Molecular characterization of group A rotavirus found in elderly patients in Ireland; predominance of G1P[8], continued presence of G9P[8], and emergence of G2P[4]

Divergence of group a rotavirus with genetic variations before and after introduction of rotavirus vaccines in northern Taiwan

Despite the development of vaccines in 2006, rotavirus is still a major cause of acute gastroenteritis worldwide. This study was performed to analyze the presence of circulating rotaviruses before and after the introduction of rotavirus vaccines to allow phylogenetic comparisons of vaccine strains in northern Taiwan.Rotavirus genotyping and sequencing of rotavirus VP7 and VP4 PCR products were performed by Reverse Transcriptase Polymerase Chain Reaction and DNA autosequencing. Phylogenies were constructed by the neighbor-joining and maximum-likelihood methods using CLUSTAL W software included in the MEGA software package (version 6.0).Between April 2004 and December 2012, a total of 101 rotavirus specimens from pediatric patients with acute gastroenteritis hospitalized in Chang Gung Children's Hospital were amplified, and their VP4 and VP7 sequences were determined. These 101 specimens consisted of 55 pre-vaccine strains (G1 [13, 23.6%], G2 [12, 21.8%], G3 [16, 29.1%], and G9 [14, 25.5%]) and 46 post-vaccine strains (G1 [25, 54.3%], G2 [12, 26.1%], G3 [5, 10.9%], and G9 [4, 8.7%]). The most common combination of the G and P types was G2P[4], accounting for 36% cases, followed by G9P[8] (25%), G1P[8] (20%), G3P[4] (15%), G3P[8] (10%), G1P[4] (5%), and G2P[8] (5%). Phylogenetic analysis showed that only the G1 and P[8] genotypes clustered in the same lineages with the rotavirus vaccine strains.Based on our results, the inclusion of G9, modified G2 and G3 with target lineages, and the combination G2P[4] and G9P[8] in the rotavirus vaccines in Taiwan is warranted as a vaccination strategy.

Unexpected predominance of rotavirus G9P[8] strain in Tunisian adult diarrheal patients

Introduction. Group A Rotavirus (RVA) is known to be a major cause of acute gastroenteritis (AGE) in children but its role as a potential pathogen in immunocompetent adults is probably underestimated.Aim. To compare RVA infections in patients from different age groups.Methodology. Fecal samples were collected from patients aged from birth to 65 years, hospitalized or consulting for AGE between 2015 and 2017. All samples were screened by RT-PCR for the detection of VP6 gene specific of RVA. RVA-positive samples were VP7 and VP4 genotyped using multiplex semi-nested RT-PCR. Full-length VP7 gene of G9-positive strains were sequenced and submitted for phylogenetic analysis.Results. Of 1371 stool specimens collected from children (<5 years; n=454), older children (5 to <15 years; n=316) and adults (15-65 years; n=601), 165 (12.0 %) were RVA-positive. RVA detection rates were significantly higher in children and adults than in older children (15.8 % and 12.1 Vs 6.3 %, respectively; P<0.001). While RVA infections were mostly detected during the coldest months in children, they were observed all year-round in patients aged >5 years. Although G1P[8] remained the most prevalent combination (41.7 %) detected in children, G9P[8] strains widely predominated in adults (58.1 %), followed by G2P[4] (12.9 %). All characterized G9 strains clustered in the modern lineage III.Conclusion. RVA play an important role in AGE not only in children but also in adults. The findings of a wide G9 predominance in patients >5 years highlights the need for continuing surveillance in both pediatric and mature populations.

Molecular characterization of group A rotavirus among children aged under 5 years in Tunisia, 2015-2017

The aim of the present study was to report the molecular characterization of human group A rotaviruses (RVAs) circulating in Tunisia. Stool specimens were collected from children under 5 years of age who had been hospitalized or were consulting for gastroenteritis in Tunisian hospitals between 2015 and 2017. All samples were screened by reverse-transcription polymerase chain reaction (RT-PCR) for the detection of the VP6 gene specific for RVA. RVA-positive samples were further analysed for G/P genotyping by semi-nested multiplex RT-PCR. Among 454 tested samples, 72 (15.8 %) were positive for RVA. G1P[8] was the most prevalent detected strain (41.7%), followed by G9P[8] (32.8%), G2P[4] (7.5%), G12P[8] (7.5%), G1P[6] (3.0%), G2P[8] (1.5%) and G3P[8] (1.5%), with mixed infections in 4.5 % of cases. In the absence of a national anti-rotavirus vaccination strategy, RVAs remain the primary aetiological agent for gastroenteritis in Tunisian children.

Viruses Associated With Foodborne Infections

Foodborne pathogens cause acute and chronic health outcomes of very different durations, severity and mortality, resulting in high costs and burdens to society. The issues of food safety and food poisoning are being increasingly emphasised, particularly in developed countries. Infection/contamination with many agents i.e., bacterial, parasitic and viral entities can result in foodborne illness. This article will focus mainly on viral agents of infection.

A range of different viruses can cause food poisoning/foodborne infection, and infection can result in a myriad of symptoms, ranging from mild, acute disease to chronic, debilitating disease and even death. Due to the inherent differences between bacteria and viruses, namely the fact that viruses do not replicate in food, while bacteria do, viruses are frequently difficult to detect. This is compounded by the fact that many of the viruses associated with enteric disease do not replicate in cell culture. These factors can lead to a lag between reporting, detection and analysis of foodborne viruses versus bacterial agents. Despite these constraints, it is now evident that there are both well-established and emerging viruses implicated in foodborne infections, and the role of molecular detection and characterisation is becoming increasingly important.

Restriction fragment length polymorphism analysis of rotavirus VP7-encoding gene from humans and animals of Northeast India: a relative study of Indian and global isolates

A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic relationship between 67 (29 Indian, 38 global) rotavirus isolates of human, bovine and porcine neonates. The assay involved direct digestion of RT-PCR amplified VP7 cDNAs with three restriction enzymes (VspI, HaeIII, NlaIV) independently. Forty-eight RFLP patterns were identified for all 67 strains, and of these 20 patterns were associated with Indian isolates. A correlation between the restriction patterns and G type was apparent through deduction of enzyme restriction sites from known sequences. Major G serotypes (G1, G2, G6, G8) with a few mixed types could be differentiated where there was a positive assortment of intrinsic serotypes from multiple host origin, and certain single or combined enzyme profiles were highly dominant in the population. Significant genetic variations were established between global and Indian isolates and none of the RFLP patterns were shared between them. These data suggest that the Indian wild-type rotavirus population is distinguishable based on the VP7 gene, and co-circulation of distinct strains in different hosts is foremost, indicating the possible likelihood of inter-species transmission.

Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: is there evidence of strain selection from vaccine pressure?

Comprehensive reviews of pre licensure rotavirus strain prevalence data indicated the global importance of six rotavirus genotypes, G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. Since 2006, two vaccines, the monovalent Rotarix (RV1) and the pentavalent RotaTeq (RV5) have been available in over 100 countries worldwide. Of these, 60 countries have already introduced either RV1 or RV5 in their national immunization programs. Post licensure vaccine effectiveness is closely monitored worldwide. This review aimed at describing the global changes in rotavirus strain prevalence over time. The genotype distribution of the nearly 47,000 strains that were characterized during 2007-2012 showed similar picture to that seen in the preceding period. An intriguing finding was the transient predominance of heterotypic strains, mainly in countries using RV1. Unusual and novel antigen combinations continue to emerge, including some causing local outbreaks, even in vaccinated populations. In addition, vaccine strains have been found in both vaccinated infants and their contacts and there is evidence for genetic interaction between vaccine and wild-type strains. In conclusion, the post-vaccine introduction strain prevalence data do not show any consistent pattern indicative of selection pressure resulting from vaccine use, although the increased detection rate of heterotypic G2P[4] strains in some countries following RV1 vaccination is unusual and this issue requires further monitoring.

Genetic diversity of porcine group A rotavirus strains in the UK

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This is the first study of rotavirus genotypes circulating in UK pigs.

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Rotavirus transmission between pigs and humans is not thought to be common in the UK.

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Human rotavirus genotype P[8] found in a UK pig.

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The uncommon rotavirus genotype P[32] is widespread in UK pig herds.

Rotavirus is endemic in pig farms where it causes a loss in production. This study is the first to characterise porcine rotavirus circulating in UK pigs. Samples from diarrheic pigs with rotavirus enteritis obtained between 2010 and 2012 were genotyped in order to determine the diversity of group A rotavirus (GARV) in UK pigs. A wide range of rotavirus genotypes were identified in UK pigs: six G types (VP7); G2, G3, G4, G5, G9 and G11 and six P types (VP4); P[6], P[7], P[8], P[13], P[23], and P[32]. With the exception of a single P[8] isolate, there was less than 95% nucleotide identity between sequences from this study and any available rotavirus sequences.

The G9 and P[6] genotypes are capable of infecting both humans and pigs, but showed no species cross-over within the UK as they were shown to be genetically distinct, which suggested zoonotic transmission is rare within the UK. We identified the P[8] genotype in one isolate, this genotype is almost exclusively found in humans. The P[8] was linked to a human Irish rotavirus isolate in the same year. The discovery of human genotype P[8] rotavirus in a UK pig confirms this common human genotype can infect pigs and also highlights the necessity of surveillance of porcine rotavirus genotypes to safeguard human as well as porcine health.

Rotavirus in adults, Brazil, 2004–2011: G2P[4] dominance and potential impact on vaccination

Objectives

The aim of this study was to monitor rotavirus (RV) infections in adults >18 years with acute gastroenteritis during 2004–2011 national Brazilian RV surveillance. In addition, to characterize the RV group A (RVA) strains in order to gain insight into the supposed vaccine selective pressure imposed to Brazilian children population.

Methods

A total of 2102 convenient fecal specimens were investigated by ELISA, PAGE, and RT-PCR.

Results

RV was detected in 203 (9.6%) of 2102 specimens, and showed a marked peak of detection in September. RVA infection was detected in 9.4% (197/2102) and RV group C (RVC) in 0.3% (6/2102). The most frequent genotypes detected in 2004 and 2005 were G9P[8] (38.5%; 5/13) and G1P[8] (54.5%; 6/11), respectively. The dominant genotype identified from 2006 to 2011 was G2P[4] (64.4%; 116/180). Detection rate varied during the 8-year period of the study from 0.7% to 12.9%.

Conclusion

The high detection rate of G2P[4] in adults provides further evidence that its dominance reflects the seasonality of RVA strains instead of the supposed selective advantage created by vaccination program. It also can be suggested that adult infections may serve as a reservoir to maintain RVA strains in childhood gastroenteritis. Considering the detection rate, the evident reduction of RVA frequency observed in children after vaccine introduction was not present in adults.

Circulation of group A rotaviruses among neonates of human, cow and pig: study from Assam, a north eastern state of India

Rotavirus (RV) infections are worldwide in distribution causing high morbidity and mortality in human and animal neonates. Human settlements in close proximity of animals aids for genetic re-assortment of the virus by interspecies transmission and consequent emergence of new viral antigenic strain. Therefore, the present study was designed to explore RV incidence in a single approach from human and animal neonates sharing similar environment. Altogether, 200 diarrheal samples from children (50), piglets (80) and calves (70) were collected during the year of 2010-2012 from various locality, farms and hospitals, initially screened through monoclonal antibody based enzyme immunoassay followed by RNA-PAGE and VP7 gene amplification by Reverse transcription PCR. The overall prevalence of rotavirus was found to be 41.5 % (83/200) where maximum numbers of positive cases were found in piglets (46.3 %) followed by human (40 %) and cow (37.1 %). Majority of samples demonstrated characteristic group A rotavirus (RVA) electropherotype of 4:2:3:2 pattern. Moreover, RNA profiles of seven samples from piglets and calves revealed variation in the migration pattern of class II, III and class IV segments. The study, for the first time from the valley, detected 43.7 % of neonatal RVA positive cases from human and animal sharing similar setting. The variation in RNA migration pattern in seven cases signifies tentative cases of gene re-assortment that warrant further evaluation.