First next-generation sequencing full-genome characterization of a hepatitis C virus genotype 7 divergent subtype

We report the near-full-length genome sequence of a hepatitis C virus (HCV) isolate from a man originating from Democratic Republic of Congo, the genotype of which could not be determined by the routinely used sequencing technique. The near-complete genome sequence of this variant BAK1 was obtained by the association of two next-generation sequencing technologies. Evolutionary analysis indicates that this isolate, BAK1, could be the first reported strain belonging to a new HCV-7b subtype. This new subtype has been incorrectly identified as genotype 2 by the Versant HCV Genotype 2.0 assay (LiPA). The requirement of three independent isolates has been filled, and a new subtype can be assigned. More examples of HCV-7 are required to better understand its origin, its pathogenicity and its relationship with genotype 2.

Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains

Directly acting antiviral drugs have contributed considerable progress to hepatitis C virus (HCV) treatment, but they show variable activity depending on virus genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the HCV near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV 1a, 1b, 3a and 4a, 16/22) and 45% for recombinant forms RF_2k/1b (5/11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in seven of 13 samples at baseline, in the NS3 (n = 3) or NS5A (n = 4) region. Of these samples, the treatment of one patient included daclatasvir, and that patient experienced a relapse. Virus sequences from pre- and posttreatment samples of four patients who experienced relapse after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proven to be successful for both genotyping and resistance-associated variant detection on several HCV types.

Symptomatic cytomegalovirus gastrointestinal infection with positive quantitative real-time PCR findings in apparently immunocompetent patients: a case series

Cytomegalovirus (CMV) gastrointestinal disease rarely occurs in immunocompetent patients, and is mainly diagnosed on the basis of histopathological findings. Real-time PCR for CMV DNA quantification is considered to be a useful diagnostic tool, but its place in the diagnostic strategy is not clearly defined. The goal of the study was to describe the clinical and paraclinical features of apparently immunocompetent patients with CMV gastrointestinal disease diagnosed according to quantitative PCR results. In this retrospective study conducted in a 1500-bed tertiary-care centre, we reviewed the case records of apparently immunocompetent patients with positive findings of CMV DNA in gastrointestinal biopsies with compatible symptoms and endoscopic findings. A total of 13 patients were included between January 2007 and December 2010. The median age was 81 years, and 54% of patients had underlying immune-modulating conditions. Diarrhoea, haematochezia and dysphagia were the main reported symptoms, and ulcers were the main endoscopic findings. The mean value of CMV DNA load in gastrointestinal biopsies was 3845 copies/μg total DNA (range, 15-15 500 copies/μg total DNA). The highest values were found in two patients who were diagnosed with adenocarcinoma in the subsequent course of CMV infection. Clinical features were similar to those in previous series in which diagnosis was based on histopathological analysis. Elderly people are more commonly affected, and a link with immune senescence is possible. Quantification of CMV DNA seems to be a useful tool for diagnosis when combined with clinical and endoscopic findings, but further studies are necessary to interpret quantitative values.

Recent evidence of underestimated circulation of hepatitis C virus intergenotypic recombinant strain RF2k/1b in the Rhône-Alpes region, France, January to August 2014: implications for antiviral treatment

Since the beginning of 2014, hepatitis C virus (HCV) recombinant forms RF2k/1b have been detected in the Rhône-Alpes French region in 10 patients originating from the Caucasus area. Circulation of this particular HCV strain is very likely to be underestimated. It is also prone to be misgenotyped when using genotyping methods based on the 5' region of the viral genome, which may lead to suboptimal treatment.

Association between hepatitis E and neurological disorders: two case studies and literature review

Hepatitis E (HEV) is an emerging disease in our developed countries, but is not routinely tested for in case of liver cytolysis. However, a growing number of extra-hepatic manifestations of HEV infection associated with acute hepatitis are reported. In this article, we discuss two cases of HEV with neurological symptoms, one with encephalitis, and the other with Parsonage Turner syndrome. All these disorders appeared concomitantly with liver cytolysis and disappeared quickly, following the viral kinetics. Only twenty cases of neurological manifestation of HEV have been described before. The use of HEV serology in patients with concurrent liver cytolysis and neurological symptoms has to be improved.

Toxicokinetics of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) in the European corn borer,Ostrinia nubilalis (Hübner)

2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), the major hydroxamic acid present in corn, and its tritiated derivative, were prepared synthetically for use in the determination of the toxicokinetics of this insect deterrent in the European corn borer (ECB),Ostrinia nubilalis. In growth studies with DIMBOA (0, 0.05, 0.2, and 0.5 mg/g diet), the mean time to pupation and adult emergence were significantly lengthened by an increase in concentration. Pupal and adult weights, for both female and male, decreased with an increase in concentration. Increased larval and pupal mortality occurred at the highest concentration of DIMBOA. DIMBOA, at concentrations of 0.2 and 0.5 mg/g diet, resulted in a decrease in the number of egg masses produced per female, and at 0.5 mg/g diet, in a decrease in the number of eggs per egg mass. Larvae fed from the neonate stage on a diet containing 0.2 mg [(3)H]- + [(1)H]DIMBOA/g diet showed an increase in the content of label from fourth to fifth instar, but levels declined at pupation and emergence. A large amount of the labeled compounds was excreted by the insect in the pupal case. In dose-related studies, both uptake and excretion increased with an increase in concentration of DIMBOA (0.05, 0.2, 0.4 mg/g diet), while a body burden (concentration in the tissues/concentration in the frass) of approximately 0.25 was maintained for all concentrations. At the highest dose of DIMBOA (0.4 mg/g), the ECB increased consumption, possibly to compensate for the toxic effects of the compound. In topical application studies, elimination of the labeled compound in the frass was rapid, reaching 65% by 4 hr and 88% by 48 hr. Accumulation of label in tissues other than hemolymph was low. The results show that the ECB does possess adaptive mechanisms to deal with the effects of this host-derived compound.

Success and failure of artesunate treatment in five transplant recipients with disease caused by drug-resistant cytomegalovirus

Cytomegalovirus (CMV) strains resistant to ganciclovir, cidofovir and/or foscarnet were genotypically and phenotypically characterised in two haematopoietic stem cell transplant recipients and three solid-organ transplant recipients with CMV disease. The anti-malaria drug artesunate led to a favourable virological and clinical response in three cases with mild CMV diseases (fever and neutropaenia) but was ineffective in two fatal CMV diseases with lung involvement in spite of a decrease in the CMV DNA load in blood and bronchoalveolar fluid.

Adult patients hospitalized for measles in France, in the 21st century

BACKGROUND

An epidemic of measles broke out in France in 2008. We designed a retrospective study focusing on adults hospitalized for measles in 2010/2011.

METHODS

A case was any patient aged more than 15 years, hospitalized (September 2010 to September 2011) with a typical rash or a biological diagnosis. Data was collected with standardized questionnaires in participating hospitals.

RESULTS

Four hundred and sixty cases were reported: sex-ratio (M/F) = 0.93, median age 26 years (σ = 8.8). Twenty-nine cases were severe (6.5%), 27 of which hospitalized in an ICU. Three hundred and twelve (68%) cases had elevated serum transaminases (EST), 155 (34%) cases had pneumonia, 34 (7%) cases had elevated serum creatinine (ESC), four (0.9%) cases had elevated serum amylase and lipase (ESAL), and three (0.7%) cases had neurological symptoms. One hundred and four (23%) patients presented simultaneously with EST and pneumonia. One patient presenting with severe pneumonia died (0.2%). One hundred and ten (24%) patients received antibiotics during a median seven days.

CONCLUSION

Measles can present as various syndromes in adults and be responsible for a high burden during outbreaks. The immediate outcome is favorable in most patients. Long-term outcome needs further investigations to identify possible late complications.

[What's new in the diagnosis and treatment of Neisseria gonorrhoeae]

Bacterial culture remains the gold standard for symptomatic infection. Nucleic Acid Amplification Tests (NAATs) have better sensitivity and specificity for rectal and pharyngeal specimens. A bacterial culture with antibiogram must be done for all NAAT positive specimens in order to modify antibiotics prescription if needed. We must fear a diffusion of extensively drug-resistant Neisseria gonorrhoeae in the future. Nevertheless, ceftriaxone 500 mg intramuscular with 1 g of azithromycin against Chlamydia trachomatis remains the treatment of N. gonorrhoeae infections. Screening of partners of identified cases and other STDs is the main measure to add to the treatment of gonorrhea.

Blood Epstein-Barr virus DNA load and risk of progression to AIDS-related systemic B lymphoma

BACKGROUND

AIDS-related lymphoma (ARL) remains the main cause of AIDS-related deaths in the combined antiretroviral therapy (cART) era. Although most ARLs are associated with the Epstein-Barr virus (EBV), whether patients with high EBV burden are more at risk of developing ARL is unknown. This study investigated the relationship between high blood EBV DNA loads and subsequent progression to ARL.

METHODS

We identified 43 cases of ARL diagnosed between 1988 and 2007 within two cohorts (ANRS SEROCO/HEMOCO and PRIMO) and for which stored serum and peripheral blood mononuclear cell (PBMC) samples were available within 3 years before ARL diagnosis. For each case, two controls matched for the cohort and CD4 cell count in the year of ARL diagnosis were selected. EBV DNA was measured in PBMCs and serum samples with a commercial kit.

RESULTS

High levels of EBV DNA in PBMCs collected a median of 10 months before diagnosis were associated with an increased risk of developing systemic B lymphoma (adjusted odds ratio 2.47; 95% confidence interval 1.15; 5.32 for each 1 log copies/10(6) PBMC increase in EBV load) but not with primary brain lymphoma.

CONCLUSION

In this study, HIV-infected patients with undetectable EBV DNA in PBMCs did not develop ARL in the following 3 years, while high levels of EBV DNA in PBMCs predicted subsequent progression to systemic B lymphoma. Clinicians should be aware of the increased risk of developing systemic B lymphoma in HIV-infected patients with a high blood EBV DNA load.

[Lymphohistiocytic activation syndrome and Burkholderia cepacia complex infection in a child revealing chronic granulomatous disease and chromosomal integration of the HHV-6 genome]

Chronic granulomatous disease (GCD) is characterized by severe infections, notably with Burkholderia cepacia complex (BCC). GCD is rarely complicated by lymphohistiocytic activation syndromes, most often secondary to bacterial or viral infections, in particular human herpes virus 6 (HHV-6). We describe the case of a 10-month-old boy who suffered from multiple organ failure due to a BCC infection and a lymphohistiocytic activation syndrome, leading to diagnosis of GCD. The initial search for HHV-6 was positive and the infection was treated, but the progression and viral sample analysis led to the chromosomal integration of the HHV-6 genome. The child's clinical condition was normal after bone marrow transplantation. This case describes a rare association between GCD and lymphohistiocytic activation syndrome and raises questions about the role played by chromosomal integration of the HHV-6 genome.

Epidemiology of viral encephalitis in 2011

Encephalitis is an inflammation of the brain structures: neurons, vessels or glial cells. However, a consensual definition of the syndrome is difficult to obtain, and it is even more difficult to define encephalitis due a specific agent. Most viruses can be responsible for infectious encephalitis, but the number of encephalitis cases is very limited with regards of the incidence of benign infections from these pathogens. Viruses responsible for encephalitis can be animal-borne, vector-borne or human-to-human transmitted, they can infect preferentially immunocompetent or immunosuppressed patients, and some of them have demonstrated their epidemic potential. Herpes simplex encephalitis is recognized worldwide as the most frequent infectious encephalitis, and the only one with a validated specific treatment. Encephalitis following some viral infections such as measles or rabies can be prevented by vaccination. Unfortunately, effective treatment currently lacks for most encephalitic viral agents identified so far.