scholarly journals Phylogenetic Classification of Global Porcine Deltacoronavirus (PDCoV) Reference Strains and Molecular Characterization of PDCoV in Taiwan

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1337
Author(s):  
Fu-Chun Hsueh ◽  
Feng-Yang Hsu ◽  
Yu-Hsuan Chen ◽  
Hsing-Chun Shih ◽  
Wei-Hao Lin ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Genetic Research ◽  
Watery Diarrhea ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Phylogenetic Characterization ◽  
Spike Gene ◽  
Phylogenetic Classification ◽  
Reference Strains

Porcine deltacoronavirus (PDCoV), a highly transmissible intestinal pathogen, causes mild to severe clinical symptoms, such as anorexia, vomiting and watery diarrhea, in piglets and/or sows. Since the first report of PDCoV infection in Hong Kong in 2012, the virus has readily disseminated to North America and several countries in Asia. However, to date, no unified phylogenetic classification system has been developed. To fill this gap, we classified historical PDCoV reference strains into two major genogroups (G-I and G-II) and three subgroups (G-II-a, G-II-b and G-II-c). In addition, no genetic research on the whole PDCoV genome or spike gene has been conducted on isolates from Taiwan so far. To delineate the genetic characteristics of Taiwanese PDCoV, we performed whole-genome sequencing to decode the viral sequence. The PDCoV/104-553/TW-2015 strain is closely related to the G-II-b group, which is mainly composed of PDCoV variants from China. Additionally, various mutations in the Taiwanese PDCoV (104-553/TW-2015) strain might be linked to the probability of recombination with other genogroups of PDCoVs or other porcine coronaviruses. These results represent a pioneering phylogenetic characterization of the whole genome of a PDCoV strain isolated in Taiwan in 2015 and will potentially facilitate the development of applicable preventive strategies against this problematic virus.

scholarly journals Genetic characterization of skull base chondrosarcomas

2015 ◽  
Vol 123 (4) ◽  
pp. 1036-1041 ◽  
Author(s):  
Hiroki Kanamori ◽  
Yohei Kitamura ◽  
Tokuhiro Kimura ◽  
Kazunari Yoshida ◽  
Hikaru Sasaki
Keyword(s):  
Skull Base ◽  
Case Series ◽  
Bone Neoplasms ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Genome Study ◽  
Skull Base Chordomas

OBJECT Although chondrosarcomas rarely arise in the skull base, chondrosarcomas and chordomas are the 2 major malignant bone neoplasms occurring at this location. The distinction of these 2 tumors is important, but this distinction is occasionally problematic because of radiological and histological overlap. Unlike chordoma and extracranial chondrosarcoma, no case series presenting a whole-genome analysis of skull base chondrosarcomas (SBCSs) has been reported. The goal of this study is to clarify the genetic characteristics of SBCSs and contrast them with those of chordomas. METHODS The authors analyzed 7 SBCS specimens for chromosomal copy number alterations (CNAs) using comparative genomic hybridization (CGH). They also examined IDH1 and IDH2 mutations and brachyury expression. RESULTS In CGH analyses, the authors detected CNAs in 6 of the 7 cases, including chromosomal gains of 8q21.1, 19, 2q22-q32, 5qcen-q14, 8q21-q22, and 15qcen-q14. Mutation of IDH1 was found with a high frequency (5 of 7 cases, 71.4%), of which R132S was most frequently mutated. No IDH2 mutations were found, and immunohistochemical staining for brachyury was negative in all cases. CONCLUSIONS To the best of the authors' knowledge, this is the first whole-genome study of an SBSC case series. Their findings suggest that these tumors are molecularly consistent with a subset of conventional central chondrosarcomas and different from skull base chordomas.

First isolation and characterization of Brucella suis from yak

Genome ◽  
2020 ◽  
Vol 63 (8) ◽  
pp. 397-405
Author(s):  
Xiaowen Yang ◽  
Ning Wang ◽  
Xiaofang Cao ◽  
Pengfei Bie ◽  
Zhifeng Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health And Safety ◽  
Host Cells ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Qinghai Province ◽  
Isolation And Characterization ◽  
Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

scholarly journals Ornithobacterium rhinotracheale: MALDI-TOF MS and Whole Genome Sequencing Confirm That Serotypes K, L and M Deviate from Well-Known Reference Strains and Numerous Field Isolates

2021 ◽  
Vol 9 (5) ◽  
pp. 1006
Author(s):  
Merima Alispahic ◽  
Lukas Endler ◽  
Michael Hess ◽  
Claudia Hess
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Identification And Characterization ◽  
Reference Strains ◽  
Ornithobacterium Rhinotracheale ◽  
Tof Ms

Ornithobacterium rhinotracheale is one of the most important bacterial agents of respiratory diseases in poultry. For correct identification and characterization of this fastidious bacterium, reliable diagnostic tools are essential. Still, phenotypic tests are used to identify O. rhinotracheale and serotyping is the most common method for characterization, despite known drawbacks and disadvantages such as divergent results, cross-reactivity between strains, or the non-typeability of strains. The intention of the present study was to evaluate MALDI-TOF MS and whole genome sequencing for the identification and characterization of O. rhinotracheale. For this purpose, a selection of 59 well-defined reference strains and 47 field strains derived from outbreaks on Austrian turkey farms were investigated by MALDI-TOF MS. The field strains originated from different geographical areas in Austria with some of the isolates derived from multiple outbreaks on farms within a year, or recurrent outbreaks over several years. MALDI-TOF MS proved a suitable method for identification of O. rhinotracheale to genus or species level except for 3 strains representing serotypes M, K and F. Phylogenetic analysis showed that most strains grouped within one cluster even though they were comprised of different serotypes, while serotypes F, K, and M clearly formed a different cluster. All field isolates from turkey farms clustered together, independent of the origin of the isolates, e.g., geographical area, multiple outbreaks within a year or recurrent outbreaks over several years. Whole genome sequencing of serotype M, K and F strains confirmed the extraordinary status and deviation from known fully-sequenced strains due to a lack of sequence similarity. This was further confirmed by alignments of single genes (16S-RNA and rpoB) and multilocus sequence typing although the demarcation was less obvious. Altogether, the results indicate that these three serotypes belong to a different species than O. rhinotracheale, and might even be members of multiple new species.

scholarly journals Genetic and phylogenetic characterization of genome segments 2 and 6 of bluetongue virus isolates in Japan from 1985 to 2008

2012 ◽  
Vol 93 (7) ◽  
pp. 1465-1473 ◽  
Author(s):  
Hiroaki Shirafuji ◽  
Tohru Yanase ◽  
Tomoko Kato ◽  
Makoto Yamakawa
Keyword(s):  
Bluetongue Virus ◽  
Phylogenetic Analyses ◽  
Control Measures ◽  
Asia Pacific ◽  
Segment Length ◽  
Genetic Characteristics ◽  
Phylogenetic Characterization ◽  
Partial Correlations ◽  
Different Origins

This study conducted genetic and phylogenetic analyses of genome segments 2 and 6 (Seg-2 and Seg-6), which encode serotype-specific structural proteins of the outer capsid, of bluetongue virus (BTV) isolated in Japan from 1985 to 2008. The Japanese strains of BTV were clearly sorted into six groups by several genetic characteristics of Seg-2, including segment length, ORF length and 5′- and 3′-terminal sequences, and were identified as serotypes 2, 3, 9, 12, 16 and 21 by phylogenetic comparisons with Seg-2 of reference and field strains of serotypes 1–24. In contrast, phylogenetic comparisons of Seg-6 also revealed some variations among the Japanese strains and partial correlations of the serotypes between the Japanese strains and the reference or field strains. Thus, the results revealed that at least six serotypes of BTV were isolated in Japan and that there were some variations in the genetic and phylogenetic characteristics of Seg-2 and Seg-6 among the Japanese strains, suggesting that BTV of several different origins has appeared sporadically in Japan. These data will be beneficial for understanding BTV epidemiology and taking better control measures against bluetongue in Japan and its neighbouring countries in the Asia-Pacific region.

Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients

2019 ◽  
Author(s):  
Farida BEHZADIAN ◽  
Elham MOASSER ◽  
Parviz OWLIA ◽  
Horieh SADERI
Keyword(s):  
Influenza A ◽  
Clinical Symptoms ◽  
Geographical Location ◽  
Neighbor Joining ◽  
M Gene ◽  
Phylogenetic Characterization ◽  
Nasal Swabs ◽  
Relationship Of ◽  
Close Relatedness

Background: A few studies have been done on the molecular analysis of Iranian influenza A isolates M gene. Methods: In 2014, nasal swabs collected from outpatients with clinical symptoms in the hospital clinics of Tehran, Iran were subjected for influenza detection and subtyping using Real-Time RT-PCR. Sequence and phylogenetic analysis performed on four randomly selected isolates from each subtype (H1N1 and H3N2) using neighbor-joining method. Results: Phylogenetic dendrograms drawn based on M nucleotide sequence of H1N1 isolates showed close relatedness with Omanian isolates while the most isolates of H3N2 have clustered with Kuwait isolates and isolates from outside of geographical location. Amino acid sequence analysis showed S31N substitution in all isolates rendering the virus resistant to adamantanes. Conclusion: This study determined the sequence identity and phylogenetic relatedness of M gene sequence got from Iranian influenza A isolates to elucidate the modality of relationship of this gene in comparison with its counterparts from other regions.

scholarly journals First Glimpse into the Genomic Characterization of People from the Imperial Roman Community of Casal Bertone (Rome, First–Third Centuries AD)

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Flavio De Angelis ◽  
Marco Romboni ◽  
Virginia Veltre ◽  
Paola Catalano ◽  
Cristina Martínez-Labarga ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Analysis ◽  
Whole Genome ◽  
Waste Products ◽  
Genetic Characteristics ◽  
The Past ◽  
Genetic Components ◽  
Starting Point ◽  
Genomic Characterization

This paper aims to provide a first glimpse into the genomic characterization of individuals buried in Casal Bertone (Rome, first–third centuries AD) to gain preliminary insight into the genetic makeup of people who lived near a tannery workshop, fullonica. Therefore, we explored the genetic characteristics of individuals who were putatively recruited as fuller workers outside the Roman population. Moreover, we identified the microbial communities associated with humans to detect microbes associated with the unhealthy environment supposed for such a workshop. We examined five individuals from Casal Bertone for ancient DNA analysis through whole-genome sequencing via a shotgun approach. We conducted multiple investigations to unveil the genetic components featured in the samples studied and their associated microbial communities. We generated reliable whole-genome data for three samples surviving the quality controls. The individuals were descendants of people from North African and the Near East, two of the main foci for tannery and dyeing activity in the past. Our evaluation of the microbes associated with the skeletal samples showed microbes growing in soils with waste products used in the tannery process, indicating that people lived, died, and were buried around places where they worked. In that perspective, the results represent the first genomic characterization of fullers from the past. This analysis broadens our knowledge about the presence of multiple ancestries in Imperial Rome, marking a starting point for future data integration as part of interdisciplinary research on human mobility and the bio-cultural characteristics of people employed in dedicated workshops.

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