New oligonucleotide primers for P-typing of rotavirus strains: Strategies for typing previously untypeable strains

Simmonds, Mirjam Kühne; Armah, George; Asmah, Richard Harry; Banerjee, Indrani; Damanka, Susan; Esona, Mathew D.; Gentsch, Jon R.; Gray, Jim; Kirkwood, Carl D.; Page, Nicola; Iturriza‐Gómara, Miren

doi:10.1016/j.jcv.2008.02.011

Cited by 154 publications

(141 citation statements)

References 27 publications

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“…The extracted RNA was used for RT-PCR using specific VP7 and VP4 consensus primer pairs (Das et al, 1994;Simmonds et al, 2008). Viral RNA was heated for 5 min at 97 C to denature the dsRNA segments and was quickly placed back on ice.…”

Section: Methodsmentioning

confidence: 99%

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Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Moussa

Fredj

Fodha

et al. 2016

Journal of Medical Microbiology

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Group A rotavirus (RVA) represents the most important aetiological agent of diarrhoea in children worldwide. From January 2009 to December 2014, a multi-centre study realized through 11 Tunisian cities was undertaken among children aged <5 years consulting or hospitalized for acute gastroenteritis. A total of 1127 faecal samples were collected. All samples were screened by ELISA for the presence of RVA antigen. RVA-positive samples were further analyzed by PAGE and used for G/P-genotyping by semi-nested multiplex RT-PCR. Globally, 270 specimens (24 %) were RVA-positive, with peaks observed annually between November and March. Nine different electropherotypes could be visualized by PAGE, six with a long profile (173 cases) and two with a short one (seven cases). Mixed profiles were detected in two cases. Among the 267 VP7 genotyped strains, the predominant G-genotype was G1 (39.6 %) followed by G3 (22.2 %), G4 (13 %), G9 (11.5 %), G2 (5.2 %) and G12 (5.2 %). Among the 260 VP4 genotyped strains, P[8] genotype was the predominant (74. 9 %). Uncommon G/Pgenotype combinations, mixed infections and untypeable strains were also detected. This is the first report, in Tunisia, of multiple detection of an emerging human RVA strain, G12 genotype. This study highlighted the need for maintaining active surveillance of emerging strains in Northern Africa.

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Section: Methodsmentioning

confidence: 99%

“…Specific primers (consensus primers VP4F/VP4R) (Simmonds et al, 2008) were used to amplify the VP8* gene which was then differentiated into VP4 genotypes by a cocktail of specific primers designed for the human VP4 genotypes P[4], P [6], P[8], P[9] and P[10] (Gentsch et al, 1992;Iturriza-Gomara et al, 2000;Simmonds et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Moussa

Fredj

Fodha

et al. 2016

Journal of Medical Microbiology

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“…Viral RNA was extracted from 10% faecal suspensions in balanced salt solution with the guanidinium isothiocyanate/silica method [Boom et al, 1990]. Complementary DNA was synthesized from the extracted viral RNA using reverse transcriptase enzyme in the presence of random hexamers [Iturriza-Gómara et al, 1999] and was further characterised by semi-nested multiplex polymerase chain reaction (PCR) using specific primers for the VP7 and VP4 genes to identify the G and P types respectively [Gentsch et al, 1992;Gouvea et al, 1990;Iturriza-Gómara et al, 2000a;IturrizaGómara et al, 2004;Simmonds et al, 2008]. Amplification products were analysed by electrophoresis using a 2% agarose gel stained with ethidium bromide in TBE buffer.…”

Section: Methodsmentioning

confidence: 99%

Frequency, clinical characteristics, and genotype distribution of rotavirus gastroenteritis in Greece (2007–2008)

Koukou

Grivea

Roma

et al. 2010

Journal of Medical Virology

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Rotavirus is the leading cause of acute gastroenteritis among young children worldwide. A prospective multi‐center study was conducted (2007–2008) in five Pediatric Hospitals to determine the prevalence, the clinical characteristics, and genotype distribution of rotavirus infection in Greece. Faecal samples were examined for the presence of group A rotavirus antigen by immunochromatography. Rotavirus strains were subjected to G and P genotyping by reverse‐transcriptase polymerase chain reaction (PCR) and sequencing. A total of 393 children (216 boys) of median age 23 months, participated in the study. Rotavirus was the cause of acute gastroenteritis in 166 children, 42.3% (CI 95%, 37.4–47.1%) of non‐hospitalized and 47.8% (CI 95%, 41.7–53.9%) of hospitalized patients. Rotavirus gastroenteritis occurred between December and April in 78.6% of the cases. Most children with RVG (77.8%) were between 3 months and 3 years old. The mean value of Clark severity score was 12.9 ± 5.1 for RVG and 10.5 ± 4.9 for non‐RVG (P < 0.01). Genotypes were determined in 117 strains and their distribution was as following: G1P[8], 49%; G2P[4], 31%; G4P[8], 10%; G9P[8], 9%; and G8P[14], 1%. In conclusion, rotavirus is a frequent cause of acute gastroenteritis in Greece. The genotypes circulating are similar with those of other European countries. J. Med. Virol. 83:165–169, 2011. © 2010 Wiley‐Liss, Inc.

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“…Therefore, failure to type is most likely to be associated with technical issues and/or low viral load, although occasionally they may represent usual genotypes, particularly in those associated with an animal rotavirus G-or P-types [21][22][23][24][25][26]. The failure to identify G-types associated with P [6], P [9], P [10], P [11] and P [14] may be associated with the presence of unusual G-types for which G genotype-specific primers were not included in the study protocol.…”

Section: Distribution According To Gendermentioning

confidence: 99%

Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance network

Iturriza‐Gómara¹,

Dallman²,

Bányai³

et al. 2010

Epidemiol. Infect.

207

254

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SUMMARYEuroRotaNet, a laboratory network, was established in order to determine the diversity of co-circulating rotavirus strains in Europe over three or more rotavirus seasons from 2006/2007 and currently includes 16 countries. This report highlights the tremendous diversity of rotavirus strains co-circulating in the European population during three years of surveillance since 2006/ 2007 and points to the possible origins of these strains including genetic reassortment and interspecies transmission. Furthermore, the ability of the network to identify strains circulating with an incidence of o1% allowed the identification of possible emerging strains such as G8 and G12 since the beginning of the study ; analysis of recent data indicates their increased incidence.

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New oligonucleotide primers for P-typing of rotavirus strains: Strategies for typing previously untypeable strains

Cited by 154 publications

References 27 publications

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

Frequency, clinical characteristics, and genotype distribution of rotavirus gastroenteritis in Greece (2007–2008)

Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance network

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