
Hasan S. Palanci ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
High Morbidity ◽  
Viral Pathogen ◽  
Virulent Strains ◽  
The World ◽  
Goose Parvovirus ◽  
Pcr Method ◽  
Definition Of

ABSTRACT: Goose parvovirus (GPV), also called Derzsy’s disease, is a viral pathogen that causes high morbidity and mortality in goslings and ducklings. In this study, we perform the molecular characterization of the GPV in Turkey. The definition of similarity to the world of GPV isolates in Turkey and construction of a phylogenetic tree was aimed. For this purpose, the presence of GPV in the liver, spleen, and intestine tissues of nine goslings with symptoms such as dysphagia, bilateral ocular swelling, eye discharge, diarrhea, and fatigue were investigated by real-time PCR method and all samples were detected as positive. According to the data obtained by molecular characterization, phylogenetic analysis of GPV has been presented in Turkey. As a result of this study, it was determined that the GPVs available in Turkey are virulent strains.

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 Budgerigar Fledgling Disease Virus SC-YB19, with an 18-Nucleotides Deletion, in China

2020 ◽  
Author(s):  
Tian Zhi-ge ◽  
Yin Chuan-ming ◽  
Cong Feng ◽  
xiaoliang hu
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Disease Virus ◽  
Economic Losses ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Genotype Variation ◽  
Sequence Position

Abstract Background: Budgerigar fledgling disease virus (BFDV) poses a serious threat to the Chinese psittacine industry, causing enormous economic losses. This study aims to reveal the etiological role of BFDV and evaluate the molecular characterization.Results: We report on BFDV, designated SC-YB19, which had an 18-nucleotide (nt) deletion in the enhancer region, corresponding to the sequence position 164–181 nt, when compared with other BFDV strains. Sequence analyses suggested that 19 nucleotide substitutions were identified with the domestic strains, APV7 and AF118150. Phylogenetic analysis indicated that SC-YB19, along with three domestic strains, formed a unique cluster, and were closely related to Polish isolates. Conclusion: Taken together, these results demonstrate that a BFDV genotype variation was co-circulating in China, and provide important insights on evolution of BFDV.

Morphological, histological and molecular characterization of Myxidium cf. rhodei infecting the kidney of Rutilus rutilus

2020 ◽  
Vol 141 ◽  
pp. 39-46
Author(s):  
MD Dorjievna Batueva ◽  
X Pan ◽  
J Zhang ◽  
X Liu ◽  
W Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rutilus Rutilus ◽  
Longitudinal Axis ◽  
Suture Line ◽  
Present Species ◽  
Supplementary Data

In the present study, we provide supplementary data for Myxidium cf. rhodei Léger, 1905 based on morphological, histological and molecular characterization. M. cf. rhodei was observed in the kidneys of 918 out of 942 (97%) roach Rutilus rutilus (Linnaeus, 1758). Myxospores of M. cf. rhodei were fusiform with pointed ends, measuring 12.7 ± 0.1 SD (11.8-13.4) µm in length and 4.6 ± 0.1 (3.8-5.4) µm in width. Two similar pear-shaped polar capsules were positioned at either ends of the longitudinal axis of the myxospore: each of these capsules measured 4.0 ± 0.1 (3.1-4.7) µm in length and 2.8 ± 0.1 (2.0-4.0) µm in width. Polar filaments were coiled into 4 to 5 turns. Approximately 18-20 longitudinal straight ridges were observed on the myxospore surface. The suture line was straight and distinctive, running near the middle of the valves. Histologically, the plasmodia of the present species were found in the Bowman’s capsules, and rarely in the interstitium of the host. Phylogenetic analysis revealed that M. cf. rhodei was sister to M. anatidum in the Myxidium clade including most Myxidium species from freshwater hosts.

scholarly journals Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families

PLoS ONE ◽  
2018 ◽  
Vol 13 (10) ◽  
pp. e0206382 ◽  
Author(s):  
Sun-Jung Kwon ◽  
Gug-Seoun Choi ◽  
Boram Choi ◽  
Jang-Kyun Seo
Keyword(s):  
Molecular Characterization ◽  
Rna Virus

scholarly journals Genome organization and molecular characterization of the three Formica exsecta viruses—FeV1, FeV2 and FeV4

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6216 ◽  
Author(s):  
Kishor Dhaygude ◽  
Helena Johansson ◽  
Jonna Kulmuni ◽  
Liselotte Sundström
Keyword(s):  
Molecular Characterization ◽  
Genome Organization ◽  
Rna Virus ◽  
Open Reading Frames ◽  
Link Type ◽  
Infection Pathways ◽  
Comparative Genomics Analysis ◽  
First Time ◽  
Negative Sense

We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.

Molecular characterization of the first human G15 rotavirus strain of zoonotic origin from the bovine species

2021 ◽  
Vol 102 (4) ◽  
Author(s):  
Takeshi Tsugawa ◽  
Yoshiki Fujii ◽  
Yusuke Akane ◽  
Saho Honjo ◽  
Kenji Kondo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Human Infection ◽  
Potential Reservoir ◽  
Group A Rotaviruses ◽  
Paediatric Outpatient ◽  
Group A ◽  
Human Infections ◽  
Bovine Species

Group A rotaviruses (RVAs) infect a wide variety of mammalian and avian species. Animals act as a potential reservoir to RVA human infections by direct virion transmission or by contributing genes to reassortants. Here, we report the molecular characterization of a rare human RVA strain Ni17-46 with a genotype G15P[14], isolated in Japan in 2017 during rotavirus surveillance in a paediatric outpatient clinic. The genome constellation of this strain was G15-P[14]-I2-R2-C2-M2-A13-N2-T9-E2-H3. This is the first report of an RVA with G15 genotype in humans, and sequencing and phylogenetic analysis results suggest that human infection with this strain has zoonotic origin from the bovine species. Given the fact that this strain was isolated from a patient with gastroenteritis and dehydration symptoms, we must take into account the virulence of this strain in humans.

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