Jan Zoll

Saffold virus, a human Theiler's-like cardiovirus, is ubiquitous and causes infection early in life.

The family Picornaviridae contains well-known human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and parechovirus). In addition, this family contains a number of viruses that infect animals, including members of the genus Cardiovirus such as Encephalomyocarditis virus (EMCV) and Theilers murine encephalomyelits virus (TMEV). The latter are important murine pathogens that cause myocarditis, type 1 diabetes and chronic inflammation in the brains, mimicking multiple sclerosis. Recently, a new picornavirus was isolated from humans, named Saffold virus (SAFV). The virus is genetically related to Theilers virus and classified as a new species in the genus Cardiovirus, which until the discovery of SAFV did not contain human viruses. By analogy with the rodent cardioviruses, SAFV may be a relevant new human pathogen. Thus far, SAFVs have sporadically been detected by molecular techniques in respiratory and fecal specimens, but the epidemiology and clinical significance remained unclear. Here we describe the first cultivated SAFV type 3 (SAFV-3) isolate, its growth characteristics, full-length sequence, and epidemiology. Unlike the previously isolated SAFV-1 and -2 viruses, SAFV-3 showed efficient growth in several cell lines with a clear cytopathic effect. The latter allowed us to conduct a large-scale serological survey by a virus-neutralization assay. This survey showed that infection by SAFV-3 occurs early in life (>75% positive at 24 months) and that the seroprevalence reaches >90% in older children and adults. Neutralizing antibodies were found in serum samples collected in several countries in Europe, Africa, and Asia. In conclusion, this study describes the first cultivated SAFV-3 isolate, its full-length sequence, and epidemiology. SAFV-3 is a highly common and widespread human virus causing infection in early childhood. This finding has important implications for understanding the impact of these ubiquitous viruses and their possible role in acute and/or chronic disease.

MDA5 Detects the Double-Stranded RNA Replicative Form in Picornavirus-Infected Cells

Summary RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C), a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions.

The mengovirus leader protein suppresses alpha/beta interferon production by inhibition of the iron/ferritin-mediated activation of NF-kappa B.

ABSTRACT In our studies on the biological function of the mengovirus leader protein, we identified a casein kinase II (CK-2) phosphorylation site in the protein. Here we report that the mengovirus leader protein can be phosphorylated by CK-2 in vitro. Expression of a recombinant leader protein in which the consensus CK-2 sequence around threonine 47 was disturbed resulted in a mutant protein that could no longer be phosphorylated. The CK-2 consensus sequence was modified by site-directed mutagenesis and subsequently introduced into a mengovirus cDNA clone to investigate the effect of the phosphorylation of the leader protein on virus replication and on the host cell response. Modifications by which the CK-2 consensus sequence was disturbed resulted in mutant viruses with reduced growth kinetics. We demonstrated that the integrity of the CK-2 phosphorylation site of the mengovirus leader protein was specifically related to the suppression of NF-κB activation and subsequent suppression of alpha/beta interferon production in infected cells. We also found that the integrity of the CK-2 phosphorylation site of the leader protein coincided with an increase of ferritin expression in the infected cell. These data indicate that the leader protein suppresses the iron-mediated activation of NF-κB and thereby inhibits alpha/beta interferon expression in the infected cell.

The mengovirus leader protein blocks interferon-alpha/beta gene transcription and inhibits activation of interferon regulatory factor 3.

Viral infection of mammalian cells triggers the synthesis and secretion of type I interferons (i.e. IFN‐α/β), which induce the transcription of genes that cause cells to adopt an antiviral state. Many viruses have adapted mechanisms to evade IFN‐α/β‐mediated responses. The leader protein of mengovirus, a picornavirus, has been implicated as an IFN‐α/β antagonist. Here, we show that the leader inhibits the transcription of IFN‐α/β and that both the presence of a zinc finger motif in its N‐terminus and phosphorylation of threonine‐47 are required for this function. Transcription of IFN‐α/β genes relies on the activity of a number of transcription factors, including interferon regulatory factor 3 (IRF‐3). We show that the leader interferes with the transactivation activity of IRF‐3 by interfering with its dimerization. Accordingly, mutant viruses with a disturbed leader function were impaired in their ability to suppress IFN‐α/β transcription in vivo. By consequence, the leader mutant viruses had an impaired ability to replicate and spread in normal mice but not in IFNAR‐KO mice, which are incapable of mounting an IFN‐α/β‐dependent antiviral response. These results suggest that the leader, by suppressing IRF3‐mediated IFN‐α/β production, plays an important role in replication and dissemination of mengovirus in its host.

Azole, polyene and echinocandin MIC distributions for wild-type, TR34/L98H and TR46/Y121F/T289A Aspergillus fumigatus isolates in the Netherlands

OBJECTIVES To determine the MIC distributions of itraconazole, voriconazole and posaconazole and non-azole drugs for wild-type cyp51A, as well as TR(34)/L98H and TR(46)/Y121F/T289A cyp51A mutants of Aspergillus fumigatus. METHODS We retrieved MIC and cyp51A sequence data for 952 clinical A. fumigatus strains isolated in or referred to our reference laboratory, during the January 2010 to December 2013 period. All MICs were determined using the EUCAST methodology and interpreted using the EUCAST breakpoints. RESULTS Three-hundred and sixty-four of the 952 strains (38%) were resistant to azoles. Of these, 225 contained the TR34/L98H mutation, 98 contained the TR(46)/Y121F/T289A mutation and 39 had no cyp51A mutations. Two isolates harboured other cyp51A mutations, of which one (P216L) has been shown to confer azole resistance. Of the TR(34)/L98H isolates, 99.6% (224/225) were resistant to itraconazole (MICs >2 mg/L), 92.4% (208/225) were resistant to voriconazole (MICs >2 mg/L) and 97.8% (220/225) were resistant to posaconazole (MICs >0.25 mg/L). All TR(46)/Y121F/T289A isolates were resistant to voriconazole (MICs >16 mg/L), 82.7% (81/98) were resistant to itraconazole with a bimodal MIC distribution and 94.9% (93/98) were resistant to posaconazole. The MICs of amphotericin B, anidulafungin and terbinafine were not affected by the presence of azole-resistance mechanisms. CONCLUSIONS The TR(34)/L98H and TR(46)/Y121F/T289A cyp51A genotypes of A. fumigatus show distinct resistance phenotypes. The mechanisms behind low-level itraconazole resistance in TR(46)/Y121F/T289A isolates warrant future research. The potential of increased azole dosing for disease caused by low-level resistant strains should be investigated.

Azole-Resistant Aspergillus fumigatus, Iran

To the Editor: Aspergillus fumigatus causes a variety of diseases in humans. The drugs recommended for treatment of Aspergillus diseases are the mold-active azole antifungal drugs (1). However, a wide range of mutations in A. fumigatus confer azole resistance, which commonly involves modifications in the cyp51A gene (2), the target for azole antifungal drugs. Azole resistance is thought to be selected for as a result of patient therapy or exposure to azole compounds in the environment; resistance in clinical A. fumigatus isolates has been increasingly reported in several European countries, Asia, and the United States (3–7). The most frequently reported resistance mechanism is a 34-bp tandem repeat (TR34) in combination with a substitution at codon 98 (TR34/L98H) (4); this mechanism is believed to have been selected for through environmental exposure to azole fungicides. Because routine in vitro susceptibility testing of clinical Aspergillus isolates is not common in many centers worldwide, the prevalence of azole resistance might be underestimated. We investigated the prevalence of azole resistance in clinical A. fumigatus isolates stored for 6 years (2003–2009) at Tehran University Mycology Reference Centre and Islamic Azad University, Ardabil Branch, Iran. We investigated 124 clinical A. fumigatus isolates obtained from patients with Aspergillus diseases (Technical Appendix Table 1). We conducted strain identification, in vitro antifungal susceptibility testing, and sequence-based analysis of the Cyp51A gene, as described (4). We performed microsatellite genotyping of all A. fumigatus isolates for which the MIC of itraconazole was ≥16 mg/L (8) by using a short tandem repeat A. fumigatus assay, and we compared the results with those reported for the Netherlands (20 isolates) and other European countries (24 isolates) (Technical Appendix Figure). The distribution of azole-resistant and wild-type A. fumigatus isolates examined in this study, according to year of isolation, is shown in online Technical Appendix Table 1. Of 124 A. fumigatus isolates, 4 grew on the wells containing itraconazole and voriconazole, indicating a multidrug-resistant phenotype. Of these resistant isolates, 3 were from patients with chronic pulmonary aspergillosis and 1 was from a patient with allergic bronchopulmonary aspergillosis (Table). Table Characteristics of 4 azole-resistant clinical Aspergillus fumigatus isolates, Iran* Sequence analysis of the CYP51A gene indicated the presence of TR34/L98H in 3 isolates and no mutations in the other isolate (Table). The first TR34/L98H isolate had been recovered in 2005, which is relatively early compared with reported isolations in other countries (Technical Appendix Table 2). Microsatellite typing of 6 short tandem repeat loci demonstrated identical patterns for 2 of the 3 azole-resistant isolates from Iran, but the TR34/L98H isolates from Iran did not cluster with those from the Netherlands and other European countries, indicating no close genetic relatedness (Technical Appendix Figure). The TR34/L98H azole resistance mechanism was first described in 1998 in the Netherlands; since then, its presence in clinical and environmental A. fumigatus isolates in multiple European countries and recently in Asia has been increasingly reported (Technical Appendix Table 2) (3–7). In the study reported here, prevalence of azole resistance in clinical A. fumigatus isolates obtained from patients in Iran was 3.2%; most isolates exhibited the TR34/L98H resistance mechanism. The fact that the first TR34/L98H isolate was found relatively early, in 2005, underscores the possibility that prevalence of azole resistance might be underestimated in many countries because in vitro susceptibility testing of A. fumigatus is not routinely performed. Microsatellite genotypic analysis of A. fumigatus isolates from the Netherlands and various European countries showed that the genetic diversity of TR34/L98H isolates is lower than that of wild-type controls (8). It has been suggested that TR34/L98H isolates might have a common ancestor that developed locally and subsequently migrated across Europe. In contrast, genotyping of TR34/L98H originating from India suggested a different dynamic; all environmental and clinical TR34/L98H isolates from India shared the same multilocus microsatellite genotype not found in any other analyzed samples, from within India or from the Netherlands, France, Germany, or the People’s Republic of China (9). The molecular epidemiology of the TR34/L98H isolates from Iran suggests that they cluster apart from the European isolates, indicating that migration from Europe to Iran, or vice versa, is unlikely. Genotyping of more TR34/L98H isolates from the Middle East and comparison with those from India would enhance understanding of the origin and geographic spread of TR34/L98H. Our study indicates that TR34/L98H was in Iran in 2005; this finding adds to the growing list of regions where acquired resistance in A. fumigatus of environmental origin is documented. From a global perspective, fungicide use is second highest in the Asia–Pacific regions (24%), preceded only by western Europe (37%) (10). For a bettering understand of the scale of this emerging public health problem and for insight into the dynamics of geographic migration, surveys of fungal culture collections for TR34/L98H and molecular typing studies are warranted. These data would be useful not only for clinical management of Aspergillus diseases but also for enabling policy makers to develop strategies that prevent resistance selection by the environmental route. Technical Appendix: Distribution of azole-resistant and azole-susceptible Aspergillus fumigatus isolates, Iran, 2003–2009; first reports of multiple-triazole-resistant A. fumigatus isolate(s) carrying the TR34/L98H mutations in the CYP51A gene, by country; and minimum spanning tree comparing genotypic relatedness of clinical azole-resistant A. fumigatus isolates carrying TR34/L98H alteration in the CYP51A gene from Iran with those reported from European countries. TR, tandem repeat. Click here to view.(160K, pdf)

Plasma from septic shock patients induces loss of muscle protein

IntroductionICU-acquired muscle weakness commonly occurs in patients with septic shock and is associated with poor outcome. Although atrophy is known to be involved, it is unclear whether ligands in plasma from these patients are responsible for initiating degradation of muscle proteins. The aim of the present study was to investigate if plasma from septic shock patients induces skeletal muscle atrophy and to examine the time course of plasma-induced muscle atrophy during ICU stay.MethodsPlasma was derived from septic shock patients within 24 hours after hospital admission (n = 21) and healthy controls (n = 12). From nine patients with septic shock plasma was additionally derived at two, five and seven days after ICU admission. These plasma samples were added to skeletal myotubes, cultured from murine myoblasts. After incubation for 24 hours, myotubes were harvested and analyzed on myosin content, mRNA expression of E3-ligase and Nuclear Factor Kappa B (NFκB) activity. Plasma samples were analyzed on cytokine concentrations.ResultsMyosin content was approximately 25% lower in myotubes exposed to plasma from septic shock patients than in myotubes exposed to plasma from controls (P < 0.01). Furthermore, patient plasma increased expression of E3-ligases Muscle RING Finger protein-1 (MuRF-1) and Muscle Atrophy F-box protein (MAFbx) (P < 0.01), enhanced NFκB activity (P < 0.05) and elevated levels of ubiquitinated myosin in myotubes. Myosin loss was significantly associated with elevated plasma levels of interleukin (IL)-6 in septic shock patients (P < 0.001). Addition of antiIL-6 to septic shock plasma diminished the loss of myosin in exposed myotubes by approximately 25% (P < 0.05). Patient plasma obtained later during ICU stay did not significantly reduce myosin content compared to controls.ConclusionsPlasma from patients with septic shock induces loss of myosin and activates key regulators of proteolysis in skeletal myotubes. IL-6 is an important player in sepsis-induced muscle atrophy in this model. The potential to induce atrophy is strongest in plasma obtained during the early phase of human sepsis.

Identification of Potential Recombination Breakpoints in Human Parechoviruses

ABSTRACT Based on a comparison of the phylogeny of two distant regions, evidence has been found for recombination within parechoviruses. However, recombination breakpoints could not be detected in this way. We searched for potential recombination breakpoints in parechovirus by analysis of complete parechovirus sequences, including a newly isolated strain. Bootscan analysis demonstrated that parechoviruses are mosaic viruses build of regions related to corresponding genomic regions of other parechoviruses. With a genetic algorithm for recombination detection, sites for recombination were found. Analysis of partial sequences, as defined by recombination breakpoints, showed phylogenetic segregation between regions.

Phylogenetic relationships of five species of Aspergillus and related taxa as deduced by comparison of sequences of small subunit ribosomal RNA

The nucleotide sequences of the genes encoding the 18S rRNA of Aspergillus flavus, A. nidulans, A. terreus and A. niger were elucidated and aligned to the sequences of A. fumigatus. In addition, the 18S rRNA sequences of the V4-V9 region of morphologically similar filamentous fungi, e.g. Penicillium chrysogenum, P. marneffei and Paecilomyces variotii, were elucidated. Phylogenetic analysis and comparison showed a very close intergeneric relationship of the genus Aspergillus to species of the genera Paecilomyces and Penicillium. However, the sequenced Aspergillus species also showed a very close relationship to Eurotium rubrum and Monascus purpureus. Phylogenetic analysis of fungal 18S rRNA sequences divided the general Aspergillus, Penicillium and Paecilomyces into two coherent clusters and showed a close intergeneric relationship which is in keeping with the existing morphological and taxonomic classification.

Genotype-phenotype complexity of the TR46/Y121F/T289A cyp51A azole resistance mechanism in Aspergillus fumigatus.

The Aspergillus fumigatus cyp51A gene TR46/Y121F/T289A mutation is a new emerging resistance mechanism with high-level voriconazole (VOR) resistance, and elevated MICs to all other medical azoles. This is highly worrisome as VOR is the primary drug for the treatment of many aspergillus diseases. The 46 base pair tandem repeat (TR46) is positioned at the same location of the cyp51A gene promoter region as has been described for other tandem repeats. The exact role of the TR46 in combination with the two amino acid changes (Y121F and T289A) in the CYP51A protein is unknown. In this study this azole resistance mechanism was investigated by recombinant analysis study combined with homology modelling. MICs of the TR46/Y121F/T289A recombinant corresponded to the MICs of the original clinical isolates containing the same mutations with high-level resistance to VOR. The TR46 or Y121F by itself has only a moderate effect on azole susceptibility. The combination of TR46/Y121F, however, appears to be highly resistant not only for VOR but also for itraconazole (ITZ). The genetic change of T289A in combination with TR46 or by itself has no significant effect on the phenotype but moderates the phenotype of the ITZ resistance only in the presence of Y121F. The striking resistant phenotype of the TR46/Y121F mutant is supported by the structural analysis of the CYP51A homology model. The A. fumigatus CYP51A Y121 residue forms an H-bond with the heme centre of the enzyme. Disruption of the H-bond by the Y121F substitution destabilizes the active centre of CYP51A which appears to be essential with respect to azole resistance. In CYP51A-azole complexes, residue T289 is in close proximity of the azole moiety of VOR. Replacement of the polar amino acid threonine by the more hydrophobic amino acid alanine might promote more stable drug-protein interactions and has thereby an impact on ITZ susceptibility, which is confirmed by the MICs of the genetic recombinants.