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This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in October 2018. Of note, the ICTV has approved, by an absolute majority, the creation of additional taxonomical ranks above those recognized previously. A total of 15 ranks (realm, subrealm, kingdom, subkingdom, phylum, subphylum, class, subclass, order, suborder, family, subfamily, genus, subgenus, and species) are now available to encompass the entire spectrum of virus diversity. Classification at ranks above genus is not obligatory but can be used by the authors of new taxonomic proposals when scientific justification is provided.

Purpose: Compression socks are frequently used in the treatment and prevention of lower-limb pathologies; however, when combined with endurance-based exercise, the impact of compression socks on haemostatic activation remains unclear., Objectives: To investigate the effect of wearing compression socks on coagulation and fibrinolysis following a marathon., Methods: Sixty-seven participants [43 males (mean ± SD: age: 46.7 ± 10.3 year) and 24 females (age: 40.0 ± 11.0 year)] were allocated into a compression (SOCK, n = 34) or control (CONTROL, n = 33) group. Venous blood samples were obtained 24 h prior to and immediately POST-marathon, and were analyzed for thrombin-anti-thrombin complex (TAT), tissue factor (TF), tissue factor pathway inhibitor (TFPI), and D-Dimer., Results: Compression significantly attenuated the post-exercise increase in D-Dimer compared to the control group [median (range) SOCK: + 9.02 (- 0.34 to 60.7) ng/mL, CONTROL: + 25.48 (0.95-73.24) ng/mL]. TF increased following the marathon run [median (range), SOCK: + 1.19 (- 7.47 to 9.11) pg/mL, CONTROL: + 3.47 (- 5.01 to 38.56) pg/mL] in all runners. No significant post-exercise changes were observed for TAT and TFPI., Conclusions: While activation of coagulation and fibrinolysis was apparent in all runners POST-marathon, wearing compression socks was shown to reduce fibrinolytic activity, as demonstrated by lower D-Dimer concentrations. Compression may reduce exercise-associated haemostatic activation when completing prolonged exercise.

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and one new order were added to the taxonomy. The current totals at each taxonomic level now stand at 9 orders, 131 families, 46 subfamilies, 803 genera and 4853 species. A change was made to the International Code of Virus Classification and Nomenclature to allow the use of the names of people in taxon names under appropriate circumstances. An updated Master Species List incorporating the approved changes was released in March 2018 ( https://talk.ictvonline.org/taxonomy/ ).

Efforts to develop tissue-engineered skin for regenerative medicine have explored natural, synthetic, and hybrid hydrogels. The creation of a bilayer material, with the stratification exhibited by native skin, is a complex problem. The mechanically robust, waterproof epidermis presents the stratum corneum at the tissue/air interface, which confers many of these protective properties. In this work, we explore the effect of high temperatures on alginate hydrogels, which are widely employed for tissue engineering due to their excellent mechanical properties and cellular compatibility. In particular, we investigate the rapid dehydration of the hydrogel surface which occurs following local exposure to heated surfaces with temperatures in the range 100-200 °C. We report the creation of a mechanically strengthened hydrogel surface, with improved puncture resistance and increased coefficient of friction, compared to an unheated surface. The use of a mechanical restraint during heating promoted differences in the rate of mass loss; the rate of temperature increase within the hydrogel, in the presence and absence of restraint, is simulated and discussed. It is hoped that the results will be of use in the development of processes suitable for preparing skin-like analogues; application areas could include wound healing and skin restoration.

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2017.

We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.

B-cell lymphoma, a common morphologic variant of non-Hodgkin lymphoma, has been associated with persistent pollutants in humans, but this association is not well-characterized in top-level predators sharing marine resources with humans. We characterized and compared blubber contaminants and hormones of a pregnant harbor porpoise (Phocoena phocoena) with B-cell lymphoma, with those in two presumed healthy fishery by-caught porpoises with no lymphoma: a pregnant adult and female juvenile. Common historic use compounds, including polychlorinated biphenyls, polybrominated diphenyl ethers, and pesticides, were evaluated in blubber samples from three porpoises. In addition, blubber cortisol and progesterone levels (ng/g) were determined in all three animals. Total pollutant concentrations were highest in the juvenile porpoise, followed by the lymphoma porpoise and the nonlymphoma adult. Blubber cortisol concentrations were 191% greater in the pregnant with lymphoma porpoise compared with the pregnant no lymphoma porpoise, and 89% greater in the juvenile female compared with the pregnant no lymphoma porpoise. Although both adults were pregnant, progesterone levels were substantially greater (90%) in the healthy compared with the lymphoma adult. Health monitoring of top-level marine predators, such as porpoise, provides a sentinel measure of contaminants that serve as indicators of potential environmental exposure to humans.

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( http://www.ictvonline.org/statutes.asp ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( http://www.ictvonline.org/ ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://talk.ictvonline.org/files/proposals/ ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).

Purpose: A hypertensive response to moderate intensity exercise (HRE) is associated with increased cardiovascular risk. The mechanisms of an HRE are unclear, although previous studies suggest this may be due to haemostatic and/or haemodynamic factors. We investigated the relationships between an HRE with haemostatic and hemodynamic indices., Methods: Sixty-four participants (57 ± 10 years, 71 % male) with indication for exercise stress testing underwent cardiovascular assessment at rest and during moderate intensity exercise, from which 20 participants developed an HRE (defined as moderate exercise systolic BP ≥ 170 mmHg/men and ≥ 160 mmHg/women). Rest, exercise and post-exercise blood samples were analysed for haemostatic markers, including von Willebrand factor (vWf), and haemodynamic measures of brachial and central blood pressure (BP), aortic stiffness and systemic vascular resistance index (SVRi)., Results: HRE participants had higher rest vWf compared with normotensive response to exercise (NRE) participants (1,927 mU/mL, 95 % CI 1,240-2,615, vs. 1,129 mU/mL, 95 % CI 871-1,386; p = 0.016). vWf levels significantly decreased from rest to post-exercise in HRE participants (p = 0.005), whereas vWf levels significantly increased from rest to exercise in NRE participants (p = 0.030). HRE participants also had increased triglycerides, rest BP, aortic stiffness and exercise SVRi (p < 0.05 for all). Rest vWf predicted exercise brachial systolic BP (β = 0.220, p = 0.043; adjusted R (2) = 0.451, p < 0.001) independent of age, sex, body mass index, triglycerides, rest brachial systolic BP and aortic stiffness., Conclusions: Increased rest blood levels of vWf are independently associated with moderate intensity exercise systolic BP. These findings implicate abnormalities in haemostasis as a possible factor contributing to HRE at moderate intensity.

A database and website ( http://www.ictvonline.org/taxonomyReleases.asp ) have been established where the history of changes in virus taxonomy from 1971 to the present day can easily be traced. Each change is linked to a source document confirming the change or, for most changes since 2002, to the taxonomic proposal approved by the International Committee on Taxonomy of Viruses (ICTV).

Aortic pulse wave velocity (PWV) and augmentation index (AIx) are independent predictors of cardiovascular risk and mortality, but little is known about the effect of air temperature changes on these variables. Our study investigated the effect of exposure to whole-body mild-cold on measures of arterial stiffness (aortic and brachial PWV), and on central haemodynamics [including augmented pressure (AP), AIx], and aortic reservoir components [including reservoir and excess pressures (P ex)]. Sixteen healthy volunteers (10 men, age 43 ± 19 years; mean ± SD) were randomised to be studied under conditions of 12 °C (mild-cold) and 21 °C (control) on separate days. Supine resting measures were taken at baseline (ambient temperature) and after 10, 30, and 60 min exposure to each experimental condition in a climate chamber. There was no significant change in brachial blood pressure between mild-cold and control conditions. However, compared to control, AP [+2 mmHg, 95 % confidence interval (CI) 0.36-4.36; p = 0.01] and AIx (+6 %, 95 % CI 1.24-10.1; p = 0.02) increased, and time to maximum P ex (a component of reservoir function related to timing of peak aortic in-flow) decreased (-7 ms, 95 % CI -15.4 to 2.03; p = 0.01) compared to control. Yet there was no significant change in aortic PWV (+0.04 m/s, 95 % CI -0.47 to 0.55; p = 0.87) or brachial PWV (+0.36 m/s; -0.41 to 1.12; p = 0.35) between conditions. We conclude that mild-cold exposure increases central haemodynamic stress and alters timing of peak aortic in-flow without differentially affecting arterial stiffness.

RNA interference is a natural defense against viruses in plants. To date, the only viral siRNAs characterized have been those for positive-sense RNA viruses with one or two genome components. Here, we characterized siRNAs derived from rice stripe virus (RSV), a member of the genus Tenuivirus with four genomic RNAs and an ambisense coding strategy. Deep sequencing of small RNAs from infected rice leaves showed that siRNAs were derived almost equally from virion and complementary RNA strands and were mostly 20-22 nucleotides long. Most viral siRNAs were produced within the coding sequences and 5' termini of the RSV genome. RSV siRNAs had a higher G and lower C content than the viral genome but a strong A/U bias at the first nucleotide and a U bias at the final one, suggesting preferential targeting of such sequences by rice Dicer-like proteins.

The new plant virus family Virgaviridae is described. The family is named because its members have rod-shaped virions (from the Latin virga = rod), and it includes the genera Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus and Tobravirus. The chief characteristics of members of the family are presented with phylogenetic analyses of selected genes to support the creation of the family. Species demarcation criteria within the genera are examined and discussed.

The complete nucleotide sequences of segments S2, S3, S5, and S8-S11 of a Rice gall dwarf virus isolate from Guangxi Province, China, (RGDV-GX) were determined, completing the sequence of this isolate. The total genome (25,567nt) was similar in organization to a recently reported Thailand isolate (RGDV-T). A previously unreported second segment-specific repeat of 7 or 8nt was detected close to the 3'-end of segments S3, S5, and S8. The 3'-UTR of RGDV-GX S4 was 139nt shorter than that of RGDV-T; the insertion in RGDV-T contains a 34-nt inverted repeat, with the 3'-terminus probably abolishing the expected stem loop structure.

An isolate of a plant reovirus causing severe stunting and dark leaf symptoms on rice from Guangdong, China, was similar in virion morphology and serologically related to rice black-streaked dwarf virus (RBSDV). The electrophoretic profiles of genome segments of the two viruses in agarose or polyacrylamide gel were indistinguishable. The four genome segments of the new isolate corresponding to RBSDV S7-S10 were amplified by ligation RT-PCR and sequenced. The size and organization of each genome segment was very similar to its counterparts in RBSDV, maize rough dwarf virus (MRDV), and mal de Rio Cuarto virus (MRCV). Sequence identity was greatest to RBSDV and MRDV (ranging from about 60-85% depending on the protein), but identities were always much lower than those between RBSDV and MRDV. These comparisons and phylogenetic analyses suggested that the virus represents a new species in genus Fijivirus group 2, tentatively named Rice black-streaked dwarf virus-2.

A filamentous virus isolated from Iris japonica with mosaic symptoms was pathogenic to I. japonica and I. bulleyana but not to 12 virus indicator species. Sequencing of the 3'-terminus of the genome showed that it was a potyvirus, most closely related to sunflower mosaic virus (63.2% identical), and phylogenetic analysis also showed a more distant grouping with tobacco etch and Colombian datura viruses. The virus was detected by RT-PCR in symptomatic I. japonica plants from several regions of China. The virus appears to be an isolate of a new species in the genus Potyvirus, tentatively named butterfly flower mosaic virus.

A potyvirus from Chinese narcissus was transmitted mechanically to three species of Narcissus and to Lycoris radiata but not to 22 other test species. In western blot, the coat protein reacted strongly with Narcissus degeneration virus (UK isolate) antiserum. Antiserum raised to the Chinese virus did not react with eighteen other potyviruses. The complete nucleotide sequence (9816 nt) had the typical genome organisation for a member of the genus Potyvirus. Sequence comparisons and phylogenetic analysis showed that the Chinese virus was different from all previously sequenced potyviruses but distantly related to onion yellow dwarf and shallot yellow stripe viruses.

Rice gall dwarf virus (RGDV) is a member of the genus Phytoreovirus within the family Reovirdae. Its genome has 12 segments of double-stranded RNA (dsRNA), of which the nucleotide sequences of segments S4, S6, and S7 were determined, providing the first complete genome sequence of RGDV. Each of the segments S4, S6, and S7 contained conserved terminal sequences conforming to the RGDV consensus, 5'-GGXA ... UGAU-3' (X = U or C). Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of 79.8, 58.6, and 53.3 kDa. These proteins appeared to be homologous to those encoded by the corresponding segments of rice dwarf virus and wound tumor virus, the other known members of the same genus, having about 20-30% amino acid identity to them. It is therefore likely that RGDV S4 and S6 encode non-structural proteins and S7 an inner core protein. Probable homologies between the segments of all known phytoreoviruses are summarized. Beyond these similarities, the RGDV proteins displayed no significant similarity to any other reported viral proteins.

The complete genome sequence of the four RNAs of rice stripe virus Zhejiang isolate was determined. In addition to polymerase modules, the pc1 protein encoded on RNA1 harbours an ovarian tumour (OTU) - like cysteine protease signature near its N-terminus, suggesting that the protein might yield the viral polymerase and one or more additional proteins by autoproteolytic cleavage and/or have deubiquitination activity. A novel inverted repeat sequence motif was found to be universal within the intergenic regions of ambisense genome segments of tenuiviruses, supporting the possibility that it may be functionally important, perhaps in regulating transcription termination.

A filamentous virus, with particles 600-650 nm long, was purified from Narcissus pseudonarcissus (daffodil) in Hangzhou and an antiserum prepared. After mechanical inoculation, the virus could be detected serologically in Narcissus species but not in some commonly used virus indicators. Infection was symptomless. The complete sequence of the genomic RNA (8281 nt) showed six predicted ORFs typical of carlaviruses. Pairwise comparisons of gene sequences and phylogenetic analysis demonstrated that the new virus should be classified as a carlavirus but that it was not closely related to members of any current species. We propose the name Narcissus symptomless virus (NSV).

The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58-59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.

Plants of Thunberg fritillary (Fritillaria thunbergii Miq.) from Zhejiang Province, were found to be co-infected with two distinct potyviruses. One was an isolate of the recently reported Thunberg fritillary mosaic virus (TFMV; Wei et al., (2005) Arch Virol 150: 1271-1280), while the other was a distinct virus that did not react with TFMV antiserum nor with antisera to 17 other potyviruses, except for a weak reaction with antibodies produced to soybean mosaic virus (SMV) Pinellia strain. Both viruses could be transmitted mechanically to their original host but not to any of a range of commonly used indicator plants. No local lesion host was identified that would enable the viruses to be propagated independently. The complete sequences of both viruses were determined; that of the new virus (9656 nt) had the typical genome organisation and recognised sequence motifs of a potyvirus, encoding a putative polyprotein of 351 kDa. Phylogenetic analysis, sequence comparisons, and the pattern of polyprotein cleavage sites all indicated that it was a member of the Bean common mosaic virus subgroup. The most closely related species are Soybean mosaic virus and Wisteria vein mosaic virus, with 68-69% amino acid identity between their polyproteins. This is sufficiently different for the new virus to be regarded as a distinct species, which we have tentatively named Fritillary virus Y.

The host range and nucleotide sequence of shallot yellow stripe virus (SYSV) from welsh onion in Shandong province, China is described. Of the plants tested, only shallot and welsh onion became infected but most shallot plants were symptomless. The complete sequence of one isolate (10429 nt) and the 3'-terminal 3540 nts of a second isolate were determined. They had c. 90% nt identity to one another and to published (partial) sequences of SYSV. SYSV was most closely related to onion yellow dwarf virus (OYDV) and resembled it in having a much larger P3 protein than other species in the genus.

A potyvirus causing mosaic symptoms in Thunberg fritillary (Fritillaria thunbergii) was found at two sites in Zhejiang province, China. The virus was readily mechanically transmitted to its original host but not to any of 17 other widely used plant virus indicators. A polyclonal antiserum raised to purified virus particles reacted with its homologous virus but not with a range of other viruses (including 16 potyvirus species). In electron microscopy, virus particles and inclusion bodies typical of a potyvirus were seen. The complete nucleotide sequence of an isolate from Ningbo was determined. It was 9723 nt long and sequence analyses predicted the standard potyvirus organisation. The partial sequence (1664 nts at the 3'-terminus) of an isolate from Panan was also determined; the two sequences had 96.9% nt identity. In sequence comparisons and phylogenetic analyses with completely sequenced potyviruses, the new virus was most closely related to Lily mottle virus (53.0% aa identity) and Leek yellow stripe virus. The most closely related incomplete sequence in the international databases was for Lycoris mild mottle virus (72.8% nt identity in their coat proteins). These results suggest that the virus studied is a new species in the genus Potyvirus, which we have tentatively named Thunberg fritillary mosaic virus.

The complete sequence of the genomic RNA of an isolate of Lily virus X (LVX) has been determined for the first time. The isolate from the Netherlands was 5823 nucleotide (nt) long excluding the 3'-poly(A) tail, making it the shortest reported potexvirus sequence. The 5'-non-coding region begins with GGAAAA like that of Scallion virus X (ScaVX) and some isolates of Cymbidium mosaic virus (CymMV), whereas those of other sequenced potexviruses probably all begin with GAAAA. The genome organisation was similar to that of other members of the genus except that a TGBp3-like region lacked a normal AUG start codon. A phylogenetic analysis based on the entire coding sequence showed that LVX was most closely related to Strawberry mild yellow edge virus and belonged in a subgroup of the genus that also contains CymMV, Narcissus mosaic virus, ScaVX, Pepino mosaic virus, Potato aucuba mosaic virus and White clover mosaic virus.

A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.

Degenerate primers were used to detect and amplify 3'-terminal genome fragments of potyviruses from medicinal aroid plants growing at 16 sites in China. Virus was detected in 7 samples of which six, all of Pinellia ternata, contained a strain of soybean mosaic virus (SMV) similar to that previously reported from this host in China. The complete sequence of one isolate and the P1 protein coding region of the other isolates were also sequenced. In all cases, the P1 proteins resembled isolates of Dasheen mosaic virus (DsMV) more closely than SMV, confirming earlier suggestions of recombination in this region. In a phylogenetic analysis of SMV, DsMV and related sequences, the aroid sequences of SMV formed a distinct group which also included a sequence published as Zantedeschia symptomless virus (AF469171). One of the P. ternata samples was also infected with a second potyvirus, the 3'-terminal sequence of which was similar to DsMV and to some sequences published as Vanilla mosaic virus. The seventh infected sample was Typhonium flagelliforme and the virus from it was identified from its sequence as zantedeschia mosaic virus (ZaMV), providing the first report of this virus from mainland China.

A Barley mild mosaic virus (BaMMV) isolate from France (BaMMV-Sil) capable of overcoming rym5-controlled resistance was inoculated to barley genotypes carrying various genes for resistance to the barley mosaic viruses. BaMMV-Sil was unable to infect genotypes carrying rym1, rym4, rym8, rym9, or rym11 but genotypes carrying rym3, rym5, rym6 or no known bymovirus resistance gene were susceptible. Plants carrying rym7 or rym10 showed partial resistance with delayed virus accumulation. The two genomic RNAs of BaMMV-Sil were sequenced and compared to published sequences and those of a further common strain isolate from the UK. Four amino acid differences were observed between BaMMV-Sil and European common strain isolates in the polypeptide encoded by RNA1, the RNA species which determines pathogenicity on the rym5 genotypes. Only two of these differences are likely to be functionally important (His rather than Gln at position1217 in the VPg cistron; His rather than Asp at position 1776 in the NIb cistron). Comparisons with related viruses in the genera Bymovirus and Potyvirus suggest that the change in the VPg, which occurs within a motif conserved amongst all viruses within the family Potyviridae, is the more likely cause of rym5 resistance-breaking.

Tuberose plants with mild mottle symptoms, growing in a glasshouse in Hangzhou, China, contained virions and inclusion bodies typical of a potyvirus. The virus was mechanically transmitted to tuberose but not to 14 other test plant species. A fragment of 4607 nucleotides, corresponding to the 3'-half of a typical potyvirus was amplified by RT-PCR using degenerate primers and sequenced. The most similar sequence in the databases was that of Tuberose mild mosaic virus (TuMMV) from Taiwan and this was the only virus significantly related to it in phylogenetic analyses. The new sequence had 71.1% nt and 76.6% aa identity to TuMMV in the coat protein. Western blot analyses using antisera raised to expressed coat protein showed that the two viruses were serologically related. Although there are no substantial biological data to distinguish the Hangzhou isolate from TuMMV, the molecular difference between the two virus isolates is similar to, or slightly greater than, that between several pairs of well-established potyvirus species. These results therefore suggest that the Hangzhou isolate should be regarded as a new member of the genus Potyvirus, and we have tentatively named it Tuberose mild mottle virus.

The new plant virus family Flexiviridae is described. The family is named because its members have flexuous virions and it includes the existing genera Allexivirus, Capillovirus, Carlavirus, Foveavirus, Potexvirus, Trichovirus and Vitivirus, plus the new genus Mandarivirus together with some related viruses not assigned to any genus. The family is justified from phylogenetic analyses of the polymerase and coat protein (CP) sequences. To help to define suitable molecular criteria for demarcation of species, a complete set of pairwise comparisons was made using the nucleotide (nt) and amino acid (aa) sequences of each fully-sequenced gene from every available accession in the family. Based on the distributions and on inspection of the data, it was concluded that, as a general rule, distinct species have less than ca. 72% identical nt or 80% identical aa between their entire CP or replication protein genes.

Degenerate primers for RT-PCR were designed and used to amplify genome fragments ( c. 750 nt in the coat protein-ORF6 region) of allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.

A potyvirus isolated from Pinellia ternata in China was characterised and shown to be related to Soybean mosaic virus (SMV). The virus was pathogenic on P. ternata and some soybean cultivars, whereas the local soybean SMV isolate HH5 did not infect P. ternata. Western blot experiments demonstrated a serological relationship between the virus from Pinellia, SMV and Watermelon mosaic virus (WMV). The complete nucleotide sequences of the Pinellia virus (isolate P-1, 9735 nt) and of the Chinese soybean SMV isolates HH5 (9585 nt) and HZ (9588 nt) were determined. A 1733 nt sequence at the 3'-terminus of a second isolate from Pinellia (isolate P-2) was also determined. The predicted polyprotein of isolate P-1 has 83% amino acid (aa) identity with those of published SMV sequences. In many parts of the genome, aa identity was about 90% but it was much lower in the P1 protein region (24-29%), where it more closely resembled Dasheen mosaic virus (62%). The partial sequence of isolate P-2 had 91% nt identity to P-1 and both isolates resembled a recent sequence in the public databases (AF469171) wrongly named Zantedeschia mosaic virus. The two complete SMV soybean sequences had 93-95% nt identity with those of the previously sequenced isolates and >97% amino acid identity. Phylogenetic analysis and comparisons of coat proteins suggest that the Pinellia, WMV and SMV potyviruses should probably be treated as strains of the same species.

An internet database (DPVweb) was established containing details of all sequences of viruses, viroids and satellites of plants that are complete or that contain at least one complete gene (n>4600). The start and end positions of each feature (genes, non-translated regions etc) were recorded and checked for accuracy. Client software was written to enable easy selection of sequences and features of a chosen virus and to analyse codon usage bias. Codon usage was analysed for each gene of one example of each fully-sequenced plant virus. There were large differences in codon preferences, related to the nucleotide composition of the genome, particularly the GC content of the third codon position. There was no effect of gene size on codon bias. Genes from the same genome usually had similar coding strategies except where constrained by the overlap of reading frames. Although some synonymous codons were consistently used with low frequency by both plants and viruses, viruses were not generally adapted to use (or avoid) those codons most frequently used by their host plants and there was no obvious association with the type of transmission. Mutational bias, rather than translational selection appears to account for the majority of the variation detected. The software is available at http://www.dpvweb.net/analysis/codons.php.

Degenerate primers were used to amplify virus sequences from imported lilies in Zhejiang province, China. Two viruses, Lily mottle virus (LMoV, genus Potyvirus) and Lily symptomless virus (LSV, genus Carlavirus) were detected, purified and completely sequenced from a mixed infection in a plant raised from bulbs imported from the Netherlands. The sequence of LMoV was 9644 nt long and encoded a polyprotein of 3095 amino acids with a calculated M(r) of 351.0 kDa that had only 45.1-54.4% identity to other completely sequenced potyviruses. Phylogenetic analysis of the complete polyproteins of members of the genus demonstrated that LMoV was distantly grouped with LYSV, BYMV and ClYVV. Two partial LMoV sequences from different cultivars were identical to one another and very similar (98.3% identical nucleotides) to the corresponding region of the complete sequence. Analysis of the coat protein sequences of LMoV isolates revealed two subgroups, corresponding to the earlier "Tulip breaking virus lily strain" and "Tulip band breaking virus" isolates. Our newly-determined isolates showed an extremely close relationship to the first of these. The LSV sequence was 8393 nucleotides long and had the typical carlavirus genome organization. The ORF1 protein was most closely related to that of Blueberry scorch virus (57.2% identical amino acids). Sequences of 1796 nt at the 3'-end of three additional LSV isolates from different cultivars were very similar (>98% identical nucleotides) to the corresponding region of the complete sequence. This is the first report of complete sequences for LMoV and LSV.

The complete sequence of an isolate of Onion yellow dwarf virus (OYDV) from Yuhang, Zhejiang province, China, was determined. It was 10538 nts in length and was predicted to encode a polyprotein 3403 amino acids (aa) long with a calculated M(r) of 385.1 kDa. The predicted P3 protein (530 aa) was larger than that of any of the potyviruses sequenced to date (344-378 aa). The additional sequence occurs at the N-terminus of the protein, does not represent a duplication from elsewhere in the OYDV genome and could not be matched to any other sequences in the databases. Similar sequences were found in 4 other Chinese OYDV isolates. Phylogenetic analysis of the amino acid sequences of the polyprotein showed that OYDV is distantly related to Pea seed-borne mosaic virus and the potyviruses of grasses and cereals.

Sugarcane or maize leaves with mosaic virus symptoms were collected from 13 sites in China. Sequence data showed that all 8 samples from maize contained Sugarcane mosaic virus (SCMV); complete sequences were determined from 2 samples and partial sequences (the CI coding region and the 3'-part of the genome) from the others. The 5 sugarcane samples all contained a virus tentatively described as Sorghum mosaic virus (SrMV) and in three of them SCMV was also detected; 2 SrMV sequences and the 3 SCMV ones were completely determined and partial SrMV sequences were obtained from the remaining 3 samples. The features of the complete sequences of SCMV and SrMV are described for the first time. Sequence comparisons and phylogenetic analysis showed three distinct groups of Chinese SCMV sequences (sugarcane isolates from Zhejiang province, a maize isolate from Guangdong and maize isolates from other provinces). The SrMV sequences were similar to one another (> 93% identical nucleotides); they resembled published sequences in the coat protein but were less similar in the 3'-UTR. The complete sequences of SCMV and SrMV had about 70% nucleotides identical to one another and to Maize dwarf mosaic virus (MDMV). MDMV was not detected in any of the samples.

Potyvirus isolates from asparagus bean ( Vigna sesquipedalis) plants in Zhejiang province, China, caused either rugose and vein banding mosaic symptoms (isolate R) or severe yellowing (isolate Y) in this host, but were otherwise similar in host range. Both isolates were completely sequenced and shown to be isolates of Bean common mosaic virus (BCMV). The complete sequences were 9992 (R) or 10062 (Y) nucleotides long and shared 91.7% identical nucleotides (93.2% identical amino acids) in their genomes and were more distantly related to the BCMV-Peanut stripe virus sequence (PStV). The isolates were much less similar to one another in the 5'-UTR and the N-terminal region of the P1 protein. In the P1, isolate Y was closer to PStV (76.1% identical amino acids) than to isolate R (64.8%). Phylogenetic analyses of the coat protein region showed that the new isolates grouped with other isolates from Vigna spp., forming the blackeye cowpea mosaic strain subgroup of BCMV with 94-98% nucleotides (96-99% amino acids) identical to one another and about 90% identity to other BCMV isolates. Other significant subgroupings amongst published BCMV isolates were detected.

Molecular analyses of viruses infecting Chinese scallion (Allium chinense G. Don) showed that the plants did not contain any of the poty-, carla- or allexiviruses that are common in garlic plants in China. The complete sequences of a potyvirus and a potexvirus were determined and these were shown to represent different viruses from any in the databases. They could be transmitted mechanically to scallion but not to other Allium species (including garlic) or to Narcissus. The potyvirus, tentatively named Scallion mosaic virus, has a distant relationship (c. 62% nucleotide identity over the entire genome) to Turnip mosaic virus and Japanese yam mosaic virus, with which it grouped in phylogenetic analyses. Its genome is 9324 nts long, encoding a 341.3 kDa polyprotein of 3001 amino acids. The potexvirus, tentatively named Scallion virus X, has a genome 6987 nts long and its organisation was similar to that of the other potexviruses but with only 46.3-63.2% nucleotides identical to them. It is most closely related to Narcissus mosaic virus but phylogenetic analyses indicate that it should be considered a distinct species. Neither of the viruses have been detected in garlic, although the two host plants are closely related.

The complete nucleotide sequence of a UK isolate of oat mosaic virus (OMV) was determined. RNA1 was 7550 nt long with one large open reading frame potentially encoding a polyprotein of 262.8 kDa with features typical of bymoviruses. RNA2 was 2284 nt in length, substantially smaller than those of other bymoviruses sequenced. It appeared that most of the P2 region had been deleted during repeated mechanical transmission of the isolate. The 3'-UTR of RNA2 was very long (> 1.25 kb) and proved to have a 532 nt slightly overlapping repeat. Phylogenetic analysis confirmed that OMV is an independent member of the genus Bymovirus.

Conserved carla- and potyvirus primers were used in RT-PCR to amplify virus fragments from garlic and other bulb crops in China and the fragments were subsequently sequenced and compared in phylogenetic analyses. Garlic plants from Henan, Hubei, Jiangsu, Shangdong and Yunnan provinces all contained at least one isolate each of Garlic latent virus (genus Carlavirus), Onion yellow dwarf virus (OYDV, genus Potyvirus) and Leek yellow stripe virus (LYSV, genus Potyvirus). The complete sequence of a Zhejiang isolate of LYSV was also determined, providing the first complete sequence of this virus. The genome was 10142 nucleotides long excluding the poly(A) tail and had the typical features of the genus Potyvirus, although some of the amino acids surrounding the polyprotein cleavage sites were unusual. Shallot yellow stripe virus (SYSV) was amplified from bunching onion (Allium fistulosum var. caespitosum) in Zhejiang province, providing the first record of SYSV in China. Lily mottle virus was amplified from dragon-teeth lily (Lilium brownii var. viridulum).