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Introduction – objectifs Responsable d’une epidemie annuelle de bronchiolite du nourrisson, le Virus Respiratoire Syncytial (VRS) est generalement associe a une problematique pediatrique de sante publique. Pourtant, ce virus a aussi un impact non negligeable et moins connu sur les autres classes d’âge, en particulier les seniors au-dela de 75 ans. Les donnees virologiques de surveillance ambulatoire de la grippe permettent aussi de suivre les epidemies de VRS, veritable facteur de confusion dans l’alerte grippe, et d’explorer leur impact par âge. L’objectif de ce travail etait d’evaluer l’impact des infections a VRS sur les differentes classes d’âge au cours des 7 derniers hivers (2007 a 2014). Materiels et methodes Analyse retrospective des donnees de surveillance ambulatoire. Les periodes epidemiques pour le VRS et pour la grippe sont bornees a partir de criteres composites cliniques et virologiques. Resultats Le VRS est responsable d’une epidemie annuelle, active entre les mois de novembre et janvier-fevrier. La duree moyenne de cette epidemie est de 12 semaines [extremes : 9–14]. Des cas d’infection a VRS sont signales dans toutes les tranches d’âge avec un impact particulierement net chez les moins de 5 ans mais aussi les seniors. L’expression clinique de l’infection a VRS, en cours d’analyse, sera presentee pour chaque tranche d’âge (0–4 ans, 5–14 ans, 15–50 ans, 51–64 ans, 65–74 ans, 75 ans et plus). Conclusion Le poids medico-economique des infections a VRS, souvent considere a travers son seul impact sur les moins de 2 ans, doit etre reconnu et meriterait d’etre mieux etudie. La promotion et le renforcement des mesures barrieres respiratoires, seul moyen de lutte disponible, ne devraient pas etre limites a la protection des nourrissons mais largement diffuses.

Respiratory viral infections are very common in young children. They sometimes occur as primary infections (and sometimes re-infections) by influenza and parainfluenza virus, respiratory syncytial virus (VRS), adenovirus, rhinovirus and coronavirus. The clinical pictures are very varied and without strict clinico-virological correlation. In adults the role of the site (frail lung, aged persons) and the type of virus play an important part. Many viral infections develop in an epidemiological way (influenza, VRS bronchiolitis, rhinovirus infections...) and several epidemics by different viruses overlap from September-October to March-April making it very difficult to decide the precise cause. Epidemics are followed thanks to networks of medical practitioners (GROG, SENTINELLE...) and by data from hospitalised patients, but precise identification of epidemic viruses is only possible and validated by virological analysis of samples taken from patients.

Cytomegalovirus (HCMV) infection is the leading cause of congenital virus infection in developed countries, affecting an estimated 1% of births. This antenatal infection can cause serious sequelae. Strategies for prevention and treatment must, therefore, be agreed upon, entailing a preliminary performance assessment of antenatal virus diagnosis techniques. Between 1992 and 1999, HCMV serology status was established for 19 456 pregnant women in four French hospitals. Seronegative patients (55.4%) were given serology screening, and antenatal diagnosis was given to 152 women who had shown seroconversion during their pregnancies (1.4%). The detection of HCMV transmission from mother to fetus was finally established in 95 cases, using polymerase chain reaction (PCR) and viral culture methods for detecting HCMV in the amniotic fluid. These results were compared with viral culture of children's urine after birth, enabling us to distinguish between children really infected in utero (30%) and non-infected children (70%). The results of the virus culture and those of PCR were identical in 94 of the 95 cases, with one discrepancy (culture−/PCR+). The two diagnosis techniques had identical sensitivity (72%), with culture proving slightly more specific than PCR (98.4% as opposed to 96.9%). Positive prediction values for culture and for PCR were, respectively, 95.6 and 91.3%. Antenatal virus diagnosis on amniotic fluid was negative with both techniques in 8 out of 29 cases of children born with HCMV infection (VPN=89%). Over half of these wrongly negative results can be explained by amniocentesis carried out too early in the pregnancy or too early with respect to the mother's primary infection.

Background: The viral isolation technique (VIT) is largely used as a gold standard for the detection of influenza A and B viruses in respiratory samples. Some recent studies have pointed out that the polymerase chain reaction (PCR) assays allow sensitive and rapid detection of influenza viruses, also providing excellent correlation with traditional methods. Objectives and design study: The aim of this study was to evaluate the efficiency of three non-nested PCR, two PCR-hybridization assays using primers defined in M and NS genes, and one PCR which uses primers defined in NP, NS and HA genes and combines the detection of H3N2 and H1N1 hemagglutinin genes using defined primers in NP, NS and HA genes (PCR3), in comparison with an IF assay (IFA) and viral isolation technique (VIT). The study was carried out on 244 nasal samples collected mainly by practitioners of the GROG surveillance network during winter 1998–1999 for the detection of influenza A virus. Results: Overall influenza viruses were detected more frequently by PCR techniques in 157 (64.3%), 147 (60.2%), 110 (45%) cases for PCR1, PCR2, PCR3, respectively, than by VIT or IFA, in 100 (40.9%) and 74 (30.3%) cases, respectively. Taking the positive culture samples as a reference, 100 (41.8%) samples were found to be positive for influenza A, and the sensitivity of IFA, PCR 1, PCR 2 and PCR3 techniques were 70, 100, 99, and 90%, respectively as compared with viral isolation cultures. On the other hand, as 86.5% of positive samples were positive with at least two different techniques, the sensitivity, specificity, VPP and VPN of each technique were recalculated taking into account a further criterion defining a positive sample: positivity with two techniques. We observe that techniques PCR 2 and particularly PCR 1 have very good sensitivity, respectively 98.6 and 100%, far better than the traditional techniques, IFA and culture, whilst maintaining acceptable specificity: 94.1 and 86.1%, respectively. In both cases they enable 141 (57.7%) A-positive influenza samples to be detected instead of the 100 (40.9%) obtained when culture is the reference test. IFA, culture and PCR 3 are highly specific (VPP=100%), but in comparison with PCR 1 and 2 their sensitivity, respectively 51.7, 69.9, 77.6%, and negative predictive value are unsatisfactory. PCR 1 and 2 are superior to the other techniques to a statistically highly significant degree in terms of sensitivity, but the difference between the two is not significant.

Human parvovirus B19 (PVB19) is a DNA virus ransmitted via the respiratory route, through parenteral dministration of products derived from blood, and vertically rom mother to fetus (Heegaard and Brown, 2002). PVB19 auses erythema infectiosum, arthropathy, transient aplasic crisis, and hydrops fetalis, but there are few reports of fatal outcome involving myocarditis (Murry et al., 2001; apadogiannakis et al., 2002; Zack et al., 2005). The patient, a 5-year-old girl, was admitted to the emerency unit after a malaise with loss of conscience for 3 min ithout convulsing. She complained of headache and abdomnal pain over 2 days, with five vomiting episodes and two iarrheic stools in a context of familial gastroenteritis. The hild was pale, with blood pressure of 92/59 mmHg, heart ate of 145 beats/min, and temperature 35 ◦C. The oxygen aturation level was 99%. A few hours later, a new episode of malaise occurred with drop in blood pressure to 46/25 mmHg and a heart rate f 54 beats/min, accompanied by loss of consciousness and lotching of the skin. The child appeared to recover following dministration of isotonic fluids to counteract hypovolemia. linical examination did not reveal other abnormal findings. ranial computer tomography and cardiac examination were ormal. There were no indications of hepatosplenomegaly, bdominal mass, meningeal syndrome, dehydration, or espiratory distress syndrome. The complementary blood xaminations showed no abnormal modifications. Tropoine, C-reactive protein, and hemoglobin were within

POORLY-KNOWN VIRUS: Coronaviruses, so named because of their sun-ray-like aspect, were discovered in the sixties. The biology of these RNA viruses is complex and poorly understood. KNOWN PATHOGENS: Coronaviruses are known pathogens in veterinary medicine, causing disease states in several domestic species. In human medicine, they can cause benign respiratory infections, but few laboratories include coronaviruses in their routine diagnostic tests. SUSPECTED PATHOGENS: There is some data in the literature suggesting coronaviruses might be implicated in more severe diseases including multiple sclerosis, necrotizing enterocolitis, and lower respiratory tract infections, particularly in infants. IMPROVING DIAGNOSTIC METHODS: Due to the lack of reliable and sensitive diagnostic techniques, it is impossible to date to correctly assess the medical impact of these ubiquitous and endemic viruses. Molecular biology techniques enabling detection of human coronavirus infections should be applied to verifying the suspected implication of these viruses in diverse disease states.

HUMAN CYTOMEGALOVIRUS (HCMV) infection is a frequent complication of renal transplantation. Treatment should start early in the course of the viral infection to obtain the best results. HCMV must be detected before clinical symptom appearance, but virus detection is not always followed by HCMV disease. Therefore, treatment is not necessary every time HCMV infection is detected in a patient. For this reason, it is very important to have an early diagnostic system to obtain a correlation between the results and the disease gravity. The objective of this study is to compare four HCMV diagnostic methods: DNA in sera by polymerase chain reaction (PCR), DNA in leukocytes by PCR, pp65 leukocytic antigenemia, and viremia to predict symptomatic HCMV infection.

Background: Immunofluorescence assay (IFA) of viral antigens in nasal aspirates is largely used for the diagnosis of respiratory syncytial virus (RSV), parainfluenzavirus (PIV) type 3 and adenovirus (AdV) infections, whilst rhinovirus (RV) are detected by virus isolation technique (VIT) only. Using the two techniques, IFA and VIT, a significant number of specimens remain negative in spite of clinical and epidemiological presumptions of viral infection. Objectives and study design: The polymerase chain reaction (PCR) should improve the sensitivity of viral detection in clinical specimens. From October 1995 to March 1996, 277 nasal aspirates from hospitalized infants were tested simultaneously by IFA, VIT, polymerase chain reaction and hybridization with a DNA enzyme immunoassay (PCR-EIA) for RSV, PIV-3, AdV and RV. Results: RSV were detected in 177 (64%) samples, PIV-3 in 23 (8%), RV in 40 (14%), and AdV in 30 (10%). PCR-EIA detected RSV in more samples 173 (62%) than IFAVIT: 109 (39%) (P < 10−7). In most cases (79%), RSV-infected infants had lower respiratory tract disease, and routine and PCR techniques were positive. Out of the 23 PIV-3 infections, 12 were IFAVIT- and PCR-EIA-positive, and 11 IFAVIT-negative and PCR-EIA-positive. For RV, 35 (87%) specimens were PCR EIA-positive and 11 (27%) culture-positive; for AdV 30 samples were PCR-EIA-positive and four were culture-positive. Simultaneous viral infections were revealed in a significantly higher proportion than in conventional techniques: 18% (50277) versus 2.5% (7277); P < 10−7. One RSV infection in four was associated with the presence of another virus, mainly PIV-3 (16 cases) and AdV (13 cases). Conclusions: PCR-EIA detects more positive-specimens than IFAVIT, 1.5 times more for RSV, 1.9 for PIV-3, 4 for RV and 10 for AdV, respectively. This increased sensitivity of viral detection by PCR-EIA compared to the IFAVIT could suggest that samples containing low levels of virus are missed by routine methods IFAVIT, and consequently, RSV or PIV-3, and above all RV or AdV are overlooked as agents of respiratory diseases. However, apart from the fact that the economic and convenient aspects of virus diagnostic cannot be missed, it is difficult to answer the following questions: what is the meaning of the detection of a viral sequences in nasal aspirates of infants. or may PCR have detected virus in patients who would not developed disease?

BACKGROUND: RT amplification reaction has revealed that various single viruses or viral co-infections caused acute bronchiolitis in infants, and RV appeared to have a growing involvement in early respiratory diseases. Because remaining controversial, the objective was to determine prospectively the respective role of RSV, RV, hMPV and co-infections on the severity of acute bronchiolitis in very young infants. METHODS AND PRINCIPAL FINDINGS: 209 infants (median age: 2.4 months) were enrolled in a prospective study of infants

Introduction Respiratory viruses are a major cause of respiratory tract infections. The prevalence of a virus-positive respiratory sample and its significance in patients requiring mechanical ventilation remain unknown.

Respiratory syncytial virus infections occur frequently in children, often localized in the upper respiratory tract. Outcome is usually quite satisfactory, but in nearly one half of the infants lower tract involvement may cause severe respiratory insufficiency leading to hospitalization in about 1% of the cases. Its frequency has been estimated at 20 to 30% of the viral infections in hospitalized infants, 10 times the frequency of the other respiratory virus. Respiratory syncytial epidemias last about 4 to 5 months with a seasonal peak in december and january. The direct detection of respiratory syncytial antigens in nasal specimens by immunofluorescence or enzymatic immunoassay is the key to rapid diagnosis. They appear as performant and more convenient than specific IgM antibodies or nucleic acid detections, and than virus isolation on cell culture, which is justified to evaluate strain sensitivity to ribavirin. Immunofluorescence has also been used to identify the subgroups A and B from 1981 to 1993, and respiratory syncytial subgroup A seems to signify more severe disease. Symptomatic assistance may require hydratation, oxygenotherapy and respiratory physical therapy. Antibiotics should not be given as a routine treatment since bacterial superinfection is infrequent, but may be indicated in cases with associated signs of complications. Indications for bronchodilators and corticosteroids are still under debate. Significant results have been obtained with ribavirin and specific anti respiratory syncytial immunoglobulins but further evaluations are still required to precise their use in clinical practice.

Community viral bronchopneumonias are frequent, mainly in children, and can be associated to all respiratory viruses: influenza- and parainfluenzavirus, respiratory syncytial virus, adenovirus, rhinovirus. The diagnostic method which proves viral infection of the respiratory tissues is selected as the direct detection by an immunofluorescence assay of viral infected cells in respiratory samples. In them, viral isolation or nucleic acid detection by PCR provide an amplification of the viruses. By using PCR-hybridation techniques viral detection is overall increased of 1.5 times for respiratory syncytial virus, 1.9 for parainfluenzavirus 3, 4 for rhinovirus and 10 times for adenovirus. This increased sensitivity raises questions about the meaning of the detection of viral sequences in nasal aspirates, with or without clinical signs. Cytomegalovirus (CMV) is a major agent of pneumonia in immunocompromised patients. All virological markers of CMV infection have to be sought (antigenemia, viremia...), but specific inclusions in pulmonary cells are the single diagnosis criteria. As pulmonary biopsies are rarely available and CMV inclusions rarely found in BAL, it has been reported useful to look for high viral loads or late m-RMA transcripts in these samples. Adenovirus pneumonia are unfrequent in these patients and mostly associated to rare or atypical strains. Such PCR-hybridization systems deserves also to be used in these cases.

Chlamydia pneumoniae has been established recently as an important human respiratory pathogen. The aim of this study was to define the incidence of Chlamydia pneumoniae in acute respiratory infections by evaluating its presence in posterior nasopharyngeal aspirates or broncho-alveolar lavage specimens by polymerase chain reaction-hybridization (PCR-EIA) as well as the titres of specific antibodies in serum by a rELISA test and a micro-immunofluorescence (MIF) test. 68 adults patients were investigated. Eight patients (11.8%) were positive by either rELISA or PCR-EIA or both, with an infection rate of 5 patients with community-acquired pneumonia, 2 asthmatic patients and 1 patients with an exacerbation of chronic obstructive pulmonary disease. Serological evidence of acute infection was found in four of these patients with rELISA test and in three others with MIF test. PCR-EIA detected Chlamydia pneumoniae DNA in four patients, but there were concordant results with rELISA and PCR-EIA in only one patient. In conclusion, Chlamydia pneumoniae appears to be a common etiologic agent of acute respiratory infections in adults. The discrepancy between serological test and PCR-EIA results reflects the difficulties in routine laboratory diagnosis of Chlamydia pneumoniae. The ambiguous results of serological tests from a single serum sample assess the utility of PCR for prompt diagnosis. When PCR is negative or no feasible, a second serology to 15/21 days of interval is necessary. Further studies with optimised techniques must be developed.

A reverse transcription-PCR and hybridization-enzyme immunoassay (RT-PCR-EIA) has been developed to identify the major agents of bronchiolitis in infants: respiratory syncytial viruses A and B (RSVA and RSVB) and parainfluenzavirus 3 (PIV3). Two primer sets (P1-P2 and P1-P3) were selected in a conserved region of the polymerase L gene. In infected cell cultures, this method detected RSVA ( n = 14), RSVB ( n = 13), and PIV3 ( n = 13), with the exclusion of PIV1 ( n = 4), PIV2 ( n = 3), measles virus ( n = 6), mumps virus ( n = 4), influenza A virus ( n = 11), and influenza B virus ( n = 4). The differentiation of the amplicons by restriction fragment length polymorphism (RFLP) showed a Pvu II site for PIV3 strains and an Ava II site for RSV strains, with RSVA distinguished from RSVB by Bgl II. The hybridization-EIA, using three internal probes specific for each virus, correlated with the immunofluorescence assay (IFA) and RFLP results. Clinical aspirates from 261 infants hospitalized with bronchiolitis were tested by IFA, viral isolation technique (VIT), and RT-PCR-EIA. RT-PCR-EIA detected RSV sequences in 103 samples (39.4%), and IFA-VIT detected RSV sequences in 109 cases (41.7%). A few samples (2.6%) were IFA-VIT positive but PCR negative, and one sample was RT-PCR-EIA positive only. RT-PCR-EIA detected PIV3 sequences in 14 of the 15 IFA-VIT-positive isolates. The two methods showed very good correlation (96.9%), but RT-PCR-EIA was clearly more efficient in typing, leaving 5% non-A, non-B isolates, while IFA failed to resolve 23% of the isolates. The two methods contradicted each other for

Nasal aspirates from 238 infants hospitalized with acute respiratory infections during the winter of 1994 and 1995 were tested for respiratory syncytial virus (RSV) by immunofluorescence assay (IFA) and the viral isolation technique (VIT) and by two PCR and hybridization methods: reverse transcription PCR 1 (RT-PCR1), which amplifies the RNAs of all RSV strains, and RT-PCR-2, which allows subgroup classification of RSV. RT-PCR-1 and RT-PCR-2 detected viral sequences in 56.7% (135 of 238) and 48.3% (115 of 238) of the samples, respectively, while only 80 (33.6%) samples were found to be positive by IFA and VIT. Of the PCR-positive specimens, 57 were missed by these routine techniques in RT-PCR-1 and 45 were missed in RT-PCR-2. Although the RSV-PCR-1 and RSV-PCR-2 techniques amplified two different sequences of the RSV genome, they gave similar results for 218 (91.6%) nasal aspirates. Compared with conventional methods, the sensitivity, specificity, and agreement were 97.5, 63.9, and 75.2%, respectively, for RT-PCR-1 and 89.7, 71.9, and 77.7%, respectively, for RT-PCR-2, and for these two RT-PCR assays, the positive predictive value (PPV) and the index of agreement (kappa) were comparable and moderate, respectively: PPV was 57.8% and kappa was 0.52 in RT-PCR-1, and PPV was 60.9% and kappa was 0.54 in RT-PCR-2. However, there was a perfect correlation between the two RT-PCRs, with a PPV of 100% and an excellent index of agreement (kappa = 0.88). Therefore, most RT-PCR results were really true positive, and VIT and IFA, which missed some of them, appeared to be less sensitive.

International audience; 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 OPEN ACCESS Viruses 2015, 7 2359 and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.

The performancs of a membrane-based EIA, the Quick Vue Influenza test, (Quidel,USA) were compared to those of an immunofluorescence assay (IFA) for the detection of influenza virus A antigens in respiratory samples from children hospitalized during the 2002-2003 winter season. A prospective study was carried out on 2 nasal swabs drawn in parallel from 33 children: 13 samples were positive and 18 negative on both the Quick Vue test and IFA. Using an in-house reverse transcription (RT)- PCR assay as a gold standard, the two discordant results were identified as a false-positive reaction of the IFA and a false-negative one of the Quick Vue test . The sensitivity, specificity, positive and negative predictive values of the Quick Vue test were 87.5%, 100%, 100% and 89.5%, respectively. In the retrospective study of frozen samples, 57 of the 70 positive samples were detected by the Quick Vue test and 5 of 50 negative samples. Using the RT-PCR as a gold standard, there were 4 false-negative and 3 false-positive results on IFA and 10 false-negative results on the Quick Vue test. Our study suggests that performances of the Quick Vue are good if the test is carried out directly on nasal secretions, but that they can be decreased when nasal aspirates are collected in transport medium and frozen.

Pre-print on MedRxiv : https://www.medrxiv.org/content/10.1101/2020.05.26.20114025v1; International audience; Temperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-values (time to obtain a log10 reduction of virus infectivity), including values for SARS-CoV-2, were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global dataset of D-values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points or any coronavirus strains belonging to Alphacoronavirus and Betacoronavirus genera.Importance: The prediction of the persistence of SARS-CoV-2 on fomites is essential to investigate the importance of contact transmission. This study collects available information on inactivation kinetics of coronaviruses in both solid and liquid fomites and creates a mathematical model for the impact of temperature and relative humidity on virus persistence. The predictions of the model can support more robust decision-making and could be useful in various public health contexts. Having a calculator for the natural clearance of SARS-CoV-2 depending on temperature and relative humidity could be a valuable operational tool for public authorities.

International audience; After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection by SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2. For each animal, rectal, nasopharyngeal swabs and serum were taken. Swabs were submitted to RT-qPCR assays targeting 2 genes of SARS-CoV-2. All dogs were tested SARS-CoV-2 negative. One cat was tested positive by RT-qPCR on rectal swab. Nasopharyngeal swabs from this animal were tested negative. This cat showed mild respiratory and digestive signs. Serological analysis confirms the presence of antibodies against the SARS-CoV-2 in both serum samples taken 10 days apart. Genome sequence analysis revealed that the cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon their pets or compromise their welfare.

Highlights • SARS-CoV-2 infects massively the olfactory mucosa in hamsters. • SARS-CoV-2 induces desquamation of the olfactory epithelium. • SARS-CoV-2 infects mainly sustentacular cells and not olfactory sensory neurons. • SARS-CoV2 infection lead to a massive recruitment of immune cells. • SARS-CoV-2 was not found in the central nervous system., Anosmia is one of the most prevalent symptoms of SARS-CoV-2 infection during the COVID-19 pandemic. However, the cellular mechanism behind the sudden loss of smell has not yet been investigated. The initial step of odour detection takes place in the pseudostratified olfactory epithelium (OE) mainly composed of olfactory sensory neurons surrounded by supporting cells known as sustentacular cells. The olfactory neurons project their axons to the olfactory bulb in the central nervous system offering a potential pathway for pathogens to enter the central nervous system by bypassing the blood brain barrier. In the present study, we explored the impact of SARS-COV-2 infection on the olfactory system in golden Syrian hamsters. We observed massive damage of the OE as early as 2 days post nasal instillation of SARS-CoV-2, resulting in a major loss of cilia necessary for odour detection. These damages were associated with infection of a large proportion of sustentacular cells but not of olfactory neurons, and we did not detect any presence of the virus in the olfactory bulbs. We observed massive infiltration of immune cells in the OE and lamina propria of infected animals, which may contribute to the desquamation of the OE. The OE was partially restored 14 days post infection. Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria.

Background: Acute respiratory infections (ARI) are recognized as an important cause of morbidity, mortality and hospitalization among children in developing countries. Human respiratory syncytial virus (HRSV) is the main cause of severe lower respiratory tract disease in infants, young children and the elderly. Identified in 2001, Human Metapneumovirus (HMPV) is a new paramyxovirus. Studies have shown the co-circulation of the subgroups of these two viruses with domination of one of the sub-groups according to the geographical zones and according of years. These two viruses encode two major surface glycoproteins, the highly conserved fusion F protein and the highly variable attachment G protein. Data are still limited in sub-Saharan African countries on prevalence, seasonality and genetic characterization of these two respiratory viruses. In Cameroon, these two viruses have been described only once (5.7 and 5% for HRSV and HMPV respectively) in patients with influenza-like illness in 2012.Objective: This study reports the prevalence, seasonality and the genetic variability of HRSV and HMPV strains in Cameroonian children for 3 consecutive epidemic seasons (September 2011-October 2014). Moreover, the genetic diversity of other respiratory viruses detected during this work is presented as a secondary objective.Methods: A prospective surveillance was conducted to identify inpatient and outpatient children less than 15 years with respiratory symptoms ≤ 5 days. The nasopharyngeal samples were tested for 17 respiratory viruses using a multiplex polymerase chain reaction. Viral distribution and demographic data were analyzed statistically. Positive samples for HRSV and HMPV were amplified by semi-nested polymerize chain reaction and then partially sequenced at the G gene. Phylogenetic analyzes were performed on the partial nucleotide and protein sequences of the G gene.Results: From September 2011 to October 2014, 822 children under 15 years were enrolled in the study. At least one virus was identified in each of 72.6% (577/822) of children, 31.7% (189/597) of whom were co-detections; 28.5% (226/822) were positive for human adenovirus, 21.4% (176/822) for influenza virus, 15.5% (127.822) for rhinovirus/enterovirus, 9.4% (77/822) for bocavirus, 9% (74/822) for HRSV, 8.2% (67/822) for human coronavirus, 6.2% (50/822) for human parainfluenzavirus, and 3.9% (32/822) for HMPV. HRSV infection was more frequent in children under 2 years (70.3%, 52/74) and hospitalized participants (70.3%, 52/74). While HRSV showed a seasonal pattern with circulation from September to December, sporadic cases of HMPV were detected throughout the year. HRSV-A (19.1%, 9/47) and HRSV-B (17%; 8/47) were observed relatively at the same frequency with (63.8%, 30/47) codetections of HRSV-A/HRSV-B. HMPV-A (71.4%; 10/14) was predominant compared to HMPV-B (28.6; 4/14). Phylogenetic analysis revealed that the HRSV strains of the study are grouped within subgroup NA-1 (for HRSV-A) and BA-9 (for HRSV-B). Cameroonian HMPV strains are grouped among the members of genotype A2b (for HMPV-A), B1 and B2 (for HMPV-B).Conclusion: This study suggests that about 70% of ARI recorded in children in Cameroon are caused by viruses. The present study is also the first report on the genetic variability of the G gene of HRSV and HMPV strains in the region. Although this work partially fills gaps for some information, additional studies are required to clarify the molecular epidemiology and evolutionary pattern of respiratory viruses in sub-Saharan Africa in general and more particularly in Cameroon.; Contexte : Les infections respiratoires aiguës (ARI) sont reconnues comme une cause importante de morbidité, de mortalité et d'hospitalisation chez les enfants dans les pays en développement. Le virus respiratoire syncytial humain (HRSV) est l’agent étiologique principal de maladie sévère des voies respiratoires basses chez les nourrissons, les jeunes enfants et les personnes âgées. Identifié en 2001, le Metapneumovirus humain (HMPV) est un nouveau paramyxovirus. Les études ont montré la cocirculation des sous groupes de ces deux virus avec la domination de l’un des sous groupes selon les zones géographiques et selon les années. Les données restent cependant limitées dans les pays de l’Afrique subsaharienne, sur la prévalence, la saisonnalité et la caractérisation génétique de ces deux virus respiratoires. Au Cameroun, ces deux virus ont été décrits seulement une seule fois (5,7 et 5% pour HRSV et HMPV respectivement) chez des patients présentant des syndromes grippaux en 2012. Objectif : Cette étude rapporte la prévalence, la saisonnalité et la variabilité génétique des souches HRSV et HMPV chez des enfants camerounais pendant 3 saisons épidémiques consécutives (de Septembre 2011 à Octobre 2014). Par ailleurs, la diversité génétique d’autres virus respiratoires détectés au cours de ce travail est présentée comme objectif secondaire.Méthodes : Une surveillance prospective a été menée pour identifier les enfants hospitalisés et ambulatoires âgés de moins de 15 ans présentant des symptômes respiratoires ≤ 5 jours. Les échantillons nasopharyngés ont été testés pour 17 virus respiratoires en utilisant une réaction multiplex de polymérisation en chaîne. La distribution virale et les données démographiques ont été analysées statistiquement. Les échantillons positifs du HRSV et HMPV ont été amplifiés par polymérisation en chaine semi nichée puis séquencés partiellement au niveau du gène G. Des analyses phylogénétiques ont été effectuées sur les séquences nucléotidiques et protéiques partielles du gène G.Résultats : De septembre 2011 à octobre 2014, 822 enfants âgés de moins de 15 ans ont été inscrits dans l’étude. Au moins un virus a été identifié chez chacun des 72,6% (597/822) d'enfants, dont 31,7% (189/597) étaient des codétections; 28,5% (226/822) étaient positifs pour l'adénovirus humain, 21,4% (176/822) pour le virus Influenza, 15,5% (127.822) pour le rhinovirus/entérovirus, 9,4% (77/822) pour le bocavirus, 9% (74/822) pour le HRSV, 8,2% (67/822) pour les coronavirus humain, 6,2% (50/822) pour le parainfluenzavirus humain et 3,9% (32/822) pour le HMPV. L’infection HRSV était plus fréquente chez les enfants de moins de 2 ans (70,3% ; 52/74) et chez les participants hospitalisés (70,3% ; 52/74). Alors que le HRSV a montré un profil saisonnier avec une circulation de septembre à décembre, des cas sporadiques de HMPV ont été détectés tout au long de l'année. HRSV-A (19,1%, 9/47) et HRSV-B (17% ; 8/47) ont été observés relativement à la même fréquence avec (63,8% ; 30/47) de cas en codétection HRSV-A/HRSV-B alors que HMPV-A (71,4% ; 10/14) était majoritaire comparé à HMPV-B (28,6 ; 4/14). L'analyse phylogénétique a révélé que les souches HRSV de l’étude sont groupées au sein du sous groupe NA-1 (pour HRSV-A) et BA-9 (pour HRSV-B). Les souches HMPV camerounaises sont groupés parmi les membres du génotype A2b (pour HMPV-A), B1 et B2 (pour HMPV-B).Conclusion : Cette étude suggère qu’environ 70% des ARI enregistrés chez des enfants au Cameroun sont causés par des virus. La présente étude est également le premier rapport sur la variabilité génétique du gène G des souches de HRSV et HMPV dans la région. Bien que ce travail comble partiellement certaines lacunes d’informations, des études supplémentaires sont requises pour une clarification de l’épidémiologie moléculaire et du mode d’évolution des virus respiratoires présents en Afrique subsaharienne en général et plus singulièrement au Cameroun.

We introduce this work with an update of the epidemiology concerning the many viral agents responsible for central nervous system (CNS) infections. The first part describes the circuit of a cerebrospinal fluid (CSF) sample in the CHU of Caen, from the collection to the analysis in the virology laboratory. We describe the results of these analysis between January 1st 2015 and December 31th 2016, and the prescriptions from the different care departments. The second part of this work reports a comparison of 2 RT-PCR method used for the detection of enteroviruses in the CSF, and an evaluation of a multiplex PCR for the detection of 14 pathogens agents involved in infectious meningitis and encephalitis.; L’introduction de cette thèse est une actualisation des données épidémiologiques concernant les nombreuses étiologies virales des infections du système nerveux central. La première partie décrit le parcours d’un échantillon de liquide céphalorachidien (LCR) au sein du CHU de Caen, de son prélèvement dans le service de soins, jusqu’à la réalisation des analyses de virologie. Nous décrivons aussi les résultats de ces analyses entre le 1er janvier 2015 et le 31 décembre 2016, ainsi que les prescriptions des différents services de soins. La seconde partie concerne la comparaison de deux méthodes de RT-PCR pour la détection des entérovirus dans le LCR, ainsi que l’évaluation d’une PCR Multiplex pour la détection de 14 micro-organismes impliqués dans les méningites et encéphalites infectieuses.