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

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.

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

Virus Evolution ◽

10.1093/ve/veaa018 ◽

2020 ◽

Vol 6 (1) ◽

Cited By ~ 4

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.

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Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus in southern China from 2007 to 2014

Journal of Veterinary Science ◽

10.4142/jvs.2017.18.3.317 ◽

2017 ◽

Vol 18 (3) ◽

pp. 317 ◽

Cited By ~ 5

Author(s):

Qiwen Wu ◽

Zhili Li ◽

Guanqun Zhang ◽

Jianqiang Niu ◽

Xiduo Zeng ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Southern China ◽

Respiratory Syndrome Virus

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Genetic Diversity Analysis of Genotype 2 Porcine Reproductive and Respiratory Syndrome Viruses Emerging in Recent Years in China

BioMed Research International ◽

10.1155/2014/748068 ◽

2014 ◽

Vol 2014 ◽

pp. 1-13 ◽

Cited By ~ 21

Author(s):

Lei Zhou ◽

Xiaorong Yang ◽

Yuan Tian ◽

Shuoyan Yin ◽

Gang Geng ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Hypervariable Region ◽

Clinical Samples ◽

Respiratory Syndrome Virus ◽

Diversity Analysis ◽

Coding Region ◽

Genotype 2 ◽

Orf5 Sequences ◽

Complete Genomic

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by its extensive genetic diversity. Here we analyzed 101 sequences of NSP2 hypervariable region, 123 ORF3 sequences, and 118 ORF5 sequences from 128 PRRSV-positive clinical samples collected in different areas of China during 2008–early 2012. The results indicated that the amino acid identities of the three genes among these sequences were 87.6%–100%, 92.5%–100%, and 77%–100%, respectively. Meanwhile, 4 novel patterns of deletion and insertion in NSP2 region or GP5 were first found. The phylogenetic analysis on these 3 genes revealed that the Chinese PRRSV strains could be divided into three subgroups; majority of genes analyzed here were clustered in subgroup 3 with multiple branches; the strains with 30-aa deletion in NSP2-coding region were still the dominant virus in the field. Further phylogenetic analysis on four obtained complete genomic sequences showed that they were clustered into different branches with the Chinese corresponding representative strains. Our analyses suggest that the genetic diversity of genotype 2 PRRSV in the field displays a tendency of increasing in recent years in China, and the 30-aa deletion in NSP2-coding region should be no longer defined as the molecular marker of the Chinese HP-PRRSV.

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Analysis of Genetic Variation of Two NADC30-like Strains of Porcine Reproductive and Respiratory Syndrome Virus in China

The Open Virology Journal ◽

10.2174/1874357901711010090 ◽

2017 ◽

Vol 11 (1) ◽

pp. 90-97

Author(s):

Zhi Zhou ◽

Jiajun Wu ◽

Shuo Zhang ◽

Bo Hou ◽

Tao Han ◽

...

Keyword(s):

Genetic Diversity ◽

Amino Acids ◽

Phylogenetic Analysis ◽

Genetic Variation ◽

North America ◽

Untranslated Region ◽

Respiratory Syndrome Virus ◽

Nucleotide Deletion ◽

Complete Genomes ◽

Swine Herds

Background: NADC30-like strains of porcine reproductive and respiratory syndrome virus first appeared in Chinese swine herds in 2012. Objective and Method: To explore the possible genetic diversity of these strains, we sequenced and analyzed the complete genomes of two NADC30-like strains. These isolates shared 95.4% homology with NADC30. Result: The two strains displayed a discontinuous deletion of 131 amino acids in NSP2, mutations of amino acids in GP3 and GP5, and a 3-nucleotide deletion in the 3′ untranslated region. Phylogenetic analysis showed that the two isolates formed a new branch and clustered in a subgroup with NADC30 isolates from North America. Conclusion: We conclude that the above two NADC30-like strains may have been introduced from North America to China, where they acquired new genetic diversity.

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