Improved assay protocol for measurement of ammonia on the Roche Cobas 8000 automated platform.

INTRODUCTION: Ammonia is a metabolite of protein catabolism that, when elevated, may be toxic for tissues, especially for the central nervous system. Elevated ammonia in blood is an indicator and a prognostic factor for hepatic and kidney disease or inherited metabolic disorders in nitrogen metabolism. The accuracy of ammonia determination is influenced by sampling condition, handling, storage and assay itself. Our and other laboratories have been experiencing high frequencies sample error flags while measuring ammonia with glutamate dehydrogenase method on Roche Cobas 8000 platform. To reduce the number of error flags we adapted Roche NH3L protocol by incorporation of an additional onboard routine step for sample pre-dilution. MATERIAL AND METHODS: The AMC NH3L is an adaptation of Roche protocol that uses four fold pre-dilution of the sample in the rerun prior to the analysis. It was assessed for 1.occurrence of absorbance error flags, 2.precision, 3.correlation with Roche method and 4.interference by hemolysis, icterus and lipemia. RESULTS: The AMC NH3L adaptation demonstrates acceptable within-run and total precision. Comparison studies show no differences between the Roche rerun application and AMC NH3L adaptation. The AMC NH3L adaptation solves 78% of absorbance errors and for samples with high ammonia concentration is less affected by interferences from icterus and hemolysis than the Roche rerun application. CONCLUSION: The AMC NH3L adaptation is less prone to instrument error flags and for samples with high ammonia concentration, is more robust to endogenous interferences. The AMC NH3L adaptation is viable alternative to the Roche protocol for the ammonia measurement.

Predominance of G9P[8] rotavirus strains throughout France, 2014-2017.

OBJECTIVES: Group A rotavirus is a major cause of acute gastroenteritis in young children worldwide. A prospective surveillance network has been set up in France to investigate rotavirus infections and to detect the emergence of potentially epidemic strains. METHODS: From 2014 to 2017, rotavirus-positive stool samples were collected from 2394 children under 5 years old attending the paediatric emergency units of 13 large hospitals. Rotaviruses were genotyped by RT-PCR with regard to their outer capsid proteins VP4 and VP7. RESULTS: Genotyping of 2421 rotaviruses showed that after a marked increase in G9P[8] (32.1%) during the 2014-2015 season, G9P[8] became the predominant genotype during the 2015-2016 and 2016-2017 seasons with detection rates of 64.1% and 77.3%, respectively, whereas G1P[8] were detected at low rates of 16.8% and 6.6%, respectively. Phylogenetic analysis of the partial rotavirus VP7 and VP4 coding genes revealed that all of these G9P [8] strains belonged to the lineage III and the P [8]-3 lineage, respectively, and shared the same genetic background (G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) as did most of previously detected G9P[8] strains and particularly the emerging G9P[8] strains from the 2004-2005 season in France. CONCLUSIONS: G9P[8] rotaviruses have become the predominant circulating genotype for the first time since their emergence a decade ago. In the absence of rotavirus immunization programmes in France, our data give an insight into the natural fluctuation of rotavirus genotypes in a non-vaccinated population and provide a base line for a better interpretation of data in European countries with routine rotavirus vaccination.

Clinical severity and molecular characteristics of circulating and emerging rotaviruses in young children attending hospital emergency departments in France.

Group A rotavirus (RVA) is the leading cause of acute gastroenteritis in young children worldwide. A prospective surveillance network has been set up to investigate the virological and clinical features of RVA infections and to detect the emergence of potentially epidemic strains in France. From 2009 to 2014, RVA-positive stool samples were collected from 4800 children <5 years old attending the paediatric emergency units of 16 large hospitals. Rotaviruses were then genotyped by RT-PCR with regard to their outer capsid proteins VP4 and VP7. Genotyping of 4708 RVA showed that G1P[8] strains (62.2%) were predominant. The incidence of G9P[8] (11.5%), G3P[8] (10.4%) and G2P[4] (6.6%) strains varied considerably, whereas G4P[8] (2.7%) strains were circulating mostly locally. Of note, G12P[8] (1.6%) strains emerged during the seasons 2011-12 and 2012-13 with 4.1% and 3.0% prevalence, respectively. Overall, 40 possible zoonotic reassortants, such as G6 (33.3%) and G8 (15.4%) strains, were detected, and were mostly associated with P[6] (67.5%). Analysis of clinical records of 624 hospitalized children and severity scores from 282 of them showed no difference in clinical manifestations or severity in relation to the genotype. The relative stability of RVA genotypes currently co-circulating and the large predominance of P[8] type strains may ensure vaccine effectiveness in France. The surveillance will continue to monitor the emergence of new reassortants that might not respond to current vaccines, all the more so as all genotypes can cause severe infections in infants.

Detection and genotyping of group A rotaviruses isolated from sewage samples in Monastir, Tunisia between April 2007 and April 2010.

AIMS: To ascertain the viral load, the distribution of G and P types of group A rotaviruses (RV-A) in sewage samples and to compare strains in clinical, animal and environmental samples. METHODS AND RESULTS: During our study from April 2007 to April 2010, 518 samples of raw and treated sewage were collected from two biological sewage treatment plants (STPs) located in the Monastir region, Tunisia. RV-A was detected by real-time RT-PCR in 375 (72·4%) sewage samples. According to the quantification results of RV-A, it appears that the viral load in raw and treated sewage of the two STPs was quite similar (P = 0·735). The genotyping of RV-A strains detected in sewage samples showed a great diversity with 10 G types and 8 P types. Most of them were described as common in humans, but we also detected genotypes commonly found in animals. All the genotypes detected in two previous studies performed in our laboratory on clinical and bovine samples were also found in environmental samples. However, some genotypes commonly found in animal were only found in sewage samples. CONCLUSION: The comparison of environmental, clinical and animal data suggests that STPs may convey not only human sewage but also animal wastes, both of them contaminated with numerous RV-A strains which are not efficiently eliminated by the sewage treatment process and may spread to surface waters. SIGNIFICANCE AND IMPACT OF THE STUDY: This work demonstrates the potential release of human and animal RV-A into water sources, representing a public health risk, by inducing gastroenteritis in population, but also by increasing the risk of zoonotic transmission and formation of reassortant viruses which could get a higher infectious potential. Our findings also suggest that monitoring of sewage may provide an additional tool to determine the epidemiology of RV-A circulating in a given community.

Distribution of G (VP7) and P (VP4) genotypes of group A bovine rotaviruses from Tunisian calves with diarrhoea.

AIMS: To investigate the incidence, viral load and genetic diversity of bovine rotaviruses strains in Tunisia. METHODS AND RESULTS: A total of 169 faecal specimens, collected from diarrhoeic calves from several farms located in the central eastern regions of Tunisia, between January 2006 and October 2010, were analysed by semi-nested multiplex RT-PCRs for P and G genotypes identification or were genotyped by DNA sequencing. Positive samples were tested by TaqMan real-time RT-PCR to quantify the viral load. Group A bovine rotaviruses were detected in 15·4% (26/169) of the total studied cases of diarrhoea. Overall, G10 was the predominant G type, detected in 12/26 samples (46·2%) and G6 accounted for 42·3% (11/26) while P[11] was the predominant P type, detected in 12/26 samples (46·2%). Two P[5] genotypes (7·7%) were found in the collection. Dual G or P combination and genotype G8 were not found. The most common VP7/VP4 combinations were G6P[11] (30·8%; n = 8) and G10P[11] (11·5%; n = 3). The combination G10P[14] was seen in one sample, and partial typing was assessed in 53·8% (n = 14) of the cases. The viral load determined by real-time RT-PCR showed an average of 1·68 × 10(9) genome copies/g of faeces. CONCLUSION: Knowledge of P and G types could help us understand the relatedness of animal rotaviruses to viruses causing disease in humans. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first time that the viral load and P types of bovine rotaviruses have been determined in Tunisia, and this study contributes to a better understanding of the epidemiology of such viruses circulating in Tunisia. Nevertheless, continuous surveillance is necessary to detect the emergence of new variants.

A major outbreak of gastroenteritis in Réunion Island in 2012: first identification of G12 rotavirus on the Island.

Between August and November 2012 a severe outbreak of gastroenteritis occurred on Réunion Island, affecting more than 50,000 cases, particularly young children. Virological analyses showed that the virus responsible for this epidemic was rotavirus. Genotyping of stool samples indicated circulation of rotavirus type G3P[8] but also G12P[8], highlighting the risk of global emergence of this genotype in the coming years.

Epidemiology and clinical features of gastroenteritis in hospitalised children: prospective survey during a 2-year period in a Parisian hospital, France.

Rotavirus is recognised as the most important agent of severe acute gastroenteritis (AGE) in young children. In a 2-year prospective survey, we investigated the epidemiology and clinical features of the viral and bacterial pathogens in children hospitalised for AGE. The study was performed in a Parisian teaching hospital from November 2001 to May 2004. Clinical data were prospectively collected to assess the gastroenteritis severity (20-point Vesikari severity score, the need for intravenous rehydration, duration of hospitalisation). Stools were systematically tested for group A rotavirus, norovirus, astrovirus and adenovirus 40/41, sapovirus and Aichi virus and enteropathogenic bacteria. A total of 457 children (mean age 15.9 months) were enrolled. Viruses were detected in 305 cases (66.7%) and bacteria in 31 cases (6.8%). Rotaviruses were the most frequent pathogen (48.8%), followed by noroviruses (8.3%) and adenoviruses, astroviruses, Aichi viruses and sapoviruses in 3.5%, 1.5%, 0.9% and 0.4%, respectively. Cases of rotavirus gastroenteritis were significantly more severe than those of norovirus with respect to the Vesikari score, duration of hospitalisation and the need for intravenous rehydration. Rotaviruses were the most frequent and most severe cause in children hospitalised for AGE, and noroviruses also account for a large number of cases in this population.

[Epidemics of gastroenteritis caused by norovirus in Parisian children]. / Épidémies parisiennes de gastro-entérites à norovirus.

During the months of October and November 2006-2008, norovirus was detected in the stools of 14 children hospitalized with acute diarrhea (no sapovirus). Nine of these noroviruses belonged to a unique GGII4 strain, which produced severe clinical symptoms, present only in 2007 and 2008 and absent in 2006. This strain, identified in Europe mainly in the elderly, seems to be on the rise in children in the Paris area over the past few years.

[Sensitivity and specificity of the VIKIA Rota-Adeno immuno-chromatographic test (bioMérieux) and the ELISA IDEIA Rotavirus kit (Dako) compared to genotyping]. / Sensibilité et spécificité du test immuno-chromatographique VIKIA Rota-Adéno (bioMérieux) et du kit Elisa IDEIA Rotavirus (Dako) par rapport aux techniques de génotypage.

The performances of two diagnostic tests for rotavirus infection in stool samples were evaluated during a prospective study in children of less than 36 months in child-care centers of Lyon from November 2004 to May 2005. The VIKIA Rota-Adeno immuno-chromatographic test (bioMérieux) and the ELISA IDEIA Rotavirus kit (Dako) were compared with a referral method, the genotyping. Fifty-seven stool samples were collected and analyzed by RT-PCR. The virus genome was detected in 29 samples. The most frequent genotypic combinations were G9P[8] with a prevalence of 75.9%. Sensitivity and specificity of the VIKIA Rota-Adeno test and the ELISA IDEIA Rotavirus kit were strictly comparable and very good: 96.6% (83.0; 99.9) and 96.4% (81.6; 99.9), respectively. The immuno-chromatographic technique were in concordance with the ELISA tests in 93.6% of cases. Thus, the VIKIA Rota-Adeno test is a good alternative for the occasional analysis of stool samples in ambulatory practice.

Unexpected substitution of dominant rotavirus G genotypes in French hospitalized children over five consecutive seasons.

The study was designed to evaluate the circulation of group A rotaviruses in French hospitalized children, and to detect unusual strains. This prospective study was conducted from 2001 to 2006 in children consulting for acute diarrhea at the pediatric emergency department in three French University Hospitals. The rotaviruses were detected by rapid test and genotyped by RT-PCR on the basis of their outer capsid proteins VP4 (P-type) and VP7 (G-type). The stools from 757 children were analyzed. G1P[8] strains were predominant (44.0%), followed by G9P[8] (17.7%), G3P[8] 13.1%, G4P[8] (9.5%), and G2P[4] (1.8%); mixed rotavirus infections occurred in 2.3%. G9 rotaviruses emerged during the 2004-2005 season (73.4%) and remained the second most prevalent strains. Few unusual strains, G6, G8, G12 and P[6]-types, were detected. The monitoring of rotavirus infections should be maintained to document strain distribution and to assess the emergence of new reassortants that may not respond to current rotavirus vaccines.

[Epidemiology and burden of rotavirus diarrhea in day care centers in Lyon, France]. / Epidémiologie et impact de la gastroentérite aiguë à rotavirus dans les crèches municipales de la ville de Lyon - saison 2004-2005.

Rotavirus is the main cause of severe, dehydrating diarrhoea in infants and young children. In industrialized countries, pediatric rotavirus gastroenteritis (PRGE) is responsible for high morbidity, particularly among children under 3 years of age attending day care centers (DCCs). The objectives of this study were to estimate the incidence, management and cost of PRGE in DCCs. We also described the nature of group A rotavirus genotypes. This study also compared the performance of different diagnostic techniques. The study was conducted from November 2004 to May 2005. Children aged less than 36 months, attending a participating DCC at least 4 times a week were included in the study. For any episode of acute gastroenteritis (AGE), defined as the occurrence of 3 or more watery or looser than normal stools and/or forceful vomiting within a 24 h period, a fecal specimen was tested by Elisa test IDEIA Rotavirus (Dako) and the immunochromatographic test VIKIA Rota-Adeno (BioMérieux). Sequencing by RT-PCR was performed to identify the rotavirus genotype. Among the 41 DCCs contacted, 18 (43.9%) agreed to participate. Out of 966 children, 547 attended a participating DCC at least 4 times a week and met the inclusion criteria. A total of 302 were included in the study. The clinical diagnosis of AGE was confirmed and validated, by the Elisa test, in 63 fecal specimens, of which 29 (46%) were positive for rotavirus antigen, with a predominance of P[8]G9 (86%). Our results showed good sensitivity and specificity for the VIKIA and Elisa methods when compared to RT-PCR. Among the PRGE cases, 36% were male and the median age was 12.2 months. The first rotavirus case was observed in December 2004 with a peak in January 2005. The incidence of PRGE cases was 2.2 [1.4-3.0] per 100 child-months in children aged less than 36 months of age, increasing to 3.4 per 100 child-months among children aged less than 24 months. Vomiting (P<0.0005) and behavior modification (P<0.001) were significantly more frequent for PRGE cases. A total of 85.7% PRGE cases sought medical attention. In 58.3% of these cases, at least one parent had to miss work for a mean duration of 2.1 days. The total cost of rotavirus cases seeking medical attention (with or without prescribed medication, days off work for parents or additional diaper consumption) was estimated at 275.54 euros/case. The PRGE incidence rate is similar to that estimated in European studies conducted in DDC. These findings confirm that rotavirus transmission occurs not only in DCCs but within the family. This is the first study to give an estimate of the incidence and the cost of rotavirus infection in DCCs in France.

Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients.

Aichi virus has been proposed as a causative agent of gastroenteritis. A total of 457 stool specimens from children hospitalized with acute diarrhea and 566 stool specimens from adults and children involved in 110 gastroenteritis outbreaks were screened for the presence of Aichi virus by reverse transcription-PCR (RT-PCR) amplification of the genomic region of the 3C and 3D (3CD) nonstructural proteins. Our results show a low incidence of Aichi virus in pediatric samples and the existence of mixed infections with other microbiological agents in some cases. From the outbreak survey, it appears that the presence of Aichi virus is an indicator of mixed infections causing gastroenteritis outbreaks and that it could be involved in half of the oyster-associated outbreaks. A second RT-PCR was developed to amplify a part of the VP1 gene. The phylogenetic analysis showed a good correlation between the two classifications based on 3CD and VP1 gene sequences and revealed the prevalence of genotype A in France. It also allowed us to partially describe an Aichi virus strain that could represent a new genotype, thus suggesting the existence of a certain diversity.

[Evaluation of seven immunochromatographic assays for the rapid detection of human rotaviruses in fecal specimens]. / Evaluation de sept réactifs d'immunochromatographie pour détecter les rotavirus humains dans les selles.

Seven commercially available immunochromatographic assays were tested for the rapid detection of group A rotaviruses in fecal samples compared to a enzyme immunoassay (Argene). Detection of rotaviruses in 80 ELISA positive frozen stool samples showed rates superior to 90% for three reagents (Rota Strip (Cypress Diagnostics), 98.8%; Rotascreen (Microgen), 95.0%; VIKIA Rota/Adeno (bioMérieux), 92.5%); from 82.5% to 88.8% for three others (Diarlex with centrifugation (Orion Diagnostica), 88.8%; Combo Rota/Adeno (All Diag), 87.5%; Rota/Adeno Combi Stick (bmd), 82.5%) and only 70.0% for Diarlex with filtration vial (Orion Diagnostica). The evaluation of the specificity, performed on one hundred fresh rotavirus negative stools, did not show any false positives with any assay. Analysis of the different technical features of these tests showed that they are quick and suitable for a clinical laboratory and do not require expensive equipment.

Molecular epidemiology of caliciviruses detected in sporadic and outbreak cases of gastroenteritis in France from December 1998 to February 2004.

We compiled sequence and epidemiological data from 172 caliciviruses detected in France from December 1998 to February 2004 in sporadic and outbreak cases. The results showed a cocirculation of strains with a majority of genogroup II (GII) noroviruses. Three groups of noroviruses, not detected before in our laboratory, emerged and spread during the period: the recombinant GGIIb and Norwalk-related strains not amplified in the polymerase gene in 2000 and a new Lordsdale variant in 2002. We observed that (i) GII-4 noroviruses were predominant in nursing home and hospital outbreaks but rare in oyster- and water-related outbreaks despite continuous circulation in the population; (ii) at the opposite, genogroup I strains were detected in the majority of environmental outbreaks; (iii) several strains were frequently found in oyster- and water-linked outbreaks (up to seven), whereas one single strain was detected when transmission was from person to person; and (iv) whereas GII noroviruses were predominant in sporadic cases where patients were under 15 years of age, GI strains were more frequent in outbreaks occurring in this age group. Finally, from a methodology point of view, this compilation shows that detection and characterization in the polymerase gene are not adequate in a significant number of cases and should be completed by amplification and sequencing in the capsid gene.