scholarly journals Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2473
Author(s):  
Zied Bouslama ◽  
Habib Kharmachi ◽  
Nourhene Basdouri ◽  
Jihen Ben Salem ◽  
Samia Ben Maiez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Animals ◽  
Genetic Characteristics ◽  
Bayesian Phylogenetic Analysis ◽  
Viral Sequencing ◽  
Virus Isolates ◽  
Virus Strains ◽  
Natural Barrier

Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.

scholarly journals Molecular epidemiological analysis of wild animal rabies isolates from India

2019 ◽  
Vol 12 (3) ◽  
pp. 352-357 ◽  
Author(s):  
Gundallhalli Bayyappa Manjunatha Reddy ◽  
Rajendra Singh ◽  
Karam Pal Singh ◽  
Anil Kumar Sharma ◽  
Sobharani Vineetha ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Fluorescent Antibody ◽  
Antibody Test ◽  
Reservoir Host ◽  
Wild Animals ◽  
Rt Pcr ◽  
Epidemiological Analysis ◽  
Nucleoprotein Gene ◽  
Single Cluster

Aim: This study was conducted to know the genetic variability of rabies viruses (RVs) from wild animals in India. Materials and Methods: A total of 20 rabies suspected brain samples of wild animals from different states of India were included in the study. The samples were subjected for direct fluorescent antibody test (dFAT), reverse transcription polymerase chain reaction (RT-PCR), and quantitative reverse transcriptase real-time PCR (RT-qPCR). The phylogenetic analysis of partial nucleoprotein gene sequences was performed. Results: Of 20 samples, 11, 10, and 12 cases were found positive by dFAT, RT-PCR, and RT-qPCR, respectively. Phylogenetic analysis showed that all Indian wild RVs isolates belonged to classical genotype 1 of Lyssavirus and were closely related to Arctic/Arctic-like single cluster indicating the possibility of a spillover of rabies among different species. Conclusion: The results indicated the circulation of similar RVs in sylvatic and urban cycles in India. However, understanding the role of wild animals as reservoir host needs to be studied in India.

scholarly journals Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

2021 ◽  
Author(s):  
Qian Yang ◽  
Dongmei Yan ◽  
Yang Song ◽  
Shuangli Zhu ◽  
Yun He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Foot And Mouth Disease ◽  
Coxsackievirus B3 ◽  
Whole Genome ◽  
Nucleotide Substitution Rate ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Heavy Burden ◽  
Group D

Abstract Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

scholarly journals Diversity and Transmission of Aleutian Mink Disease Virus in Feral and Farmed American Mink and Native Mustelids

2021 ◽  
Author(s):  
Jenni Virtanen ◽  
Andrzej Zalewski ◽  
Marta Kołodziej-Sobocińska ◽  
Marcin Brzeziński ◽  
Teemu Smura ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
American Mink ◽  
Virus Transmission ◽  
Wild Animals ◽  
Tissue Samples ◽  
Multiple Introductions ◽  
Aleutian Mink Disease Virus ◽  
Pine Martens

Abstract Aleutian mink disease virus (AMDV), which causes Aleutian disease (AD), is widely spread both in farmed mink and wild mustelids. However, only limited data is available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR positive individuals in American mink, polecats, otters, stone martens, and pine martens, and used phylogenetic analysis of NS1 region to study transmission. In addition, we used metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22% in otters to 62% and 64% in stone martens and feral mink, respectively. All studied antibody positive mink were also PCR positive, whereas only 10, 15, and 18% of antibody positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate sub-clusters in the phylogenetic tree and no signs of recent virus transmission between farmed and wild animals was observed despite frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps-of-knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.

scholarly journals Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Artem Baidaliuk ◽  
Sébastian Lequime ◽  
Isabelle Moltini-Conclois ◽  
Stéphanie Dabo ◽  
Laura B Dickson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Aedes Aegypti ◽  
Evolutionary History ◽  
Host Population ◽  
Viral Metagenomics ◽  
Insect Host ◽  
Genome Sequences ◽  
Geographical Clustering ◽  
Virus Isolates

Abstract Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing agent virus (CFAV) was the first described ISF of mosquitoes more than four decades ago. Despite evidence for widespread CFAV infections in A.aegypti populations and for CFAV potential to interfere with arbovirus transmission, little is known about CFAV evolutionary history. Here, we generated six novel CFAV genome sequences by sequencing three new virus isolates and subjecting three mosquito samples to untargeted viral metagenomics. We used these new genome sequences together with published ones to perform a global phylogenetic analysis of CFAV genetic diversity. Although there was some degree of geographical clustering among CFAV sequences, there were also notable discrepancies between geography and phylogeny. In particular, CFAV sequences from Cambodia and Thailand diverged significantly, despite confirmation that A.aegypti populations from both locations are genetically close. The apparent phylogenetic discrepancy between CFAV and its A.aegypti host in Southeast Asia indicates that other factors than host population structure shape CFAV genetic diversity.

scholarly journals FEATURES OF EPISOTIC PROCESS AND MOLECULAR-GENETIC CHARACTERISTICS OF VIRUS ISOLATES OF RABIES IN TVER REGION

2018 ◽  
Vol 63 (3) ◽  
pp. 115-123
Author(s):  
A. M. Gulukin ◽  
A. A. Shabejkin ◽  
V. V. Makarov ◽  
O. N. Zaykova ◽  
T. V. Grebennikova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rabies Virus ◽  
Molecular Genetic ◽  
Phylogenetic Group ◽  
N Gene ◽  
Genetic Characteristics ◽  
Temporal Features ◽  
Epizootic Process ◽  
Tver Region ◽  
Virus Isolates

Rabies epidemic situation in the Tver Region has been studied. Animals of different species that had confirmed clinical rabies were statistically analyzed. It was established that the features of the course of epizootics in the Tver region correspond to the regularities characteristic of rabies of the natural-focal type. As a result of sequencing of the rabies virus N gene and phylogenetic analysis, the isolates studied were assigned to the central phylogenetic group. With the help of the geoinformatic system, nosological maps of the Tver region were obtained and the spatial- temporal features of the course of the epizootic process of rabies infection were studied.

Genetic diversity and phylogenetic analysis of Aleutian mink disease virus isolates in north-east China

2018 ◽  
Vol 163 (5) ◽  
pp. 1241-1251 ◽  
Author(s):  
Xue Leng ◽  
Dongxu Liu ◽  
Jianming Li ◽  
Kun Shi ◽  
Fanli Zeng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Disease Virus ◽  
East China ◽  
Aleutian Mink Disease Virus ◽  
North East ◽  
Virus Isolates

Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus isolates in East China

2014 ◽  
Vol 24 ◽  
pp. 193-201 ◽  
Author(s):  
Xiaomin Wang ◽  
Kongwang He ◽  
Wenwen Zhang ◽  
Zhongtao Zhou ◽  
Aihua Mao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
East China ◽  
Respiratory Syndrome Virus ◽  
Virus Isolates

scholarly journals Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato

Plant Disease ◽  
2018 ◽  
Vol 102 (11) ◽  
pp. 2268-2276 ◽  
Author(s):  
Antonis Giakountis ◽  
Iason Tsarmpopoulos ◽  
Elisavet K. Chatzivassiliou
Keyword(s):  
Genetic Diversity ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Protein Sequence ◽  
Coat Protein Sequence ◽  
Tomato Plants ◽  
Satellite Rnas ◽  
Virus Isolates ◽  
Limited Genetic Diversity

Worldwide, Cucumber mosaic virus (CMV) is the causal agent of many economically important diseases. Based on immunological or molecular analysis, three distinct subgroups of CMV isolates can be identified (IA, IB, and II). In addition, some CMV isolates are associated with satellite RNAs (satRNAs), a type of noncoding transcript that may alter the symptoms of CMV infections. This study presents an analysis of CMV isolates occurring in legumes in Greece in respect to their genetic diversity, and the presence and diversity of their satRNA. Phylogenetic analysis of the CMV coat protein sequence of 18 legume and 5 tomato CMV isolates collected throughout Greece classified them within subgroups IA and IB, with a limited genetic diversity. The CMV satRNAs found in nine field legumes exhibiting mild symptoms and in one tomato with a necrotic syndrome contained a functional necrogenic motif; therefore, they were grouped within the necrogenic group of CMV-satRNAs. The necrotic phenotype was expressed in all legume CMV isolates containing necrogenic satRNAs when mechanically inoculated onto tomato plants. To our knowledge, this is the first observation that legumes host necrogenic CMV-satRNAs. The possible role of legumes in the epidemiology of CMV and necrogenic satRNA complex is discussed.

scholarly journals Frequent Reassortments May Explain the Genetic Heterogeneity of Rotaviruses: Analysis of Finnish Rotavirus Strains

2002 ◽  
Vol 76 (23) ◽  
pp. 11793-11800 ◽  
Author(s):  
Leena Maunula ◽  
Carl-Henrik von Bonsdorff
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Heterogeneity ◽  
The Other ◽  
Nucleotide Sequencing ◽  
Genetic Reassortment ◽  
Genetic Clusters ◽  
Virus Isolates

ABSTRACT The predominant rotavirus electropherotypes (e-types) during 17 epidemic seasons (1980 through 1997) in Finland were established, and representative virus isolates were studied by nucleotide sequencing and phylogenetic analysis. The virus isolates were either P[8]G1 or P[8]G4 types. The G1 and G4 strains formed one G1 lineage (VP7-G1-1) and one G4 lineage, respectively. Otherwise, they belonged to two P[8] lineages (VP4-P[8]-1 and -2) unrelated to their G types. Phylogenetic analysis of partial sequences of all 11 RNA segments obtained from the strains also revealed genetic diversity among gene segments other than those defining P and G types. With the exception of segments 1, 3, and 10, the sequences of the other segments could be assigned to 2 to 4 different genetic clusters. The results of this study suggest that, in addition to the RNA segments encoding VP4 and VP7, the other RNA segments may segregate independently as well. In total, the 9 predominant e-types represented 7 different RNA segment combinations when the phylogenetic clusters of their 11 genes were determined. The extensive genetic diversity and number of e-types among rotaviruses are best explained by frequent genetic reassortment.

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