New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method

Group A rotaviruses (RVAs) infect a wide variety of mammalian and avian species. Animals act as a potential reservoir to RVA human infections by direct virion transmission or by contributing genes to reassortants. Here, we report the molecular characterization of a rare human RVA strain Ni17-46 with a genotype G15P[14], isolated in Japan in 2017 during rotavirus surveillance in a paediatric outpatient clinic. The genome constellation of this strain was G15-P[14]-I2-R2-C2-M2-A13-N2-T9-E2-H3. This is the first report of an RVA with G15 genotype in humans, and sequencing and phylogenetic analysis results suggest that human infection with this strain has zoonotic origin from the bovine species. Given the fact that this strain was isolated from a patient with gastroenteritis and dehydration symptoms, we must take into account the virulence of this strain in humans.

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Molecular characterization of group A rotaviruses detected in children with gastroenteritis in Ireland in 2006–2009

Epidemiology and Infection ◽

10.1017/s0950268811000306 ◽

2011 ◽

Vol 140 (2) ◽

pp. 247-259 ◽

Cited By ~ 18

Author(s):

O. CASHMAN ◽

P. J. COLLINS ◽

G. LENNON ◽

B. CRYAN ◽

V. MARTELLA ◽

...

Keyword(s):

Sequence Analysis ◽

Irish Population ◽

Surveillance Activity ◽

Human Rotavirus ◽

Group A Rotaviruses ◽

Group A ◽

Hospital Acquired ◽

Rotavirus Infections ◽

Pcr Genotyping

SUMMARYCommunity and hospital-acquired cases of human rotavirus are responsible for millions of gastroenteritis cases in children worldwide, chiefly in developing countries, and vaccines are now available. During surveillance activity for human rotavirus infections in Ireland, between 2006 and 2009, a total of 420 rotavirus strains were collected and analysed. Upon either PCR genotyping and sequence analysis, a variety of VP7 (G1–G4 and G9) and VP4 (P[4], P[6], P[8] and P[9]) genotypes were detected. Strains G1P[8] were found to be predominant throughout the period 2006–2008, with slight fluctuations seen in the very limited samples available in 2008–2009. Upon either PCR genotyping and sequence analysis of selected strains, the G1, G3 and G9 viruses were found to contain E1 (Wa-like) NSP4 and I1 VP6 genotypes, while the analysed G2 strains possessed E2 NSP4 and I2 VP6 genotypes, a genetic make-up which is highly conserved in the major human rotavirus genogroups Wa- and Kun-like, respectively. Upon sequence analysis of the most common VP4 genotype, P[8], at least two distinct lineages were identified, both unrelated to P[8] Irish rotaviruses circulating in previous years, and more closely related to recent European humans rotaviruses. Moreover, sequence analysis of the VP7 of G1 rotaviruses revealed the onset of a G1 variant, previously unseen in the Irish population.

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Molecular Characterization of a Subgroup Specificity Associated with the Rotavirus Inner Capsid Protein VP2

Journal of Virology ◽

10.1128/jvi.02492-07 ◽

2008 ◽

Vol 82 (6) ◽

pp. 2752-2764 ◽

Cited By ~ 17

Author(s):

Sarah M. McDonald ◽

John T. Patton

Keyword(s):

Monoclonal Antibody ◽

Capsid Protein ◽

Neutralizing Antibodies ◽

Bovine Rotavirus ◽

Single Region ◽

Molecular Determinants ◽

High Resolution Structure ◽

Group A Rotaviruses ◽

Group A

ABSTRACT Group A rotaviruses are classified into serotypes, based on the reactivity pattern of neutralizing antibodies to VP4 and VP7, as well as into subgroups (SGs), based on non-neutralizing antibodies directed against VP6. The inner capsid protein (VP2) has also been described as a SG antigen; however, little is known regarding the molecular determinants of VP2 SG specificity. In this study, we characterize VP2 SGs by correlating genetic markers with the immunoreactivity of the SG-specific monoclonal antibody (YO-60). Our results show that VP2 proteins similar in sequence to that of the prototypic human strain Wa are recognized by YO-60, classifying them as VP2 SG-II. In contrast, proteins not bound by YO-60 are similar to those of human strains DS-1 or AU-1 and represent VP2 SG-I. Using a mutagenesis approach, we identified residues that determine recognition by either YO-60 or the group A-specific VP2 monoclonal antibody (6E8). We found that YO-60 binds to a conformationally dependent epitope that includes Wa VP2 residue M328. The epitope for 6E8 is also contingent upon VP2 conformation and resides within a single region of the protein (Wa VP2 residues A440 to T530). Using a high-resolution structure of bovine rotavirus double-layered particles, we predicted these epitopes to be spatially distinct from each other and located on opposite surfaces of VP2. This study reveals the extent of genetic variation among group A rotavirus VP2 proteins and illuminates the molecular basis for a previously described SG specificity associated with the rotavirus inner capsid protein.

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Genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan in 2004–2005

Infection Genetics and Evolution ◽

10.1016/j.meegid.2006.10.002 ◽

2007 ◽

Vol 7 (2) ◽

pp. 247-253 ◽

Cited By ~ 12

Author(s):

Tung Gia Phan ◽

Pattara Khamrin ◽

Trinh Duy Quang ◽

Shuvra Kanti Dey ◽

Fumihiro Yagyu ◽

...

Keyword(s):

Acute Gastroenteritis ◽

Genetic Characterization ◽

Group A Rotavirus ◽

Group A

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Genetic characterization of coagulase-positive staphylococci isolated from healthy pigeons

Polish Journal of Veterinary Sciences ◽

10.1515/pjvs-2015-0081 ◽

2015 ◽

Vol 18 (3) ◽

pp. 627-634 ◽

Cited By ~ 5

Author(s):

M. Kizerwetter-Świda ◽

D. Chrobak-Chmiel ◽

M. Rzewuska ◽

A. Antosiewicz ◽

B. Dolka ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Genetic Relatedness ◽

Genetic Characterization ◽

Restriction Patterns ◽

Feral Pigeons ◽

Group A ◽

Biochemical Identification ◽

Group B ◽

Coagulase Positive Staphylococci

AbstractCoagulase-positive staphylococci (CoPS) are opportunistic veterinary pathogens, of whichStaphylococcus aureus,S. delphiniandS. intermediuscan be isolated from pigeons. The biochemical identification ofS. delphiniandS. intermediusisolates may be incorrect, because of their phenotypic similarity. The purpose of the present study was to isolate and identify CoPS from domestic and feral pigeons and to determine their genetic relatedness by PFGE. A total number of 31 isolates of CoPS were obtained, 15 were identified asS. delphinigroup B, six asS. aureus,four asS. delphinigroup A, three asS. intermediusand three asS. schleiferisubsp.coagulans. The results indicate that S.delphinigroup B is the predominant CoPS species among pigeons studied. PFGE restriction patterns ofS. delphinigroup A andS. delphinigroup B form separate clusters, demonstrating their genetic heterogeneity. Indistinguishable or very similar PFGE patterns observed amongS. delphinigroup B isolates from domestic and feral pigeons confirm the possibility of CoPS transmission between these birds.

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