Hepatitis C subtype distribution in chronically infected patients with mild liver fibrosis in France: the GEMHEP study.

Treatment options for Hepatitis C infection have greatly improved with direct-acting antiviral (DAA) combinations achieving high cure rates. Nevertheless, the cost of this treatment is still high and access to treatment in many countries has been preferentially reserved for patients with more severe fibrosis (F3 and F4). In this French nationwide study, we investigated the epidemiological characteristics and genotype distribution of hepatitis C virus (HCV) in treatment-naive patients with METAVIR fibrosis stages between F0 and F2 in order to identify patient profiles that became eligible for unrestricted treatment in a second period. Between 2015 and 2016 we collected data from nine French university hospitals on a total of 584 HCV positive patients with absent, mild or moderate liver fibrosis. The most represented genotypes were genotype 1b (159/584; 27.2%), followed by genotype 1a (150/584; 25.7%); genotype 3 (87/584: 14.9%); genotype 4 (80/584; 13.7%). Among genotype 4: 4a was predominantly encountered with 22 patients (27.5% of genotype 4). Genotypes 1b and 1a are currently the most frequent virus types present in treatment-naive patients with mild fibrosis in France. They can be readily cured using the available DAA. Nevertheless, non-a/non-d genotype 4 is also frequent in this population and clinical data on the efficacy of DAA on these subtypes is missing. The GEMHEP is the French group for study and evaluation of viral hepatitis on a national scale. Data collection on epidemiological and molecular aspects of viral hepatitis is performed on a regular basis in all main French teaching hospitals and serves as a basis for surveillance of these infections. Analysis and trends are regularly published on behalf of the GEMHEP group. Data collection was performed retrospectively over the 2015-2016 period, covering nine main university hospitals in France. A total of 584 hepatitis C positive patients were included in this study. Genotyping of the circulating viruses showed a high prevalence of genotypes 1b and 1a in our population. The epidemiology of hepatitis C is slowly changing in France, particularly as a consequence of the rise of 'non-a non-d' genotype 4 viruses mainly originating from African populations. More data concerning treatment efficacy of these genotypes is needed in order to guide clinical care.

Acute flaccid paralysis following enterovirus D68 associated pneumonia, France, 2014.

Human enterovirus D68 (EV-D68) is known to be associated with mild to severe respiratory infections. Recent reports in the United States and Canada of acute flaccid paralysis (AFP) in children with detection of EV-D68 in respiratory samples have raised concerns about the aetiological role of this EV type in severe neurological disease. This case study is the first report of AFP following EV-D68 infection in Europe.

Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries.

Human enterovirus 71 (EV-71) is a cause of seasonal epidemics of hand, foot and mouth disease, and of less common but severe neurological manifestations. Uncertainty persists regarding the circulation of virus populations in several geographical areas and the timescale of their dissemination. We determined EV-71 sequences at loci 1D (VP1 capsid protein) and 3CD (non-structural proteins) in 86 strains recovered in Austria, France and Germany and performed an evolutionary genetic study of extant virus populations. Phylogenetic analyses positioned 78 of the 86 sequences within two clades among subgenogroups C1 and C2. A minor sequence cluster was assigned to subgenogroup C4. Analyses incorporating the available sequences estimated the substitution rate in genogroup C at 3.66 x 10(-3) and 4.46 x 10(-3) substitutions per site year(-1) for loci 1D and 3CD, respectively, assuming a relaxed molecular-clock model for sequence evolution. Most of the 'European' strains belonged to clades C1b and C2b, which originated in 1994 [95 % confidence interval (CI), 1992.7-1995.8] and 2002 (95 % CI, 2001.6-2003.8), respectively. Estimates of divergence times for locus 3CD were consistent with those measured for locus 1D. Intertwining between clades representing EV-71 subgenogroups and clades corresponding to other enterovirus types (notably early coxsackievirus A prototype strains) in the 3CD phylogeny is highly indicative of ancestral recombination events. Incongruent phylogenetic patterns estimated for loci 1D and 3CD show that a single tree cannot model the epidemic history of circulating EV-71 populations. The evolutionary timescale of genogroup C estimated for both loci was measured only in decades, indicating recent dissemination.

Major 5'terminally deleted enterovirus populations modulate type I IFN response in acute myocarditis patients and in human cultured cardiomyocytes.

Major 5'terminally deleted (5'TD) group-B enterovirus (EV-B) populations were identified in heart biopsies of patients with fulminant myocarditis or dilated cardiomyopathy suggesting that these 5'TD forms are key drivers of host-cell interaction in EV cardiac infections. To date, early emergence of EV-B 5'TD forms and its impact on type 1 IFN response during acute myocarditis remains unknown. Using quantitative RACE-PCR assay, we identified major EV-B 5'TD RNA populations in plasma or heart samples of acute myocarditis cases. Deletions identified within the 5' non-coding region of EV-B populations only affected secondary-structural elements of genomic RNA domain I and were distinguished in two major groups based on the extent of RNA structural deletions. Proportions of these two respective EV-B 5'TD population groups were positively or negatively correlated with IFN-ß levels in plasma samples of myocarditis patients. Transfection of synthetic CVB3/28 RNAs harboring various 5'terminal full-length or deleted sequences into human cultured cardiomyocytes demonstrated that viral genomic RNA domain I possessed essential immunomodulatory secondary-structural elements responsible for IFN-ß pathway induction. Overall, our results highlight the early emergence of major EVB-TD populations which deletions affecting secondary-structures of RNA domain I can modulate innate immune sensing mechanisms in cardiomyocytes of patients with acute myocarditis.

Census and analysis of persistent false-negative results in serological diagnosis of human immunodeficiency virus type 1 group O infections.

Human immunodeficiency viruses (HIV) have a high level of genetic diversity. The outlier variants of HIV type 1 (HIV-1) group O are distantly related to HIV-1 group M. Their divergence has an impact on serological diagnosis, with a risk of false-negative results. In this study, we report 20 failure cases, involving patients with primary or chronic infection, in France and Cameroon between 2001 and 2008. Our results indicate that some assays detected group O infection much less efficiently than others. Two major reasons for these false-negative results were identified: the presence or absence of a group O-specific antigen (and the designed sequence) for the detection of antibodies and the greater envelope variability of group O than of group M strains. This study highlights the complexity of screening for these divergent variants and the need to evaluate test performance with a large panel of strains, due to the extensive diversity of group O variants.

Impact of rapid enterovirus molecular diagnosis on the management of infants, children, and adults with aseptic meningitis.

Enteroviruses (EV) are the main etiological agents of aseptic meningitis. Diagnosis is made by detecting the genome using RT-PCR. The aim of the study was to evaluate the impact of a positive diagnosis on the management of infants, children, and adults. During 2005, 442 patients were admitted to hospital with suspected meningitis. Clinical and laboratory data and initial treatment were recorded for all patients with enteroviral meningitis. The turnaround time of tests and the length of hospital stay were analyzed. The results showed that EV-PCR detected EV in 69 patients (16%), 23% (16/69) were adults. About 18% of CSF samples had no pleocytosis. After positive PCR results, 63% of children were discharged immediately (mean 2 hr 30 min) and 95% within 24 hr. Infants and adults were discharged later (after 1.8 and 2 days, respectively). The use of antibiotics was significantly lower in children than in infants and adults. The PCR results allowed discontinuation of antibiotics in 50-60% of all patients treated. Patients received acyclovir in 16% of cases (7% children vs. 50% adults) and 23% (11% vs. 69%) underwent a CT scan. Clinical data were compared between patients whose positive EV-PCR results were available within 24 hr (n = 32) and those whose results were available > 24 hr after collection of CSF (n = 14). Duration of antibiotic treatment (difference: 2.3 days; P = 0.05) was reduced between the two groups. No statistical difference in the length of stay was observed. The EV-PCR assay should be performed daily in hospital laboratory practice and considered as part of the initial management of meningitis.

[Epidemiologic characteristics and prevention of viral nosocomial infections]. / Particularités épidémiologiques et prévention des infections nosocomiales virales.

OBJECTIVES: To describe epidemiological features of viral nosocomial infections (VNI) and their prevention principles. EPIDEMIOLOGY: Many factors lead to underestimate VNI: difficulty to distinguish between community-acquired and nosocomial infections for seasonal viral diseases, incubation time leading to symptoms after patient discharge, difficulty for diagnosis. Population at high risks of VNI are the children, the elderly and the immunocompromized patients. The risk of severe diseases is high in this last population. The main reservoir of virus is infected symptomatic or asymptomatic individuals. Asymptomatic carriers, especially health care workers, are a major source of transmission. Main routes of transmission are the fecal-oral route, the respiratory route, cutaneous or mucous contact and blood and body fluids exposure. A review of the main virus involved in VNI is presented. PREVENTION: Preventive measures, such as strict adherence to standard precautions and, in some instances, to isolation procedures, are critical to control VNI. In a major outbreak situation, it may be necessary to consider cohort isolation. Specific control measures rely on immunization, antiviral drug prophylaxis (varicella-zooster, herpes, influenza, exposure to blood) and clinical and biological screening of organ, blood, tissue and cell donors.

[Genotyping and molecular epidemiology of non polyomyelitic enteroviruses]. / Génotypage et épidémiologie moléculaire des entérovirus non poliomyélitiques.

Nonpolio enteroviruses can be reliably identified with molecular and computer tools for taxonomic, diagnostic and epidemiologic purposes. Seroneutralization tests can efficiently be replaced by genotyping assays using the VP1 capsid protein encoding gene to identify enterovirus strains isolated in cell cultures. Genotyping showed the close genetic relatedness between human enterovirus serotypes and animal enteroviruses and also rhinoviruses currently classified in a separate genus within the Picornaviridae family. Enterovirus genotyping can be done prospectively within 2 to 5 days in a greater number of meningitis patients, using cerebrospinal fluid specimens and hence can help in providing a prompt response to health alert. In the molecular epidemiology of human enteroviruses, recent advances were made by investigating genetic diversity within individual serotypes (genotypes, lineages) and the patterns of circulation and transmission of virus variants involved in epidemics (echovirus 30, enterovirus 71). The observation of epidemiologic features such as the frequent viral immigration of strains from different geographical origins speaks in favour of developing molecular identification of enteroviruses. Recombinant enterovirus strains can also be identified by genotyping. Homologous recombination is a major contributor to the genetic diversity in enteroviruses. Molecular signatures of recombination events are observed in circulating strains, suggesting the occurrence of frequent co-infections during their circulation within the general population. The role of genetic recombination in the emergence of virus variants and its involvement in the epidemiology of human enteroviruses should be investigated.

The epidemiology and virology of hepatitis C virus genotype 5 in central France.

BACKGROUND: We previously reported high prevalence of hepatitis C virus genotype 5a (HCV 5) (14%) in Central France. AIM: To identify the risk factors associated with HCV5 infection and to characterize local HCV5 lineages. METHOD: A case-control study and phylogenetic analysis were conducted. RESULTS: In all, 131 HCV5 and 343 HCV non 5 infected patients were enrolled. No HCV5 patient was born in sub-Saharan Africa and only two were injection drug user. HCV5 contamination was associated with living in a rural area called Vic le Comte (VLC) in non-transfused patients (OR = 17.7), with transfusion in patients living outside VLC (OR = 3.8) and with receiving injections in patients from VLC (OR = 3.1). More than 80% of the patients from outside VLC were contaminated by transfusion and those from VLC mainly by an iatrogenic factor - injections performed before 1972 by the local physician. Phylogenetic analysis of HCV5 isolates evidenced no distinct genetic cluster, but close relationships between the isolates of spouse pairs and between blood donors and recipients. CONCLUSIONS: Our results suggest that HCV5 spread in our district by iatrogenic route before 1972 and then via transfusion to the whole district. Collaborative studies are underway to study viral sequences from different parts of Africa and Europe to estimate the origin of our HCV 5a strains.

[Fatal case of enterovirus A71 hand, foot, and mouth disease infection]. / Décès d'un nourrisson dans un contexte de syndrome pieds-mains-bouche associé à l'entérovirus A71.

Hand, foot, and mouth disease associated with enterovirus (EV) infections is a common pediatric pathology that is usually considered as benign. However, neurological complications of varying severity, sometimes fatal, are possible, particularly when EV-A71 is involved. Several Asian countries are regularly affected by large-scale epidemics of EV infections with substantial morbidity and mortality, where early screening and appropriate therapeutic management are a public health challenge. In 2016, Europe experienced an epidemic of unusual magnitude, associated with increasing cases of severe neurological complications in Spain and France, mainly affecting children. Virological diagnosis is based on EV genome detection in peripheral clinical specimens (vesicles or oral ulcerations, throat, nasopharyngeal aspirate, stool) in addition to cerebrospinal fluid and blood. EV-A71 is rarely detected in cerebrospinal fluid, which renders the diagnosis of EV-A71-associated encephalitis challenging. We report the case of a 27-month-old child with hand, foot, and mouth disease turning into rapidly progressive and fatal cardiopulmonary failure associated with EV-A71 infection, in France in 2016. EV infections associated with hand, foot, and mouth disease warrant specific epidemiological surveillance outside the Asian region.

Effectiveness of interferon plus ribavirin combination in the treatment of naive patients with hepatitis C virus type 5. A French multicentre retrospective study.

AIM: To assess the rate of sustained virological response in naïve hepatitis C virus-type 5 patients treated by standard interferon or pegylated-interferon [corrected] (peg-interferon) and ribavirin combination for 48 weeks. PATIENTS AND METHODS: A total of 87 hepatitis C virus patients were included from 12 centres in France; 28 patients received interferon plus ribavirin and 59 were treated with peg-interferon plus ribavirin. RESULTS: Baseline characteristics were: mean age 58 +/- 11 years, sex ratio 1, 66% had metavir fibrosis score >or=F2, 21% were cirrhotics and 53% had pretherapeutic viral load >or=800,000 IU/mL. Sustained virological response was achieved in 64% and 58% of hepatitis C virus-5 patients treated with interferon and peg-interferon, respectively (NS). In adherent patients, sustained virological response was obtained in 75% of patients. Sustained virological response in hepatitis C virus-5 patients (60%) was significantly higher than sustained virological response in hepatitis C virus-1 patients (37%) (P = 0.0499) and not significantly different from sustained virological response in hepatitis C virus-2-3 patients (63%) (P = 0.8098). CONCLUSIONS: Combination therapy is effective in 60% of hepatitis C virus-5-infected patients. Sustained virological response seems better in hepatitis C virus-5 patients than in hepatitis C virus-1 patients, and is similar to that of hepatitis C virus-2-3 patients. More studies are needed to determine optimal duration of treatment in hepatitis C virus-5 patients.

[From prospective molecular diagnosis of enterovirus meningitis...to the prevention of antibiotic resistance]. / Du diagnostic moléculaire initial prospectif des méningites à entérovirus...à la lutte contre l'antibiorésistance.

Meningitis initially presents with intense manifestations that are not generally specific to a given etiology. The first major question for the physician is to decide whether to initiate a probabilistic treatment. Enteroviruses are a major cause of aseptic meningitis, which is benign in immunocompetent patients. Molecular diagnosis is now becoming the gold standard and its prospective use at the time of patient admission, on the sole basis of clinical suspicion of meningitis, has yielded more reliable data. Cytological and biochemical data from CSF analyses are of low predictive value to influence the initial decision to treat with antibiotics. In addition, cases of meningitis during winter are not uncommon. Adults are concerned in about 25% of cases. Thus, if molecular diagnostic tools are not rapidly available, patient management may be inconsistent, leading to unnecessary scans, laboratory investigations and treatment (including overconsumption of antibiotics). Current progress in the automation and practicability of viral genomic detection yields the result within a few hours after admission. Rapid molecular viral diagnosis of a benign disease that does not require treatment but which is initially worrying is of unquestionable advantage. It is of benefit to both the patient and the community because of its input on health economics, the needless consumption of drugs and, as a result, resistance to antibiotics. The diagnosis of meningitis can no longer remain a retrospective diagnosis after elimination of all the possible causes, since not prescribing unnecessary laboratory tests and not treating are true therapeutic decisions.

[Non Hodgkin's and Hodgkin's lymphomas and HIV: frequency, outcome and immune response under HAART; Clermont-Ferrand University Hospital, 1991-2003]. / Lymphomes non hodgkiniens et hodgkiniens et infection VIH: fréquence, pronostic et reconstitution immune sous trithérapie antirétrovirale; CHU de Clermont-Ferrand, 1991-2003.

OBJECTIVES: The authors had for aim to identify cases of non Hodgkin's (NHL) and Hodgkin's (HL) lymphomas in HIV1-infected patients to assess 1) their incidence, before and after 1996, 2) the clinical features and outcome under treatment together with the survival rate of the patients, 3) the immune reconstitution of lymphoma-free patients under HAART. PATIENTS AND METHODS: A retrospective study was made of HIV1-infected patients managed at the Clermont-Ferrand University Hospital from 1991 to 2003 for the diagnosis and treatment of HIV1-related lymphomas. RESULTS: Forty-one patients were included: 35 NHL and 6 HL giving a cumulative incidence rate estimate from 2.4% between 1991 and 1996 to 3.4% between 1997 and 2003 while other opportunistic diseases were decreasing. A high proportion of aggressive and disseminated disease was observed among NHL cases. Complete remission was achieved in 17 (49%) and 5 (83%) NHL and HL cases respectively. The mean survival was 109+/-54 months and was correlated with CD4 cell count at lymphoma diagnosis (univariate analysis). Among responding patients, 5 died: 3 from opportunistic infections, 1 commited suicide, and 1 from hepatic carcinoma. For responding patients, the mean increase of CD4 cell count under HAART was 58/mm3 over a 2 year-period and 192/mm3 over a 5 year-period of follow-up. CONCLUSIONS: The incidence of lymphomas in HIV-infected patients has not decreased since the introduction of HAART. The immune status assessed by CD4 cell count on diagnosis is correlated with survival. Immune restoration in lymphoma-free patients under HAART is poor.

Varicella outbreak in Sudanese refugees from Calais.

We describe an outbreak of varicella in 31 Sudanese refugees (all except one were male, mean age: 26 ± 1), from the Calais migrant camp and sheltered in a French transit area. The attack rate was 39%. Adults are scantly immunized against varicella zoster virus in East Africa and may be exposed to epidemics once in France.

Identification of a duplicated V3 domain in NS5A associated with cirrhosis and hepatocellular carcinoma in HCV-1b patients.

BACKGROUND: The NS5A protein of the hepatitis C virus has been shown to be involved in the development of hepatocellular carcinoma. OBJECTIVES: In a French multicenter study, we investigated the clinical and epidemiological features of a new HCV genotype 1b strain bearing a wide insertion into the V3 domain. STUDY DESIGN: We studied NS5A gene sequences in 821 French patients infected with genotype 1b HCV. RESULTS: We identified an uncharacterized V3 insertion without ORF disruption in 3.05% of the HCV sequences. The insertion comprised 31 amino-acids for the majority of patients; 3 patients had 27 amino-acids insertions and 1 had a 12 amino-acids insertion. Sequence identity between the 31 amino-acids insertions and the V3 domain ranged from 48 to 96% with E-values above 4e(-5), thus illustrating sequence homology and a partial gene duplication event that to our knowledge has never been reported in HCV. Moreover we showed the presence of the duplication at the time of infection and its persistence at least during 12 years in the entire quasispecies. No association was found with extrahepatic diseases. Conversely, patients with cirrhosis were two times more likely to have HCV with this genetic characteristic (p=0.04). Moreover, its prevalence increased with liver disease severity (from 3.0% in patients without cirrhosis to 9.4% in patients with both cirrhosis and HCC, p for trend=0.045). CONCLUSIONS: We identified a duplicated V3 domain in the HCV-1b NS5A protein for the first time. The duplication may be associated with unfavorable evolution of liver disease including a possible involvement in liver carcinogenesis.

Prospective analysis of 61 cases of enteroviral meningitis: interest of systematic genome detection in cerebrospinal fluid irrespective of cytologic examination results.

BACKGROUND: Enteroviruses are the most commonly identified cause of viral meningitis. Detection of the enterovirus genome in cerebrospinal fluid (CSF) using reverse-transcription polymerase chain reaction (PCR) has proved to be useful in diagnosis and is more rapid and sensitive than viral cultures. In routine practice, cytologic examination results of CSF are obtained swiftly and PCR indication is performed as a second step. OBJECTIVES: The aim of this study was to determine, by analysis of complete data from CSF results for 61 cases of proven enteroviral meningitis, whether cytologic CSF findings can be used to establish viral etiology and to indicate if PCR assay should be performed. STUDY DESIGN: From a prospective study of children admitted during 1997 for suspected enterovirus meningitis in which PCR and viral cultures of CSF were systematically performed, we selected 61 patients with proven enterovirus meningitis. We compared global white cell count (WCC), relative percentage of lymphocytes/neutrophils, PCR and culture for enterovirus, patient age, and clinical data. RESULTS: 92% of patients (56/61) had positive PCR in CSF and in 48% (29/61) enterovirus was isolated in CSF. Nine patients (14.75%) had WCC<10/mm(3); eight of them had positive PCR and two had positive culture. There were comparable numbers of CSF with a predominance of lymphocytes (n=25) and CSF with a predominance of neutrophils (n=22), and of positive PCR and positive cultures of CSF in the two groups. Results were not influenced by the age of the patients. CONCLUSION: Irrespective of other CSF parameters, it seems difficult to dispense with PCR assay for enterovirus genome detection. It should be introduced as a true rapid routine test. Early reporting of a positive PCR result could result in a considerable saving in health resources.

Nosocomial rotavirus infections in adult renal transplant recipients.

We conducted a 24-month survey of hospital-acquired rotavirus infections in 20 renal transplant recipients who received their graft during 1988. Four cases of nosocomial rotavirus infection were diagnosed (20% of patients), 3-34 days after graft. Two patients presented with severe diarrhoea and two with fever alone. The cases occurred mainly during the winter months and remained sporadic. None of our patients was found to have chronic excretion of rotaviruses. Contacts from paediatric cases can be ruled out. We concluded that rotavirus nosocomial infections were frequent in adult renal transplant recipients and suggest that screening for rotavirus is regularly performed in these immunodeficient patients who are very susceptible to hypovolaemia.

An outbreak due to echovirus type 30 in a neonatal unit in France in 1997: usefulness of PCR diagnosis.

Between February and August 1997, 53 patients with enterovirus meningitis were hospitalized in Clermont-Ferrand, France. All but one were children. Echovirus type 30 was involved in 70% of cases with identified serotype. The outbreak ceased on August 8. Two months later, a neonate was admitted to the neonatal unit with an echovirus type 30 meningitis thought to be acquired at delivery. Twenty days later a nosocomial outbreak of echovirus type 30 involving five neonates occurred. Two of them presented with meningitis and two with febrile seizure; One was asymptomatic. The retrospective examination of the maternal sera in a neutralization test, using the index case strain as a source of antigen, showed that none of the neonates was passively immunized before hospitalization. The use of genome detection in cerebrospinal fluid allowed rapid diagnosis and infection was contained by re-inforcing hygiene measures. Prospective examination of stools in the neonatal and paediatric units showed no further occurrences of the disease. No sporadic case was observed in the general population. Hence, nosocomial infections can occur a long time after an outbreak in the general population; rapid diagnosis with molecular tools is useful both for a definite diagnosis in patients already hospitalized, and to act as a rapid alert, even in intervals between seasonal outbreaks.