scholarly journals Phylogenetic Characterization of the 5′ Untranslated Region of Untypable HCV Genotypes Circulating in Pakistan

Intervirology ◽  
2020 ◽  
pp. 1-6
Author(s):  
Usman Ghani ◽  
Irshad Ur Rehman ◽  
Muhammad Ali ◽  
Ayyaz Khan ◽  
Sana Ullah ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Phylogenetic Characterization ◽  
Genotype Identification ◽  
Molecular Phylogenetic ◽  
Hcv Genotyping ◽  
Viral Isolates ◽  
Genotype 3A

<b><i>Introduction:</i></b> Commercial methods for HCV genotyping is challenged by the increased prevalence of untypable genotypes in Pakistan. <b><i>Objective:</i></b> The aim of the current study was to perform nucleotide sequencing of 5′ UTR region for genotyping of viral isolates circulating in Peshawar, Pakistan. <b><i>Methods:</i></b> The total number of commercially untypable samples were 94 in which 18 samples were sequenced for the characterization of 5′ UTR region. Post-sequencing analysis was performed for genotype identification (<i>n</i> = 18) and molecular phylogenetic analysis. <b><i>Results:</i></b> The current study reveals different genotypes, that is, 10/18 viral isolates were found to be genotype 3a (55.55%), 3 isolates (genotype 3b, 16.66%), 2 isolates (genotype 6h/6g, 11.11%), 2 (6g/d, 11.11%), and 1 sample (genotype 1c, 5.55%). In addition, genotype 3a is the dominant representative of HCV circulating in Pakistan and has been increasing across the country. <b><i>Conclusion:</i></b> The current study also reveals that genotype 6 (2 were genotype 6h/6g and 2 were 6g/d) is also circulating in Pakistan and not restricted to South China and Hong Kong.

scholarly journals Molecular phylogenetic characterization of common murine rodents from Manipur, Northeast India

2015 ◽  
Vol 90 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Dhananjoy S. Chingangbam ◽  
Joykumar M. Laishram ◽  
Hitoshi Suzuki
Keyword(s):  
Northeast India ◽  
Phylogenetic Characterization ◽  
Molecular Phylogenetic ◽  
Murine Rodents

scholarly journals Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease

2008 ◽  
Vol 66 (3) ◽  
pp. 579-589 ◽  
Author(s):  
Panagiotis G. Xenoulis ◽  
Blake Palculict ◽  
Karin Allenspach ◽  
Jörg M. Steiner ◽  
Angela M. Van House ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Small Intestine ◽  
Microbial Communities ◽  
Bowel Disease ◽  
Phylogenetic Characterization ◽  
Molecular Phylogenetic ◽  
Inflammatory Bowel

Morphological, physiological, molecular and phylogenetic characterization of new environmental isolates of Acanthamoeba spp. from the region of Bratislava, Slovakia

Biologia ◽  
2010 ◽  
Vol 65 (1) ◽  
Author(s):  
Viera Nagyová ◽  
Arpád Nagy ◽  
Štefan Janeček ◽  
Jozef Timko
Keyword(s):  
Pcr Amplification ◽  
Temperature Tolerance ◽  
Environmental Isolates ◽  
Environmental Distribution ◽  
Pathogenic Potential ◽  
Phylogenetic Characterization ◽  
Group I ◽  
Genotype Identification

AbstractProtozoa of the genus Acanthamoeba are organisms that can be generally found in the environment. The focus of this study is the detection of the presence of Acanthamoeba in different water sources and samples taken from airconditioning units. The identification of Acanthamoeba isolates was based on the morphology of cysts and trophozoites as well as PCR amplification with a genus specific primer pair JDP1 and JDP2. Growth characteristics and temperature tolerance were monitored. The pathogenic potential was tested in vitro on Vero cell cultures. Genotype identification was based on the sequencing of the GTSA.B1 PCR amplimer of 18S ribosomal DNA. The data obtained revealed that the isolates belong to T3 and T4 genotypes. One T3 and one T4 isolate contain a group I intron. The 933 base pair intron found in a genotype T4 isolate is considerably larger compared to formerly described introns of Acanthamoeba griffini (genotype T3) and A. Lenticulata (genotype T5). This is the first report detailing the environmental distribution of the Acanthamoeba genotypes in the region of Bratislava, Slovakia.

scholarly journals Diversity of Wolbachia Endosymbionts in Heteropteran Bugs

2003 ◽  
Vol 69 (10) ◽  
pp. 6082-6090 ◽  
Author(s):  
Yoshitomo Kikuchi ◽  
Takema Fukatsu
Keyword(s):  
Phylogenetic Analysis ◽  
Fragment Length Polymorphism ◽  
Universal Primers ◽  
Multiple Infections ◽  
Polymorphism Analysis ◽  
Phylogenetic Characterization ◽  
Molecular Phylogenetic ◽  
Pcr Products ◽  
Horizontal Transfers

ABSTRACT An extensive survey of Wolbachia endosymbionts in Japanese terrestrial heteropteran bugs was performed by PCR detection with universal primers for wsp and ftsZ genes of Wolbachia, cloning of the PCR products, restriction fragment length polymorphism analysis of infecting Wolbachia types, and molecular phylogenetic characterization of all the detected Wolbachia strains. Of 134 heteropteran species from 19 families examined, Wolbachia infection was detected in 47 species from 13 families. From the 47 species, 59 Wolbachia strains were identified. Of the 59 strains, 16 and 43 were assigned to A group and B group in the Wolbachia phylogeny, respectively. The 47 species of Wolbachia-infected bugs were classified into 8 species with A infection, 28 species with B infection, 2 species with AA infection, 3 species with AB infection, 5 species with BB infection, and 1 species with ABB infection. Molecular phylogenetic analysis showed little congruence between Wolbachia phylogeny and host systematics, suggesting frequent horizontal transfers of Wolbachia in the evolutionary course of the Heteroptera. The phylogenetic analysis also revealed several novel lineages of Wolbachia. Based on statistical analyses of the multiple infections, we propose a hypothetical view that, in the heteropteran bugs, interactions between coinfecting Wolbachia strains are generally not intense and that Wolbachia coinfections have been established through a stochastic process probably depending on occasional horizontal transfers.

scholarly journals Evidence of independent introductions of RHDV2 strains in Poland based on the genome analysis of viral isolates from 2016–2018

2021 ◽  
Author(s):  
Andrzej Fitzner ◽  
Andrzej Kesy ◽  
Krzysztof Bulenger ◽  
Wieslaw Niedbalski
Keyword(s):  
Sequence Similarity ◽  
Structural Proteins ◽  
Genome Sequences ◽  
Phylogenetic Characterization ◽  
Vp60 Gene ◽  
Reference Sequences ◽  
Sequence Encoding ◽  
Domestic Rabbits ◽  
Viral Isolates

The aim of this study was the molecular epidemiology of independently introduced RHDV2 strains in Poland. The nucleotide sequences of RHDV2 diagnosed in domestic rabbits in 2018 in the voivodeships of Swietokrzyskie (strain PIN), Malopolskie (strain LIB) and Mazowieckie (strain WAK), and RHDVa from 2015 (strain F77-3) recognized in wild rabbits in Kujawsko-Pomorskie voivodeship were compared to the genome sequences of the first native RHDV2 strains from 2016–2017. The reference sequences available in public databases, the representative for a classical RHDV (G1-G5 genogroups), RHDVa (G6), non-pathogenic caliciviruses (RCV, GI.3 and GI.4) as well as original and recombinant RHDV2 isolates were included for this analysis. Nucleotide sequence similarity among the most distanced RHDV2 strains isolated in Poland in 2018 was from 92.3% to 98.2% in the genome sequence encoding ORF1, ORF2 and 3’UTR, between 94.8–98.7% in the VP60 gene and between 91.3-98.1% in non-structural proteins (NSP) region. The diversity between three RHDV2 and RHDVa from 2015 was up to 16.3% in the VP60 region. Similarities are shown for the VP60 tree within the RHDV2 group, however, the nucleotide analysis of NSP region revealed the differences between older and new native RHDV2 strains. The Polish RHDV2 isolates from 2016-2017 clustered together with RHDV G1/RHDV2 recombinants, first identified in the Iberian Peninsula in 2012, while all strains from 2018 are close to the original RHDV2. The F77-3 strain clustered to well supported RHDVa (G6) genetic group, together with other Polish and European RHDVa isolates. Based on the results of phylogenetic characterization of RHDV2 strains detected in Poland between 2016–2018 and the chronology of their emergence it can be concluded that RHDV2 strains of 2018 and RHDV2 strains of 2016–2017 were introduced independently thus confirming their different origin and simultaneous pathway of spreading.

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