Correction to: Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here.

Recommendations for the nomenclature of enteroviruses and rhinoviruses.

Enteroviruses (EVs) and rhinoviruses (RVs) are significant pathogens of humans and are the subject of intensive clinical and epidemiological research and public health measures, notably in the eradication of poliovirus and in the investigation and control of emerging pathogenic EV types worldwide. EVs and RVs are highly diverse in their antigenic properties, tissue tropism, disease associations and evolutionary relationships, but the latter often conflict with previously developed biologically defined terms, such as "coxsackieviruses", "polioviruses" and "echoviruses", which were used before their genetic interrelationships were understood. This has created widespread formatting problems and inconsistencies in the nomenclature for EV and RV types and species in the literature and public databases. As members of the International Committee for Taxonomy of Viruses (ICTV) Picornaviridae Study Group, we describe the correct use of taxon names for these viruses and have produced a series of recommendations for the nomenclature of EV and RV types and their abbreviations. We believe their adoption will promote greater clarity and consistency in the terminology used in the scientific and medical literature. The recommendations will additionally provide a useful reference guide for journals, other publications and public databases seeking to use standardised terms for the growing multitude of enteroviruses and rhinoviruses described worldwide.

ICTV Virus Taxonomy Profile: Picornaviridae.

The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.

Improved replication efficiency of echovirus 5 after transfection of colon cancer cells using an authentic 5' RNA genome end methodology.

Oncolytic virotherapy is a promising novel form of cancer treatment, but the therapeutic efficiency needs improvement. A potential strategy to enhance the therapeutic effect of oncolytic viruses is to use infectious nucleic acid as therapeutic agent to initiate an oncolytic infection, without administrating infectious viral particles. Here we demonstrate improved viral replication activation efficiency when transfecting cells with 5' end authentic in vitro transcribed enterovirus RNA as compared to genomic RNA with additional non-genomic 5' nucleotides generated by conventional cloning methods. We used echovirus 5 (E5) as an oncolytoc model virus due to its ability to replicate in and completely destroy five out of six colon cancer cell lines and kill artificial colon cancer tumors (HT29 spheroids), as shown here. An E5 infectious cDNA clone including a hammerhead ribozyme sequence was used to generate in vitro transcripts with native 5' genome ends. In HT29 cells, activation of virus replication is approximately 20-fold more efficient for virus genome transcripts with native 5' genome ends compared to E5 transcripts generated from a standard cDNA clone. This replication advantage remains when viral progeny release starts by cellular lysis 22 h post transfection. Hence, a native 5' genomic end improves infection activation efficacy of infectious nucleic acid, potentially enhancing its therapeutic effect when used for cancer treatment. The clone design with a hammerhead ribozyme is likely to be applicable to a variety of oncolytic positive sense RNA viruses for the purpose of improving the efficacy of oncolytic virotherapy.

Automated correlation dimension analysis of optically injected solid state lasers.

Nonlinear lasers are excellent systems from which to obtain high signal-to-noise experimental data of nonlinear dynamical variables to be used to develop and demonstrate robust nonlinear dynamics analysis techniques. Here we investigate the dynamical complexity of such a system: an optically injected Nd:YVO(4) solid state laser. We show that a map of the correlation dimension as a function of the injection strength and frequency detuning, extracted from the laser output power time-series data, is an excellent mirror of the dynamics map generated from a theoretical model of the system. An automated computational protocol has been designed and implemented to achieve this. The correlation dimension map is also contrasted with prior research that mapped the peak intensity of the output power as an experimentally accessible measurand reflecting the dynamical state of the system [Valling et al., Phys. Rev. A 72, 033810 (2005)].

Recent Korean isolates of duck hepatitis virus reveal the presence of a new geno- and serotype when compared to duck hepatitis virus type 1 type strains.

Duck hepatitis was first reported in 1985 in Korea. The complete nucleotide sequence of two past Korean isolates, DHV-HS and DHV-HSS, isolated in 1994 and 1995, and four recent Korean isolates, AP-03337, AP-04009, AP-04114 and AP-04203 isolated in 2003 and 2004, were determined. Phylogenetic analysis using the 3D protein sequence confirmed that the previously characterized duck hepatitis virus type 1 strains and the six Korean isolates described here constitute a monophyletic group and form two clades/genotypes in which all except the four recent Korean isolates form one group (A) and the recent Korean isolates of 2003 and 2004 constitute a second group (B). Phylogenetic analysis of the VP1 protein supported the division into two different groups. Antisera raised against viruses of group A showed significant neutralizing cross-reaction against a member of the same genotype but not to a strain of group B and vice versa. These results demonstrated that the two genotypes also could be regarded as two different serotypes.

Enterovirus infection in human pancreatic islet cells, islet tropism in vivo and receptor involvement in cultured islet beta cells.

AIMS/HYPOTHESIS: It is thought that enterovirus infections cause beta-cell damage and contribute to the development of Type 1 diabetes by replicating in the pancreatic islets. We sought evidence for this through autopsy studies and by investigating known enterovirus receptors in cultured human islets. METHODS: Autopsy pancreases from 12 newborn infants who died of fulminant coxsackievirus infections and from 65 Type 1 diabetic patients were studied for presence of enteroviral ribonucleic acid by in situ hybridisation. Forty non-diabetic control pancreases were included in the study. The expression and role of receptor candidates in cultured human islets were investigated with receptor-specific antibodies using immunocytochemistry and functional assays. RESULTS: Enterovirus-positive islet cells were found in some of both autopsy specimen collections, but not in control pancreases. No infected cells were seen in exocrine tissue. The cell surface molecules, poliovirus receptor and integrin alphavbeta3, which act as enterovirus receptors in established cell lines, were expressed in beta cells. Antibodies to poliovirus receptor, human coxsackievirus and adenovirus receptor and integrin alphavbeta3 protected islets and beta cells from adverse effects of poliovirus, coxsackie B viruses, and several of the arginine-glycine-aspartic acid motifs containing enteroviruses and human parechovirus 1 respectively. No evidence was found for expression of the decay-accelerating factor which acts as a receptor for several islet-cell-replicating echoviruses in established cell lines. CONCLUSIONS/INTERPRETATION: The results show a definite islet-cell tropism of enteroviruses in the human pancreas. Some enteroviruses seem to use previously identified cell surface molecules as receptors in beta cells, whereas the identity of receptors used by other enteroviruses remains unknown.

Influence of a drink containing different antioxidants and Lactobacillus plantarum 299v on plasma total antioxidant capacity, selenium status and faecal microbial flora.

The aim of the study was to investigate whether a supplement of antioxidants to subjects with a high working pace can influence the antioxidant capacity. The study was parallel and double blind with 98 subjects randomised into two groups. One of the groups was given a test drink with antioxidants for 4 weeks (450 ml/day) while the other group took a corresponding amount of placebo drink. The test drink contained: 2 mg beta-carotene/100 ml, 40 mg alpha-tocopherol/100 ml, 80 mg ascorbic acid/100 ml, 2 mg pyridoxine/100 ml, 15 mg magnesium/100 ml, 0.2 mg manganese/100 ml, 1 mg zinc/100 ml, 0.1 mg copper/100 ml and 10 microg selenium/100 ml. Consumption of the test drink for 4 weeks increased the total plasma antioxidant capacity by 7% (ferric reducing ability of plasma method, P<0.05 compared with the placebo group), and the content of selenium and selenoprotein P in serum was raised by 16-17% (P<0.001 compared with the placebo group). No significant changes were found in the placebo group. The test drink also contained Lactobacillus plantarum 299v (5 x 10(7) cfu/ml) and 4 weeks' consumption led to a significant increase of Lb. plantarum 299v in the faeces. In conclusion, consumption of a drink rich in different antioxidants can increase the antioxidant capacity in subjects with a high working pace. This can be valuable since it may increase the protection against reactive oxygen radicals.

Comparative analysis of two coxsackievirus B3 strains: putative influence of virus-receptor interactions on pathogenesis.

Strain-specific differences in the interaction of coxsackievirus B3 (CVB3) with the coxsackievirus-adenovirus receptor (CAR) and the decay-accelerating factor (DAF) co-receptor proteins were investigated using a non-haemagglutinating (CVB3) and a haemagglutinating (CVB3-HA) strain of CVB3. A panel of receptor-transfected hamster CHO cells, expressing either CAR (CHOCAR cells), DAF (CHODAF cells), or both receptor proteins (CHODC cells) were used to study the interplay of CAR and DAF receptor molecules with regard to binding and infection with CVB3 and CVB3-HA. Despite clear differences in their binding phenotypes, both virus strains were found to primarily depend on the CAR receptor protein for initialization of productive infections. Cytopathic effects induced by CVB3-HA were influenced by co-expression of DAF receptor proteins. The cardiotropic potential of both virus strains was investigated in A.BY/SnJ mice. Despite comparable virus replication of both CVB3 strains in individual myocytes, the number of infected heart muscle cells was significantly lower in CVB3-HA infected mice. Infections of pancreata correlated with myocardial infections. Together these data suggest that even small differences in virus-receptor interactions, influencing virus binding and virus spread, may have an impact on the pathogenesis of CVB-induced diseases.

Phylogenetic analysis of Ljungan virus and A-2 plaque virus, new members of the Picornaviridae.

In addition to the viruses belonging to the nine proposed genera of the Picornaviridae, Enterovirus, Rhinovirus, Cardiovirus, Aphtovirus, Hepatovirus, Parechovirus, Kobuvirus, Erbovirus and Teschovirus, two new members of this family have recently been discovered. Three strains of Ljungan virus (LV) were isolated from bank voles (Clethrionomys glareolus) and A-2 plaque virus (A-2) was isolated from human sera. To study the genetic relationship between these recently discovered viruses and the members of the family Picornaviridae, an evolutionary analysis has been carried out using the amino acid sequences of the two nonstructural proteins 2C and 3D. Phylogenetic analysis using prime members of the nine genera support the division of picornaviruses into the proposed genera. The study also supports a previous suggestion based on analysis of partial sequences of the structural proteins that LV is more related to the genus of Parechovirus than to other picornaviruses, but also shows that the three LV strains used in the comparison constitute a distinct monophyletic group, clearly separated from the parechoviruses. The analyses using the 2C and 3D sequences clearly showed that A-2 was related to the genera of Rhinovirus and Enterovirus, but it was not possible to group the A-2 with high confidence into one of the genera. Comparison using the VP1 protein sequences of Enterovirus and Rhinovirus showed that although the A-2 virus is positioned between the two genera, the virus is more related to the genus of Enterovirus than to Rhinovirus. Our analysis of the three LV strains based on the phylogenetic analysis of the 2C and 3D proteins suggests that the strains used in this study constitute a monophyletic group clearly related to Parechovirus of Picornaviridae. The taxonomic position of the A-2 virus is presently uncertain but available data indicate that this virus may be classified as a member of the genus of Enterovirus.

Molecular analysis of the echovirus 18 prototype: evidence of interserotypic recombination with echovirus 9.

Echovirus 18 (EV18) is one of the echovirus serotypes associated with human diseases and in particular aseptic meningitis. To facilitate studies of the molecular epidemiology of EV18 and the evolution of enteroviruses in general, the complete nucleotide (nt) sequence was determined for the echovirus 18 prototype strain (Metcalf, EV18M). Excluding the poly A sequence, the genome consists of 7410 nt divided into a 740 nt 5' untranslated region (5' UTR), a 6567 nt long open reading frame coding for a 2189 amino acid (aa) polyprotein and a 103 nt 3' UTR. Molecular analysis of the EV18M genome showed a typical enterovirus-like organization. Phylogenetic analysis of the structural and non-structural genes revealed a pattern of different relationships to other echo- and coxsackieviruses. Similarity analysis demonstrated that the Hill strain of echovirus 9 is most likely the result of a previous recombination event between ancestors of the echovirus 9 strain Barty (5' half of the genome) and EV18M (3' half). Using a maximum likelihood approach, the recombination point was mapped to the 2C gene.

Characterization of background signals in wavelength-modulation spectrometry in terms of a fourier based theoretical formalism.

The detectability of wavelength-modulation (WM) diode-laser spectrometric techniques is frequently limited by various background signals. A new theoretical formalism for WM spectrometry, based on Fourier analysis and therefore capable of handling a variety of phenomena including the characterization and the analysis of analytical as well as background WM signals, was recently presented [Appl. Opt. 38, 5803 (1999)]. We report a detailed characterization of WM background signals from multiple reflections between pairs of surfaces in the optical system that act as etalons and from the associated intensity modulation in terms of this new formalism. The agreement between the background signals from a thin glass plate and those predicted by the formalism is good, which verifies the new Fourier analysis-based formalism.

Background signals in wavelength-modulation spectrometry with frequency-doubled diode-laser light. I. Theory.

Various types of background signals appear when wavelength-modulated (WM) diode-laser light is frequency doubled. We present a theoretical analysis of such background signals in terms of a previously derived formalism for WM spectrometry that is based on a Fourier series. Explicit expressions for various nf harmonics of the background signals are derived. The analysis shows that 2f detection will be plagued by significant background signals when frequency-doubled WM diode-laser light is used. It also demonstrates that 4f and 6f detection will experience background signals but not, however, to the same extent as 2f detection. The analysis illustrates clearly how the various nf harmonics of the background signals depend on entities such as modulation amplitude, associated intensity modulation, dispersion of the frequency-doubling material, laser power, and detuning. The background signals can take both positive and negative values, depending on the relation between these entities. Guidelines for how to minimize these background signals are given.

Background Signals in Wavelength-Modulation Spectrometry by use of Frequency-Doubled Diode-Laser Light. II. Experiment.

In an accompanying paper [Appl. Opt. 40, 783-793 (2001)], we predict the existence of background signals from a frequency-doubled wavelength-modulated diode-laser system. We now demonstrate and characterize various nf harmonics of such background signals from a system producing light in the 422-nm region by use of a single-pass KNbO(3) crystal with respect to the modulation amplitude, the laser center frequency, and the crystal temperature. It is demonstrated that 2f detection is plagued by considerably larger amounts of background signal than is detection at other higher, even harmonics. This result implies that 4f or 6f detection is often to be preferred in comparison with 2f detection when frequency-doubled wavelength-modulation spectrometry (WMS) is to be used. This preference is illustrated by the detection of Ca in an acetylene-air flame. It is also shown that the background signals have a much stronger dependence on the modulation amplitude than do the analytical signals. This difference implies that the optimum detectability for frequency-doubled WMS is often reached for modulation amplitudes lower than those normally used. An analysis of the effect of a finite temperature stability of the doubling crystal on the drift of the background signals as well as on the detectability is included. The results verify the theoretical description given in our accompanying paper.

Periodic oscillation within the chaotic region in a semiconductor laser subjected to external optical injection.

We report on the experimental observation of periodic windows within the chaos of the output of a semiconductor laser that is subjected to external optical injection. Continuously sampled spectra of the slave-laser output as the injection level is increased reveal the general behavior of the system as well as features that suggest that the periodic oscillation forms a distinct island within the chaotic region in the parameter space.

Molecular analysis of the prototype coxsackievirus B5 genome.

To facilitate studies of the phylogenetic relationship between enteroviruses, in particular the prototype strain (Faulkner) of coxsackievirus B5 (CVB5F) and other CVB5 isolates and to facilitate studies of the interactions between CVB5F and the target cell, the complete nucleotide sequence of the prototype has been determined. The complete sequence was collected from three overlapping reverse transcription polymerase chain reaction (RT-PCR) generated amplicons. Molecular analysis of the CVB5F genome verified that this strain is more related to other CVB5 isolates and to swine vesicular disease virus strains than to other enteroviruses. In addition, comparison of the amino acid sequence derived from the structural genes indicated a division of group B coxsackievirus into subgroups, where CVB1, CVB3 and CVB5 constitute one group, CVB2 and CVB4 from a second group and CVB6 prototype forms a branch of its own. This observation, supported by reports describing the interactions between CVB and the cell surface, may reflect that these subgroups of group B coxsackieviruses have evolved to use slightly different approaches to carry out the complete infectious cycle within the cell.

Genomic and phylogenetic characterization of coxsackievirus B2 prototype strain Ohio-1.

The human picornavirus coxsackievirus B2 (CVB2) is often linked to several infections, from mild respiratory diseases to more severe illnesses such as myocarditis. In this study, we report the complete genome sequence of CVB2 prototype strain Ohio-1. The genome sequence was determined from reverse transcribed viral RNA, amplified with long distance PCR and used for non-radioactive sequencing. The full length PCR amplicons were used for in vitro transcription and the obtained cRNA was lipofected onto green monkey kidney cells, in order to confirm that the PCR generated sequence reflects a viable virus RNA. The CVB2 genome sequence shows a typical enterovirus genome organization with a total length of 7411 nucleotides. Phylogenetic analysis, using the CVB2 polyprotein in comparison with other enterovirus polyproteins, clearly shows that CVB2 clusters with the coxsackievirus B-like enteroviruses and is more related to coxsackievirus B4 (CVB4) than any other published CVB serotype. The grouping of CVB2 and CVB4 as one subgroup has earlier been reported in connection with receptor usage and ability to replicate in different cell lines. The exposed viral capsid proteins of CVB2 (VP1-VP3) show high similarity to other CVB proteins, except in regions that are likely to be surface epitopes.

Purification of full-length enterovirus cDNA by solid phase hybridization capture facilitates amplification of complete genomes.

The aim of the study was to develop a method for the selective purification of full-length enterovirus single strand (ss) cDNA for subsequent amplification of complete enterovirus genomes by long distance PCR. As a model system we have used the prototype strain of echovirus 5 (EV5). Due to inefficient first strand cDNA synthesis using EV5 RNA as template, only a few molecules of EV5 sscDNA were completely reverse transcribed and no amplification products were observed when long distance polymerase chain reaction (LD-PCR) was used for amplification of complete EV5 genomes. To purify the complete EV5 cDNA present, an oligonucleotide, derived from the conserved 5' end of an enterovirus genome, was immobilized on paramagnetic beads and complete EV5 sscDNA was captured and purified from the less than full-length cDNAs. LD-PCR using the purified EV5 cDNA resulted in amplification of complete EV5 genomes. Transfection of the EV5 RNA transcribed from these uncloned amplicons resulted in production of replicating viruses. This demonstrates that solid phase hybridization capture of sscDNA is an efficient method that can be used for enrichment and purification of full-length enterovirus sscDNAs.

Echovirus 5: infectious transcripts and complete nucleotide sequence from uncloned cDNA.

Echovirus 5 (EV5) may be isolated from various neurological and exanthematic diseases. To determine the relationship of EV5 to other enteroviruses and for studies of its interactions with the target cell, the complete nucleotide sequence of EV5 was determined. Three overlapping fragments, collectively representing the complete genome, were amplified with RT-PCR and sequenced. Analysis of the EV5 sequence revealed a typical enterovirus-like organization of the genome. To verify that the cDNA generated sequence was derived from infectious viruses, complete EV5 genomes were amplified in one amplicon by long distance PCR. Transfection of in vitro transcribed RNA from these amplicons into cell cultures resulted in replicating EV5. Comparison of the overall nucleotide and amino acid sequences demonstrates that EV5 can be regarded as a coxsackievirus B-like enterovirus. Variable sequences between EV5 and the well characterized coxsackievirus B3 (CVB3) are for the most part observed for amino acid residues that correspond to exposed sequences in the CVB3 capsid. This observation indicates that the reported EV5 strain recently diverged from group B coxsackieviruses.

Enterobacteriaceae found in high numbers in fish, minced meat and pasteurised milk or cream and the presence of toxin encoding genes.

Enterobacteriaceae were found in high numbers after storage at 7 degrees C in 6% of consumers packs of pasteurised milk or cream, in 31% of retailed fish and in 100% of retail packs of minced meat. Seventy two fresh-water fishes, 40 packs of minced meat and 430 milk packs were sampled. One hundred and eighty four isolates were randomly picked from Tryptone glucose extract (TGE) agar (30 degrees C for 3d) or Violet red bile glucose (VRBG) agar (37 degrees C for 1d). In minced meat, Serratia liquefaciens, Hafnia alvei, Rahnella aquatilis were frequently encountered. On fish, the most frequently found species were R. aquatilis, and in milk, the dominating species were S. liquefaciens, H. alvei and R. aquatilis. One to three isolates of Citrobacter freundii were found in all three food categories. Using a polymerase chain reaction (PCR) technique, the gene of Escherichia coli heat-labile toxin (lt) was indicated in one fish isolate of R. aquatilis whereas heat-stable toxin genes (s.t.) were indicated in four H. alvei isolates, two originating from fish and two from minced meat. Positive PCR-reaction for vero cytotoxin genes were found in one H. alvei strain originating from fish (vt1), in two S. liquefaciens strains from minced meat (vt2), and in a C. freundii reference strain. One of the st-positive H. alvei strains from meat harboured the eaeA gene involved in the attaching phenotype of enteropathogenic E. coli.