G26P[19] rotavirus A strain causing acute gastroenteritis in the American continent

In Brazil, the rotavirus A genotype G26 was first identified in suckling piglets, while the P[19] genotype has not been identified in any animal species so far. This report details the genetic characterisation of a G26P[19] RVA strain detected from an eight year-old child, vaccinated with Rotarix^®, hospitalised with acute diarrhoeal disease in Rio de Janeiro in 2015. Most likely, the genome constellation (I5-R1-C1-M1-A8-N1-T1-E1-H1) observed in the G26P[19] Brazilian strain was a result of interspecies transmission events between humans and pigs. In addition, a rearrangement in the NSP5 gene was observed downstream of the 3’ non-coding region.

Key words:
rotavirus A; G26P(19); reassortment; rearrangement

Authorship

Mariela M Gómez ⁺+ Corresponding author: marie@ioc.fiocruz.br / marielamartinezgomez@gmail.com

Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz-FiocruzBrazilRio de Janeiro, RJ, BrazilFundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Virologia Comparada e Ambiental, Rio de Janeiro, RJ, Brasil

Marcelle FM da Silva

Eduardo M Volotão

Alexandre M Fialho

Christian S Mazzoco

Myrna S Rocha

Hospital Municipal Jesus, Rio de Janeiro, RJ, BrasilHospital Municipal JesusBrazilRio de Janeiro, RJ, BrazilHospital Municipal Jesus, Rio de Janeiro, RJ, Brasil

José Paulo G Leite

+ Corresponding author: marie@ioc.fiocruz.br / marielamartinezgomez@gmail.com

JPG and MMG - Conceptualisation; MMG - writing of the original draft; MMG, MFMS and EMV - methodology, interpretation of data, formal analysis, investigation, writing, review and editing; AMF and CSM - methodology, interpretation of the data; MSR - is the doctor who evaluated the patient and collected the stool sample. All authors participated in conducting the study had full access to the data, read and approved the final manuscript.

SCIMAGO INSTITUTIONS RANKINGS

Hospital Municipal Jesus, Rio de Janeiro, RJ, BrasilHospital Municipal JesusBrazilRio de Janeiro, RJ, BrazilHospital Municipal Jesus, Rio de Janeiro, RJ, Brasil

Figures | Tables

Figures (1)
Tables (1)

Thumbnail

Schematic representation of the structure of normal and rearranged NSP5 gene of Brazilian G26P[19] RVA strain (RVA/Human-wt/BRA/rj24598/2015/G26P[19]). Insertion of “AGTTAT” sequence at position 616; duplication of a 281 bp long nucleotide segment; *deletion of a nucleotide at position 733. NTR: non-translated region. The numbering of the nucleotides is in respect to the expected complete gene segment based on RVA/Pig-tc/USA/Gottfried/1975/G4P[6] NSP5 prototype sequence, accession number GU199491.

Thumbnail

TABLE
Genotype constellation comparison of Brazilian G26P[19] RVA (RVA/Human-wt/BRA/rj24598/2015/G26P[19]), and RVA reference strains of interest available at GenBank

Schematic representation of the structure of normal and rearranged NSP5 gene of Brazilian G26P[19] RVA strain (RVA/Human-wt/BRA/rj24598/2015/G26P[19]). Insertion of “AGTTAT” sequence at position 616; duplication of a 281 bp long nucleotide segment; *deletion of a nucleotide at position 733. NTR: non-translated region. The numbering of the nucleotides is in respect to the expected complete gene segment based on RVA/Pig-tc/USA/Gottfried/1975/G4P[6] NSP5 prototype sequence, accession number GU199491.

TABLE Genotype constellation comparison of Brazilian G26P[19] RVA (RVA/Human-wt/BRA/rj24598/2015/G26P[19]), and RVA reference strains of interest available at GenBank

Strain	Genotypes
Strain	VP7	VP4	VP6	VP1	VP2	VP3	NSP1	NSP2	NSP3	NSP4	NSP5
RVA/Human-wt/BRA/rj24598/2015/G26P[19]	G26	P[19]	I5	R1	C1	M1	A8	N1	T1	E1	H1
RVA/Human-wt/BRA/rj24598/2015/G26P[19]	990 bp	2328 bp	1263 bp	3233 bp	2701 bp	2508 bp	1494 bp	979 bp	1008 bp	723 bp	913 bp
RVA/Human-wt/VNM/30378/2009/G26P[19]	G26 (98,0%)	P[19] (98,6%)	I5 (98,0%)	R1 (85,7%)	C1 (90,2%)	M1 (88,3%)	A8 (79,3%)	N1 (94,0%)	T1 (98,2%)	E1 (97,4%)	H1 (92,5%)
RVA/Human-wt/NPL/07N1760/2007/G26P[19]	G26 (94,0%)	P[19] (93,8%)	I12	R1 (85,2%)	C1 (90,7%)	M1 (86,6%)	A8 (81,1%)	N1 (90,0%)	T1 (95,6%)	E1 (91,6 %)	H1 (93,7%)
RVA/Pig-wt/JPN/TJ4-1/2010/G26P[7]	G26	P[7]	X	X	X	X	X	X	X	X	X
RVA/Pig-wt/BRA/BRA381/2012/G26P[13]	G26 (93,8%)	P[13]	X	X	X	X	X	X	X	X	X
RVA/Pig-wt/IND/TRJRV/SW21/2014/G26P[X]	G26	X	X	X	X	X	X	X	X	X	X
RVA/Human-tc/THA/Mc323/1989/G9P[19]	G9	P[19] (93,5%)	I5	R1	C1	M1	A8	N1	T1	E1	H1
RVA/Pig-wt/BRA/ROTA09/2013/G3P[13]	G3	P[13]	I5 (89,4%)	R1 (92,5%)	C1 (93,1%)	M1 (91,2%)	A8 (94,9%)	N1 (87,5%)	T7	E1 (90,1%)	H1
RVA/Pig-wt/BRA/ROTA10/2013/G9P[23]	G9	P[23]	I5 (89,0%)	R1 (90,3%)	C1 (92,2%)	M1 (91,3%)	A8 (82,0%)	N1 (87,6%)	T1 (88,5%)	E1 (93,3%)	H1 (94,5%)
RVA/Pig-wt/BRA/ROTA17/2013/G5P[6]	G5	P[6]	I5 (91,0%)	R1 (91,5%)	C1 (93,0%)	M1 (89,7%)	A8 (91,4%)	N1 (87,8%)	T7	E1 (88,5%)	H1 (98,3%)

The length of the obtained sequences in this study are shown, the ones in italic means partial open reading frame (ORF) sequenced, otherwise the complete ORF was obtained. Percentage between brackets refers to the nucleotide identity value obtained after comparison with the rj24598 Brazilian strain, highest values are shown in bold. The “X” indicates the unavailability of sequence data in the GenBank. Gene segments of typical human Wa-like RVA origin are coloured green; blue is used to indicate gene segments of presumable porcine origin.

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G26P[19] rotavirus A strain causing acute gastroenteritis in the American continent

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[1] + Corresponding author: marie@ioc.fiocruz.br / marielamartinezgomez@gmail.com