Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice.

BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale.

Le virus de l'artérite virale équine : de l'épidémiologie moléculaire à l'émergence de variants pathogènes.

Equine arteritis virus (EAV) is the causative agent of equine viral arteritis, a disease observed only in equids. EAV is the prototype of the family Arteriviridæ within the order Nidovirales. EAV is an enveloped, positive-sense, single-stranded RNA virus with a considerable variation in the genome as observed in other RNA viruses. During natural infections, EAV may cause abortion and persistent subclinical infections in stallions which can shed the virus in the semen for years, or even lifetime. Chronically infected stallions represent the natural reservoir of the virus. They ensure the persistence and the evolution of the virus, making possible the emergence of new variants potentially virulent. The genetic heterogeneity of EAV during persistent infection in the stallion is considerably greater than that generated during epidemics. Recent studies facilitated the understanding of EAV evolution and genetic variability. With recent advances in molecular biological techniques and the increasing number of sequences available in databases, molecular epidemiological studies have reported specific molecular hallmarks of EAV strains during and outside of epidemics. These new data should facilitate a better understanding and the determination of the origin of new EAV outbreaks.

Evaluation of two magnetic-bead-based viral nucleic acid purification kits and three real-time reverse transcription-PCR reagent systems in two TaqMan assays for equine arteritis virus detection in semen.

This study showed that under specifically defined conditions with respect to nucleic acid extraction method and testing reagents, a previously described real-time reverse transcription-PCR (rRT-PCR) assay (T1 assay) provides sensitivity equal to or higher than that of virus isolation for the detection of equine arteritis virus in semen.

[Variation of coronavirus tropism]. / Changement de tropisme des coronavirus.

Viral tropism is defined as the group of target cells which can be infected by this virus. Knowing viral tropism is knowing the target organ, and the animal species used as host. The variation of tropism allow for virus to evolve, cross species barriers, and infect a new host. Coronavirus family is a very large group of viruses which infect birds and mammals. These RNA viruses can rapidly evolve. In the history of coronaviruses, several examples of variations of tropism have been described, and have as consequences the emergence of a new infection (coronavirus associated with SARS, porcine respiratory coronavirus), or a new expression of the clinical presentation of the infection (fatal infectious peritonitis in cats and ferrets).

Evaluation of the presence of equine viral herpesvirus 1 (EHV-1) and equine viral herpesvirus 4 (EHV-4) DNA in stallion semen using polymerase chain reaction (PCR).

In the horse, the risk of excretion of two major equine pathogens (equine herpesvirus types 1 (EHV-1) and 4 (EHV-4)) in semen is unknown. The objective of our study was to assess the possible risks for the horizontal transmission of equine rhinopneumonitis herpesviruses via the semen and the effect of the viruses on stallion fertility. Samples of stallion semen (n=390) were gathered from several different sources. Examination of the semen involved the detection of viral DNA using specific PCR. The mean fertility of the stallions whose sperm tested positive for viral DNA and the mean fertility of stallions whose sperm did not contain viral DNA, were compared using the Student's t-test. EHV-4 viral DNA was not detected in any of the semen samples. EHV-1 DNA was identified in 51 of the 390 samples, (13%). One hundred and eighty-two samples came from 6 studs and there was significant difference (p<0.05) among the proportion of stallions whose semen tested positive for viral DNA from 0 to 55% between the studs. There was a significant difference (p<0.014) between the fertility of stallions whose semen tested positive for viral DNA and those whose semen was free from viral DNA. The stallions that excreted the EHV-1 virus in their semen appeared to be more fertile than the non-excretors, but this difference was in fact related to the breeding technique since higher proportion of excretors were found among those whose semen was used fresh rather than preserved by cooling or freezing. In conclusion, this study suggests that the EHV-1 virus may be transmitted via the semen at mating or by artificial insemination as demonstrated with other herpes viruses in other species.

Genetic diversity of human respiratory syncytial virus isolated among children with acute respiratory infections in Southern Cameroon during three consecutive epidemic seasons, 2011-2013.

BACKGROUND: Human respiratory syncytial virus (HRSV) is the main viral cause of severe lower respiratory tract disease in infants and young children. The aim of this study was to describe for the first time the genetic variability of HRSV in Cameroonian patients living in Yaounde for three consecutive epidemic seasons. METHODS: HRSV-positive nasopharyngeal samples detected in children less than 15 years in Yaounde were collected from September 2011 to December 2013. Semi-nested RT-PCR, sequencing, and phylogenetic analyses of the second hypervariable region of the G gene were performed. RESULTS: A total of 57 HRSV-positive samples were collected during the study period. Among these, 46 (80.7%) could be amplified in the G gene. HRSV group A (HRSV-A) and group B (HRSV-B) co-circulated in this population at 17.4 and 82.6%, respectively. HRSV-A strains clustered in the NA-1 genotype while HRSV-B strains clustered in the BA-9 genotype. HRSV-A strains accounted for 33.3% (2/6), 4.3% (1/23), and 29.4% (5/17) of the viruses isolated in 2011, 2012, and 2013, respectively. CONCLUSIONS: This study reports molecular epidemiology data of HRSV in Cameroon for the first time. Additional studies are required to clarify evolutionary patterns of HRSV throughout sub-Saharan Africa to support antiviral and vaccine development.

Comparative molecular epidemiology of two closely related coronaviruses, bovine coronavirus (BCoV) and human coronavirus OC43 (HCoV-OC43), reveals a different evolutionary pattern.

Bovine coronaviruses (BCoVs) are widespread around the world and cause enteric or respiratory infections among cattle. The current study includes 13 samples from BCoVs collected in Normandy during an 11-year period (from 2003 to 2014), 16 French HCoV-OC43s, and 113 BCoVs or BCoVs-like sequence data derived from partial or complete genome sequences available on GenBank. According to a genotyping method developed previously for HCoV-OC43, BCoVs and BCoVs-like are distributed on three main sub-clusters named C1, C2, and C3. Sub-cluster C1 includes BCoVs and BCoVs-like from America and Asia. Sub-cluster C2 includes BCoVs from Europe. Sub-cluster C3 includes prototype, vaccine, or attenuated BCoV strains. The phylogenetic analyses revealed the monophyletic status of the BCoVs from France reported here for the first time. Moreover, BCoV exhibits a relative genetic stability when compared to HCoV-OC43 we previously described from the same region. The numerous recombination detected between HCoV-OC43 were much less frequent for BCoV. The analysis points thus to the influence of different evolutive constraints in these two close groups.

Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes.

Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome's high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.

Development of an efficient qRT-PCR assay for quality control and cellular quantification of respiratory samples.

BACKGROUND: Sample quality is a fundamental parameter for the successful diagnosis of respiratory viruses. This parameter depends upon the concentration of epithelial cells. Respiratory samples are usually heterogeneous, which makes relative quantification of the viral load, against the quantity of cells, the most suitable measurement. The quantification of viral load in the field of respiratory viruses is a vital piece of information. Quantification is required from RNA or DNA viral genomes extracted. OBJECTIVES: To design (RT-)PCR assays for reference genes, which show stable expression during viral infection, to be used as cellular controls and cellular quantification tools. STUDY DESIGN: Assays were designed for two reference genes: hypoxanthine phosphoribosyltransferase 1 (HPRT1) and ubiquitin C (UBC). The glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH) was used as a reference for this study. The transcriptional activity of the three genes was studied during infection with respiratory syncytial virus and adenovirus. The HPRT1 q(RT-)PCR assay was used on clinical samples. RESULTS: All the analysis methods concluded that the three reference genes were stably expressed during viral infection. The HPRT1 q(RT-)PCR assay indicated that the majority of clinical samples (n=301, 69%) had a cellular load of between 100 and 10,000 cells/PCR. The data showed that the concentration decreased as the age of patient increased. CONCLUSIONS: A new tool has been developed and commercialized for quality control and evaluation of cellular concentration in respiratory samples.

First detection of equine coronavirus (ECoV) in Europe.

Equine coronavirus (ECoV) is involved mainly in enteric infections. Following the recent description of ECoV in 2000, this study reports for the first time the presence of ECoV in France and, on a wider scale, in Europe. ECoV was molecularly detected from diarrheic and respiratory specimens. Sequencing and phylogenetic analyses demonstrated that European strains are most closely related to the reference North American strain (ECoV-NC99) than the Asian strain (ECoV-Tokachi09).

Emergence of novel equine arteritis virus (EAV) variants during persistent infection in the stallion: origin of the 2007 French EAV outbreak was linked to an EAV strain present in the semen of a persistently infected carrier stallion.

During the summer of 2007, an outbreak of equine viral arteritis (EVA) occurred in Normandy (France). After investigation, a link was suggested between an EAV carrier stallion (A) and the index premise of the outbreak. The full-length nucleotide sequence analysis of a study reference strain (F27) isolated from the lung of a foal revealed a 12,710 nucleotides EAV genome with unique molecular hallmarks in the 5'UTR leader sequence and the ORF1a sequence encoding the non-structural protein 2. The evolution of the viral population in the persistently infected Stallion A was then studied by cloning ORFs 3 and 5 of the EAV genome from four sequential semen samples which were collected between 2000 and 2007. Molecular analysis of the clones confirmed the likely implication of Stallion A in the origin of this outbreak through the yearly emergence of new variants genetically similar to the F27 strain.

Neuropathogenic and non-neuropathogenic variants of equine herpesvirus 1 in France.

Equine herpesvirus 1 (EHV-1) is a common pathogen of the horse which may induce mild respiratory distress, abortion, neonatal death and neurological disease. A single nucleotide polymorphism in the EHV-1 DNA polymerase (ORF30 A(2254) to G(2254)) has been associated with clinical signs of Equine herpes myeloencephalopathy (EHM). The aim of this work was to analyze the ORF30 genomic region among a panel of EHV-1 DNA extract in order to estimate the prevalence of the EHV-1 neuropathogenic genotype in France. Samples coming from cases associated with EHM, horses with respiratory symptoms and aborted mares, each obtained between 2002 and 2009, were investigated. DNA was directly extracted from biological samples and allelic discrimination was performed using real-time PCR. Thirty of the 125 analysed horses (24%) presented the G(2254) genotype of ORF 30. Among them, 7/16 were provided by EHM cases, 1/24 by respiratory cases and 22/85 by abortion cases. Concerning EHM, the 7 G(2254) genotype of ORF30 were all isolated in 2009 during two outbreaks where mortality was observed. Regarding the 22 G(2254) genotype of ORF 30, 17 were identified in foetuses on which EHV-1 was detected by PCR, without any certainty of viral implication in the abortion. These findings clearly suggest that other factors need to be considered for a better understanding of the impact of DNA polymerase genotype upon EHV-1 neuropathogenic phenotype.

Identification of equid herpesvirus-5 in respiratory liquids: a retrospective study of 785 samples taken in 2006-2007.

During a case control study undertaken in 2006-2007, a screening and consensus polymerase chain reaction (PCR) was performed to evaluate the potential role of equid herpesviruses (EHV) in several occurrences of respiratory disorders in 661 horses. Of 785 bronchoalveolar or tracheal lavage fluid samples submitted for analysis, 20 were positive for EHV-5 DNA by sequential analysis of the consensus PCR product. Nineteen of those samples were confirmed using a specific EHV-5 PCR. No particular changes in cytological profile could be associated with the detection of EHV-5 in contrast to suggestions in previous reports of natural or experimental respiratory viral infections in horses or ponies. This is the first description of EHV-5 isolation in equine respiratory fluids in Europe, but further investigations are needed to determine the potential pathogenic role of this gammaherpesvirus in the horse.

Herpesviruses in respiratory liquids of horses: putative implication in airway inflammation and association with cytological features.

The objectives of this study were to estimate the prevalence and the potential role of equine herpesviruses (EHVs) detection in both bronchoalveolar lavage (BAL) and tracheal wash (TW). The population included a control group (CTL; 37 TW and 25 BAL) and a pathological group (PAT; 259 TW and 387 BAL), including horses either suffering from respiratory diseases including syndrome of tracheal inflammation, inflammatory airway disease, recurrent airway obstruction, or submitted to respiratory investigation because of exercise intolerance or poor performance. Each respiratory liquid was submitted to a standardised cytological analysis, mentioning the morphological abnormalities of exfoliated epithelial cells (ECAb) and ciliocytophthoria (CCPh) as markers of potential viral infection, as well as PCR assays including a consensus PCR and virus-specific PCR for both equine alphaherpesviruses (EHV-1; EHV-4) and gammaherpesviruses (EHV-2; EHV-5). The EHV infections were more prevalent in the TW of PAT group (P=0.004), with the highest prevalence being for EHV-2 (P=0.006). The EHV detection in BALs was not significantly different between groups. The EHVs detection in TW was correlated to the polymorphonuclear neutrophil (PMN) counts in the respiratory liquid but not with CCPh or ECAb. CCPh or ECAb were associated with both consensus PCR and EHV-2 and EHV-5 virus-type PCR in the BAL only. The significant detection of EHVs in the TW of PAT group in association with the PMN increased counts could lead to further investigations about their putative role in equine syndrome of tracheal inflammation.

Combined antimicrobial resistance in Enterococcus faecium isolated from chickens.

Nineteen E. faecium strains isolated from chicken caecum samples, collected in slaughterhouses and highly resistant to vancomycin or gentamicin, were coresistant to erythromycin, and/or tetracyclines, and/or streptogramins, and/or avilamycin. Multiple antibiotic resistance was related to the presence in various combinations of aac(6')-aph(2"), erm(B), emtA, mef(A), tet(L), tet(M), and vanA genes.