scholarly journals First isolation and whole-genome characterization of a G9P[14] rotavirus strain from a diarrheic child in Egypt

2020 ◽  
Vol 101 (9) ◽  
pp. 896-901
Author(s):  
Ashraf Shoeib ◽  
Daniel E. Velasquez Portocarrero ◽  
Yuhuan Wang ◽  
Baoming Jiang
Keyword(s):  
Interspecies Transmission ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genome Characterization ◽  
Animal Virus ◽  
Genotype Constellation ◽  
Group A ◽  
First Time ◽  
Unique Genotype

An unusual group A rotavirus (RVA) strain (RVA/Human-tc/EGY/AS997/2012/G9[14]) was isolated for the first time in a faecal sample from a 6-month-old child who was hospitalized for treatment of acute gastroenteritis in Egypt in 2012. Whole-genome analysis showed that the strain AS997 had a unique genotype constellation: G9-P[14]-I2-R2-C2-M2-A11-N2-T1-E2-H1. Phylogenetic analysis indicated that the strain AS997 had the consensus P[14] genotype constellation with the G9, T1 and H1 reassortment. This suggests either a mixed gene configuration originated from a human Wa-like strain and a P[14]-containing animal virus, or that this P[14] could have been acquired via reassortment of human strains only. The study shows the possible roles of interspecies transmission and multiple reassortment events leading to the generation of novel rotavirus genotypes and underlines the importance of whole-genome characterization of rotavirus strains in surveillance studies.

scholarly journals Whole genomic analysis of a porcine-like human G5P[6] rotavirus strain isolated from a child with diarrhoea and encephalopathy in Japan

2013 ◽  
Vol 94 (7) ◽  
pp. 1568-1575 ◽  
Author(s):  
Satoshi Komoto ◽  
Yoshimasa Maeno ◽  
Mayuko Tomita ◽  
Tsuyoshi Matsuoka ◽  
Masaharu Ohfu ◽  
...  
Keyword(s):  
Stool Specimen ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Asian Countries ◽  
Dynamic Interactions ◽  
Genotype Constellation ◽  
Porcine Rotavirus ◽  
Porcine Origin ◽  
Unique Genotype

An unusual rotavirus strain, Ryukyu-1120, with G5P[6] genotypes (RVA/Human-wt/JPN/Ryukyu-1120/2011/G5P[6]) was identified in a stool specimen from a hospitalized child aged 4 years who showed diarrhoea and encephalopathy. In this study, we sequenced and characterized the complete genome of strain Ryukyu-1120. On whole genomic analysis, this strain was found to have a unique genotype constellation: G5-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1. The VP6 and NSP1 genotypes I5 and A8 are those commonly found in porcine strains. Furthermore, phylogenetic analysis indicated that each of the 11 genes of strain Ryukyu-1120 appeared to be of porcine origin. Thus, strain Ryukyu-1120 was found to have a porcine rotavirus genetic backbone and is likely to be of porcine origin. To our knowledge, this is the first report of whole-genome-based characterization of the emerging G5P[6] strains in Asian countries. Our observations will provide important insights into the origin of G5P[6] strains and the dynamic interactions between human and porcine rotavirus strains.

scholarly journals Isolation and characterization of a rare group A rotavirus G13P[18] strain from a diarrhoeic foal in Japan

2020 ◽  
Vol 101 (8) ◽  
pp. 800-805
Author(s):  
Manabu Nemoto ◽  
Hidekazu Niwa ◽  
Hiroshi Kida ◽  
Tohru Higuchi ◽  
Yasuhiro Orita ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Group A Rotavirus ◽  
Isolation And Characterization ◽  
Genotype Constellation ◽  
Group A ◽  
First Time ◽  
Rare Group

A rare genotype G13P[18] group A rotavirus (RVA/Horse-tc/JPN/MK9/2019/G13P[18]) was isolated from a diarrhoeic foal for the first time in 28 years. The genotype constellation of the virus was assigned to G13-P[18]-I6-R9-C9-M6-A6-N9-T12-E14-H11 and was the same as that of the first isolated strain, RVA/Horse-tc/GBR/L338/1991/G13P[18]. Phylogenetic analysis suggests that the virus is related to RVA/Horse-tc/GBR/L338/1991/G13P[18] and is distant from typical equine rotaviruses of the G3P[12] and G14P[12] genotypes.

scholarly journals Detection and Whole-Genome Characterization of a G8P[1] Group A Rotavirus Strain from Deer

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Srivishnupriya Anbalagan ◽  
Jessica Peterson
Keyword(s):  
Whole Genome ◽  
Genome Characterization ◽  
First Report ◽  
Rotavirus A ◽  
Group A Rotavirus ◽  
Group A

Rotavirus A strain 14-02218-2, with genome constellation G8P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, was isolated from newborn fawns. The 14-02218-2 rotavirus strain is related to bovine and bovine-like rotavirus strains. To our knowledge, this is the first report on whole-genome-based characterization of a deer rotavirus G8P[1] strain.

The first detection and whole genome characterization of the G6P[15] group A rotavirus strain from roe deer

2016 ◽  
Vol 191 ◽  
pp. 52-59 ◽  
Author(s):  
Urska Jamnikar-Ciglenecki ◽  
Urska Kuhar ◽  
Sabina Sturm ◽  
Andrej Kirbis ◽  
Nejc Racki ◽  
...  
Keyword(s):  
Roe Deer ◽  
Whole Genome ◽  
Genome Characterization ◽  
Group A Rotavirus ◽  
Group A

scholarly journals Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4

2021 ◽  
Vol 11 ◽  
Author(s):  
Fortunate Mokoena ◽  
Mathew Dioh Esona ◽  
Luyanda Mapaseka Seheri ◽  
Martin Munene Nyaga ◽  
Nonkululelo Bonakele Magagula ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Sub Saharan Africa ◽  
Interspecies Transmission ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Eastern Ethiopia ◽  
Single Strain ◽  
Ion Torrent Pgm ◽  
Genotype Constellation ◽  
Genotype 2

Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.

scholarly journals Whole-genome characterization of hemolytic uremic syndrome-causing Shiga toxin-producing Escherichia coli in Sweden

Virulence ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 1296-1305
Author(s):  
Ying Hua ◽  
Milan Chromek ◽  
Anne Frykman ◽  
Cecilia Jernberg ◽  
Valya Georgieva ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hemolytic Uremic Syndrome ◽  
Shiga Toxin ◽  
Whole Genome ◽  
Genome Characterization ◽  
Uremic Syndrome

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.

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