scholarly journals Phylogenetic analysis of canine parvoviruses from Turkey

2020 ◽  
Vol 76 (01) ◽  
pp. 6334-2020
Author(s):  
ZEYNEP AKKUTAY-YOLDAR ◽  
TAYLAN KOÇ B.
Keyword(s):  
High Mortality ◽  
Phylogenetic Trees ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Canine Parvovirus ◽  
Mortality And Morbidity ◽  
Identity Match ◽  
Genomic Characterization

Canine parvovirus (CPV) type 2 is the causative agent of acute hemorrhagic enteritis and high mortality in the affected dogs. Numerous studies have been done to understand the origin of the virus and to exhibit new variants and circulating strains. This report describes the detection and genomic characterization of CPV strains from indoor and outdoor dogs in Ankara, Turkey. Samples were sent to our laboratory due to clinical symptoms in puppies. We tested blood and swab samples to determine the presence of canine parvovirus (CPV) in three puppies and two adult dogs by reverse transcription-polymerase chain reaction (RT-PCR) using VP2 (capsid protein) region primers of canine parvoviruses. Following that, to provide molecular characterization data Maximum Likelihood (ML) method was used for phylogenetic analyses. Constructed phylogenetic trees from the aligned nucleotide sequences revealed that our CPV strains demonstrated high genetic similarities, with 100% identity match on nucleotide alignments with each other and classified in CPV-2b genotypes.They have placed on a monophyletic clade as a sister branch with CPV VAC S quantum with 98.9% nucleotide homology. Our findings suggest that CPV-2b is actual and frequently seen variant in Turkey and shows high similarities with other CPV variants and a bit less with FPVs in Turkey and around the world. CPV causes high mortality and morbidity in dogs and to develop effective vaccines for protection of dogs in Turkey where there are few numbers of studies that have been done, field strains should be isolated and characterised.

scholarly journals Risk and Environmental Factors Associated with the Presence of Canine Parvovirus Type 2 in Diarrheic Dogs from Thessaly, Central Greece

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 590
Author(s):  
Maria Kantere ◽  
Labrini V. Athanasiou ◽  
Alexios Giannakopoulos ◽  
Vassilis Skampardonis ◽  
Marina Sofia ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Clinical Symptoms ◽  
Gastrointestinal Disease ◽  
Environmental Parameters ◽  
Canine Parvovirus ◽  
Geographical Information ◽  
Factors Associated ◽  
Working Dogs ◽  
Canine Parvovirus Type 2

Canine parvovirus type 2 (CPV-2) primarily infects dogs, which are the main host reservoir, causing severe gastrointestinal disease associated with immunosuppression. The present study was conducted in Thessaly, Greece and aimed to identify risk and environmental factors associated with CPV-2 infection in diarrheic dogs. Fecal samples were collected from 116 dogs presenting diarrhea and were tested by polymerase chain reaction (PCR) for the presence of CPV-2 DNA. Supplementary data regarding clinical symptoms, individual features, management factors and medical history were also gathered for each animal during clinical evaluation. Sixty-eight diarrheic dogs were found to be positive for the virus DNA in their feces. Statistical analysis revealed that CPV-2 DNA was less likely to be detected in senior dogs, while working dogs, namely hounds and shepherds, had higher odds to be positive for the virus. Livestock density and land uses, specifically the categories of discontinuous urban fabric and of human population density, were identified as significant environmental parameters associated with CPV-2 infection by using Geographical Information System (GIS) together with the Ecological Niche Model (ENM). This is the first description of the environmental variables associated with the presence of CPV-2 DNA in dogs’ feces in Greece.

Genetic characterization of canine parvovirus type 2 subtypes in Maputo, Mozambique

2016 ◽  
Vol 199 (4) ◽  
pp. 543-549 ◽  
Author(s):  
J. Figueiredo ◽  
C. Miranda ◽  
R. Souto ◽  
E. Silva ◽  
J. Fafetine ◽  
...  
Keyword(s):  
Genetic Characterization ◽  
Canine Parvovirus ◽  
Canine Parvovirus Type 2

scholarly journals Detection and Partial Characterization of Simian Immunodeficiency Virus SIVsm Strains from Bush Meat Samples from Rural Sierra Leone

2005 ◽  
Vol 79 (4) ◽  
pp. 2631-2636 ◽  
Author(s):  
Cristian Apetrei ◽  
Michael J. Metzger ◽  
David Richardson ◽  
Binhua Ling ◽  
Paul T. Telfer ◽  
...  
Keyword(s):  
Sierra Leone ◽  
Phylogenetic Trees ◽  
The Past ◽  
Immunodeficiency Virus ◽  
Bush Meat ◽  
Cercocebus Atys ◽  
Meat Samples ◽  
The Relationship

ABSTRACT Human immunodeficiency virus type 2 (HIV-2) originated from simian immunodeficiency viruses (SIVs) that naturally infect sooty mangabeys (SMs; Cercocebus atys). In order to further investigate the relationship between HIV-2 and SIVsm, the SIV specific to the SM, we characterized seven new SIVsm strains from SMs sold in Sierra Leone markets as bush meat. The gag, pol, and env sequences showed that, while the viruses of all seven SMs belonged to the SIVsm-HIV-2 lineage, they were highly divergent viruses, in spite of the fact that most of the samples originated from the same geographical region. They clustered in three lineages, two of which have been previously reported. Two of the new SIVsm strains clustered differently in gag and env phylogenetic trees, suggesting SIVsm recombination that had occurred in the past. In spite of the fact that our study doubles the number of known SIVsm strains from wild SMs, none of the simian strains were close to the groups in which HIV-2 was epidemic (groups A and B).

scholarly journals African Basil (Ocimum gratissimum) Is a Reservoir of Divergent Begomoviruses in Uganda

Plant Disease ◽  
2020 ◽  
Vol 104 (3) ◽  
pp. 853-859
Author(s):  
Happyness G. Mollel ◽  
Joseph Ndunguru ◽  
Peter Sseruwagi ◽  
Titus Alicai ◽  
John Colvin ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Plant Viruses ◽  
Wild Plants ◽  
Bipartite Begomoviruses ◽  
Ocimum Gratissimum ◽  
Genomic Characterization ◽  
Open Access Article

Begomoviruses are plant viruses that cause major losses to many economically important crops. Although they are poorly understood, begomoviruses infecting wild plants may have an important role as reservoirs in the epidemiology of viral diseases. This study reports the discovery and genomic characterization of three novel bipartite begomoviruses from wild and cultivated African basil (Ocimum gratissimum) plants collected in Uganda, East Africa. Based on the symptoms shown by the infected plants, the names proposed for these viruses are Ocimum yellow vein virus (OcYVV), Ocimum mosaic virus (OcMV), and Ocimum golden mosaic virus (OcGMV). Genome and phylogenetic analyses suggest that DNA-A of OcGMV is mostly related to begomoviruses infecting tomato in Africa, whereas those of OcYVV and OcMV are closely related to one another and highly divergent within the Old World begomoviruses. The DNA-A of all characterized begomovirus isolates are of a recombinant nature, revealing the role of recombination in the evolution of these begomoviruses. The viruses characterized here are the first identified in O. gratissimum and the first in Ocimum spp. in the African continent and could have important epidemiological consequences for cultivated basils and other important crops. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Genomic characterization of two avian paramyxovirus type 2 isolates from chickens in China

Virus Genes ◽  
2011 ◽  
Vol 43 (1) ◽  
pp. 55-59 ◽  
Author(s):  
Xiaojiao Li ◽  
Shouping Zhang ◽  
Hongwei Wang ◽  
Jixun Zhao ◽  
Guozhong Zhang
Keyword(s):  
Avian Paramyxovirus ◽  
Genomic Characterization

scholarly journals Absent from DNA and protein: genomic characterization of nullomers and nullpeptides across functional categories and evolution

2020 ◽  
Author(s):  
Ilias Georgakopoulos-Soares ◽  
Ofer Yizhar Barnea ◽  
Ioannis Mouratidis ◽  
Martin Hemberg ◽  
Nadav Ahituv
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Significant Proportion ◽  
Scoring Function ◽  
Amino Acid Sequences ◽  
Dna Fingerprints ◽  
Functional Categories ◽  
Coding Sequences ◽  
A Genome ◽  
Genomic Characterization

AbstractNullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be that they have a detrimental impact on an organism. Here, we identified all possible nullomers and nullpeptides in the genomes and proteomes of over thirty species and show that a significant proportion of these sequences are under negative selection. We assign nullomers to different functional categories (coding sequences, exons, introns, 5’UTR, 3’UTR and promoters) and show that nullomers from coding sequences and promoters are most likely to be selected against. Utilizing variants in the human population, we annotate variant-associated nullomers, highlighting their potential use as DNA ‘fingerprints’. Phylogenetic analyses of nullomers and nullpeptides across evolution shows that they could be used to build phylogenetic trees. Our work provides a catalog of genomic and proteome derived absent k-mers, together with a novel scoring function to determine their potential functional importance. In addition, it shows how these unique sequences could be used as DNA ‘fingerprints’ or for phylogenetic analyses.

scholarly journals Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9752
Author(s):  
Minh Hoang ◽  
Cheng-Nan Wu ◽  
Chuen-Fu Lin ◽  
Huong Thanh Thi Nguyen ◽  
Van Phan Le ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Surface ◽  
Contact Potential ◽  
Vp2 Gene ◽  
Feline Panleukopenia Virus ◽  
Feline Parvovirus ◽  
Canine Parvovirus Type 2

Background Canine parvovirus type 2 (CPV-2) and feline parvovirus (FPV) are known as the main causes of several serious diseases and have a severe impact on puppies and kittens, respectively. FPV and new CPV-2 variants are all able to infect cats, causing diseases indistinguishable from feline panleukopenia. However, FPV only replicates efficiently in feline cells in vitro and replicates in dogs in the thymus and bone marrow without being shed in feces. In our previous study, the genotypes of six parvoviral isolates were unable to be identified using a SimpleProbe® real-time PCR assay. Methods In the present study, we characterized previously unidentified FPV-like viruses isolated from dogs in Vietnam. The six isolates were utilized to complete VP2 gene sequencing and to conduct phylogenetic analyses. Results Sequence analysis of the six parvoviral strains identified the species as being similar to FPV. Phylogenetic analysis demonstrated that the complete VP2 genes of the strains are similar to those of FPV. The FPV-like strains contain a Thr101 mutation in the VP2 protein, which is different from prototype FPV strains. Discussion Our data provide evidence for the existence of changes in the charge, protein contact potential and molecular surface of the core of the receptor-binding size with an Ile101 to Thr101 mutation. This is also the first study to provide reliable evidence that FPV may be a threat to the Vietnamese dog population.

scholarly journals Genomic Characterization of Human and Environmental Polioviruses Isolated in Albania

1999 ◽  
Vol 65 (8) ◽  
pp. 3534-3539 ◽  
Author(s):  
Maurizio Divizia ◽  
Leonardo Palombi ◽  
Ersilia Buonomo ◽  
Domenica Donia ◽  
Vito Ruscio ◽  
...  
Keyword(s):  
Paralytic Poliomyelitis ◽  
Nucleotide Position ◽  
First Case ◽  
Genomic Characterization ◽  
Stool Samples ◽  
Intertypic Recombinant ◽  
Data Banks

ABSTRACT Between April and December 1996, a serious outbreak of poliomyelitis occurred in Albania; almost 140 subjects were involved, and the episode presented an unusually high mortality rate (12%). During the outbreak, water samples from the Lana River in Tirana, Albania, and stool samples from two cases of paralytic poliomyelitis were collected and analyzed for the presence of polioviruses. Six polioviruses were isolated from the environmental and human samples, according to standard methods. All the samples were characterized by partial genomic sequencing of 330 bases across the 5′ untranslated region (5′-UTR) (nucleotide positions 200 to 530) and of 300 bases across the VP1 region (nucleotide positions 2474 to 2774). Comparison of these sequences with those present in data banks permitted the identification of environmental isolates Lana A and Lana B as, respectively, a Sabin-like type 2 poliovirus and an intertypic recombinant poliovirus (Sabin-like type 2/wild type 1), both bearing a G instead of an A at nucleotide position 481. The two other environmental polioviruses were similar to the isolates from the paralytic cases. They were characterized by a peculiar 5′-UTR and by a VP1 region showing 98% homology with the Albanian epidemic type 1 isolates reported by other authors. This study confirms the environmental circulation in Albania of recombinant poliovirus strains, likely sustained by a massive vaccination effort and by the presence in the environment of a type 1 poliovirus, as isolated from the Lana River in Tirana about 2 months before the first case of symptomatic acute flaccid paralysis was reported in this town.

scholarly journals First Molecular Characterization of Poxviruses in Cattle, Sheep, and Goats in Botswana

2021 ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Virus Diseases ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments

Abstract BackgroundPoxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former presenting also zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, and there was no prior attempt of using molecular tools to diagnose the diseases and characterize the pathogens.MethodsA high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in samples from four cattle (from Mahalapye, Kasane, and Molepolole), one sheep (from Jwaneng), and one goat (from Kasane). Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes.ResultsThe HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR, and the inspection of the multiple sequence alignments showed that the LSDV sequences of Botswana were more like those of common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel isolates and cattle isolates of the PCPV group. The Botswana ORFV from goat differed from the ORFV collected in sheep.ConclusionsThis study is the first report on the genetic characterization of pox virus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose pox virus diseases of ruminants.

scholarly journals First molecular characterization of poxviruses in cattle, sheep, and goats in Botswana

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Boitumelo Magret Modise ◽  
Tirumala Bharani Kumar Settypalli ◽  
Tebogo Kgotlele ◽  
Dingrong Xue ◽  
Kebonyemodisa Ntesang ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Small Ruminants ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Multiple Sequence Alignments ◽  
Prior Use

Abstract Background Poxviruses within the Capripoxvirus, Orthopoxvirus, and Parapoxvirus genera can infect livestock, with the two former having zoonotic importance. In addition, they induce similar clinical symptoms in common host species, creating a challenge for diagnosis. Although endemic in the country, poxvirus infections of small ruminants and cattle have received little attention in Botswana, with no prior use of molecular tools to diagnose and characterize the pathogens. Methods A high-resolution melting (HRM) assay was used to detect and differentiate poxviruses in skin biopsy and skin scab samples from four cattle, one sheep, and one goat. Molecular characterization of capripoxviruses and parapoxviruses was undertaken by sequence analysis of RPO30 and GPCR genes. Results The HRM assay revealed lumpy skin disease virus (LSDV) in three cattle samples, pseudocowpox virus (PCPV) in one cattle sample, and orf virus (ORFV) in one goat and one sheep sample. The phylogenetic analyses, based on the RPO30 and GPCR multiple sequence alignments showed that the LSDV sequences of Botswana were similar to common LSDV field isolates encountered in Africa, Asia, and Europe. The Botswana PCPV presented unique features and clustered between camel and cattle PCPV isolates. The Botswana ORFV sequence isolated from goat differed from the ORFV sequence isolated from sheep. Conclusions This study is the first report on the genetic characterization of poxvirus diseases circulating in cattle, goats, and sheep in Botswana. It shows the importance of molecular methods to differentially diagnose poxvirus diseases of ruminants.

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