Full genomic characterization of a group C rotavirus isolated from a child in south Korea

Abstract

During an epidemiological survey of human rotavirus infection in Seoul, Korea, from 2010 to 2011, one isolate of group C rotavirus (GCRV), named CAU10-312, was detected in a 5-year-old child admitted to the hospital with acute gastroenteritis, and its complete genomic sequence was determined. The 11 gene segments of the strain possessed G4-P[2]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotypes. The genotype of strain CAU10-312 appears to be closely related to strains from Bangladesh (DhakaC13 and BS347), India (v508), and England (Bristol), but distinct from Far East Asian strains, Chinese (Wu82 and YNR001) and Japanese (OH567 and BK0830). These findings may clarify the relationship of the genetics, evolutionary biology, and epidemiology of GCRVs and suggest that two very distinct genotype strains are in circulation in the world.

Whole genome sequences of Japanese porcine species C rotaviruses reveal a high diversity of genotypes of individual genes and will contribute to a comprehensive, generally accepted classification system

“…Whole genome analyses are useful for researching rotavirus evolution, including gene reassortment events and interspecies transmission, as well as following up epidemic and nosocomial transmission events. To our knowledge, whole genome sequences of many strains were analyzed in human RVC (Baek et al, 2013;Chen et al, 2015;; however only a few RVC whole genome sequences are available in animals (Marton et al, 2015a, b;Soma et al, 2013). In porcine RVC, only one whole genome sequence is available to date (Bremont et al, 1992;Bremont et al, 1993;Qian et al, 1991).…”

Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment

“…Only 20 complete genome sequences were available at the time of database interrogation. (Baek et al, 2013;Marton et al, 2015;Yamamoto et al, 2011), the type I and type II backbones in human RVCs appeared well conserved, and the two Italian RVC strains were found to be representative members of the two major genome configurations. The origin of VP3 genetic diversity in human RVCs is unclear.…”

“…Genotype designation was assigned to all gene segments of RVC on the basis of previous literature (Jiang et al, 1999;Martella et al, 2007;Matthijnssens et al, 2008;Baek et al, 2013) and lineage numbers were allocated according to Yamamoto et al (2011). Nucleotide intragenotypic cut-off values for each gene segment were calculated with Geneious v6.2 software package (Kearse et al, 2012).…”

“…The limited number of genomic sequence data on RVCs hinders the establishment of a proper classification system for complete genomic designation of RVC strains (Mawatari et al, 2014;Moutelíkov a et al, 2014), similar to the classification system developed for RVAs (Matthijnssens et al, 2008). Implementing a classification system based on the 11 genome segments would be important to better understand the epidemiology of RVC infections (Baek et al, 2013;Marton et al, 2015;Yamamoto et al, 2011;Zhirakovskaia et al, 2016). Available genome sequence information suggests that at least two major human lineages can be distinguished based on backbone gene combinations.…”

Reassortant human group C rotaviruses in Hungary

“…breaks associated with RVC have been also reported, 23 predominantly from Japan (Adah et al, 2002;Baek et al, 2013;24 Bányai et al, 2006;Esona et al, 2008;Hamano et al, 1999;25 Kumazaki and Usuku, 2014;Medici et al, 2009;Rodger et al, 26 1982;Schnagl et al, 2004). Methods to detect and differentiate 27 RVC infection from gastroenteritis caused by other rotavirus spe-28 cies rely on antigen detection, genomic RNA fingerprinting and 29 reverse transcription (RT)-PCR coupled with nucleotide sequencing 30 (Fujii et al, 1992;Gouvea et al, 1991;Khamrin et al, 2011;Meleg 31 et al, 2008;Rodger et al, 1982).…”