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

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.

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

PLoS ONE ◽

10.1371/journal.pone.0258318 ◽

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.

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Molecular Characterization of Corynebacterium pseudotuberculosis Isolated over a 15-Year Period in Switzerland

Veterinary Sciences ◽

10.3390/vetsci8080151 ◽

2021 ◽

Vol 8 (8) ◽

pp. 151

Author(s):

Jessica Schlicher ◽

Sarah Schmitt ◽

Marc J. A. Stevens ◽

Roger Stephan ◽

Giovanni Ghielmetti

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Chronic Disease ◽

Economic Impact ◽

Molecular Characterization ◽

Geographical Origin ◽

Toxin Gene ◽

Caseous Lymphadenitis ◽

Sequence Types

Corynebacteriumpseudotuberculosis biovar Ovis is the etiological agent of the contagious and chronic disease caseous lymphadenitis (CLA) in sheep and goats. The economic impact of CLA in Switzerland remains largely unknown, and the transmission modalities, as well as the genetic diversity of circulating strains, are poorly understood. This work presents further characterization data for 215 C. pseudotuberculosis isolates from sheep, goats and a dromedary originating from Switzerland and the Principality of Liechtenstein, collected over a 15-year period. The isolates were classified into the two biovars Ovis and Equi, analyzed for the presence of the diphtheria-like toxin gene and characterized using MLSA. All sheep and goat isolates were classified as C. pseudotuberculosis biovar Ovis. The isolate from a dromedary was classified as biovar Equi. No isolates harboring the diphtheria-like toxin gene were detected. Phylogenetic analysis of the concatenated sequences of four genes revealed the existence of 24 clusters. There was no correlation between MLSA sequence types, year of isolation and the geographical origin of the isolates. These findings confirm the presence of several MLSA sequence types in the study area and over a 15-year period. Moreover, no sheep- and goat-specific MLSA sequence types were found.

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

Diseases of Aquatic Organisms ◽

10.3354/dao03514 ◽

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.

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

PLoS ONE ◽

10.1371/journal.pone.0206382 ◽

2018 ◽

Vol 13 (10) ◽

pp. e0206382 ◽

Cited By ~ 1

Author(s):

Sun-Jung Kwon ◽

Gug-Seoun Choi ◽

Boram Choi ◽

Jang-Kyun Seo

Keyword(s):

Molecular Characterization ◽

Rna Virus

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

PeerJ ◽

10.7717/peerj.6216 ◽

2019 ◽

Vol 6 ◽

pp. e6216 ◽

Cited By ~ 3

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.

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

Journal of General Virology ◽

10.1099/jgv.0.001581 ◽

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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The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Viruses ◽

10.3390/v12030258 ◽

2020 ◽

Vol 12 (3) ◽

pp. 258 ◽

Cited By ~ 7

Author(s):

Dominique L. Chaput ◽

David Bass ◽

Md. Mehedi Alam ◽

Neaz Al Hasan ◽

Grant D. Stentiford ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Geographical Origin ◽

Rna Virus ◽

Geographic Origin ◽

South American ◽

Reassortment Event ◽

Coding Regions ◽

Whole Genomes ◽

History Of ◽

Negative Sense

Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.

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Molecular characterization of small and medium segments of Crimean-Congo hemorrhagic fever virus in Turkey

Future Virology ◽

10.2217/fvl-2020-0003 ◽

2020 ◽

Vol 15 (4) ◽

pp. 247-254

Author(s):

Murat Karamese ◽

Erkan Ozmen ◽

Hakan Aydin ◽

Mehmet Ozkan Timurkan ◽

Mesud Fakirullahoglu

Keyword(s):

Infectious Disease ◽

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Molecular Characterization ◽

Hemorrhagic Fever ◽

Fever Virus ◽

Crimean Congo Hemorrhagic Fever ◽

Hemorrhagic Fever Virus ◽

Relationship Of

Aim: The objective was to investigate the genotypic relationship of S and M segments in Crimean-Congo hemorrhagic fever virus (CCHFV) by phylogenetic analysis in 25 patients from seven endemic cities in Turkey. Materials & methods: A total of 25 samples from patients with CCHF were included between 2012 and 2015. Phylogenetic tree analyses were inferred using MEGA version-6.0 and distances were calculated by Kimura’s 2-parameter. Results: Phylogenetic analysis showed that all isolated viruses (n = 25) were in the predicted clades such as clade V- Europe-1 regarding both S and M segments of the CCHFV. Conclusion: Further epidemiological, molecular and phylogenic studies should be performed in both reservoir animals/vectors and humans to determine the incidence of tick-borne infectious disease and to help to develop vaccines for prevention of the disease.

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Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽

10.3390/v12020183 ◽

2020 ◽

Vol 12 (2) ◽

pp. 183 ◽

Cited By ~ 11

Author(s):

Tohru Suzuki ◽

Yoshihiro Otake ◽

Satoko Uchimoto ◽

Ayako Hasebe ◽

Yusuke Goto

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Molecular Characterization ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Wild Ruminant ◽

Genome Sequence Analysis ◽

Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

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