Duck astroviruses (DAstVs) are known to cause duck viral hepatitis; however, little is known regarding their molecular biology. Here, we report the complete sequence of a DAstV associated with a recent outbreak of fatal hepatitis in ducklings in China. Sequence analyses indicated that the genome of DAstV possessed a typical astrovirus organization and also exhibited two unique features. The polyadenylated genome comprised 7722 nt, which is the largest among astroviruses sequenced to date. The ORF2 of DAstV was not in the same reading frame as either ORF1a or ORF1b, which was distinct from all other astroviruses. Sequence comparisons and phylogenetic analyses revealed that DAstV was more closely related to turkey astrovirus (TAstV) type 2, TAstV-3 and TAstV/MN/01 (a possible new TAstV serotype) than to TAstV-1 or other astroviruses. These findings suggest that astroviruses may transmit across ducks and turkeys.Astroviruses are non-enveloped, single-stranded, positivesense RNA viruses, which have been demonstrated to infect both mammalian and avian hosts (Monroe et al., 2005). The genomes of these viruses range in size from 6.1 to 7.3 kb, consisting of three ORFs (1a, 1b, and 2) (Finkbeiner et al., 2008). All astroviruses share a rather conserved frameshift slippery sequence in the overlap region between ORF1a and ORF1b, which directs the synthesis of an ORFla/lb fusion polyprotein (Jiang et al., 1993;Lewis et al., 1994;Lewis & Matsui, 1996;Marczinke et al., 1994). ORF1a and ORF1b encode the non-structural proteins, which include several transmembrane helical motifs, a serine protease, a nuclear localization signal (NLS), and an RNA-dependent RNA polymerase (RdRp) motif (Jiang et al., 1993;Lewis et al., 1994;Willcocks et al., 1994). ORF2 encodes the capsid protein that is required for virion formation.Astroviruses in ducks have been associated with a fatal hepatitis which occurred in the UK, historically known as duck hepatitis virus type 2 (DHV-2) (Asplin, 1965; Gough et al., 1984Gough et al., , 1985. Originally thought to be a picornavirus, DHV-2 was later characterized as an astrovirus by morphology and renamed duck astrovirus 1 (DAstV-1) (Gough et al., 1984(Gough et al., , 1985Monroe et al., 2005). DHV-1 and a later described serotype 3 (DHV-3), isolated in the USA (Haider & Calnek, 1979), are still classified as picornaviruses (Stanway et al., 2005). Recently, DHV-1 was confirmed as a picornavirus belonging to a novel genus (Ding & Zhang, 2007;Kim et al., 2006;. It has also been proposed that DHV-1 be renamed duck hepatitis A virus (DHAV) genotype A (DHAV-A) and that two other newly discovered DHV serotypes (Kim et al., 2007; be designated DHAV-B and DHAV-C (Fu et al., 2008;Wang et al., 2008). More recently, a 391 nt RdRp sequence has been determined for DAstV-1 and DHV-3 and comparisons indicate that they are both astroviruses (Todd et al., 2009). In this study, we report the complete genomic sequence of a DAstV strain associated with a fatal hepatitis which occurred in China in 2008. The genomic features ...

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The nucleotide sequences of the complete VP1, VP0, VP3, and partial 3D regions of seven duck hepatitis virus (DHV) serotype 1 (DHV-1) strains isolated in China between 2001 and 2007 and one DHV-1 strain originally obtained from ATCC were determined and compared with previously available DHV sequences in GenBank. Phylogenetic analysis on the basis of VP1 sequences demonstrated three distinct genetic groups. There was an excellent concordance among the genetic groups assigned based on the complete VP0, VP3, and the partial 3D regions. In view of the growing importance of molecular techniques in diagnosis, we propose that the three genetic groups should be termed DHV types A, B, and C. All DHV-1 strains grouped in genotype A, whereas the new serotype strains isolated in Taiwan and the new serotype strains isolated in South Korea clustered into genotypes B and C, respectively, suggesting a potential genetic correlates of serotype. In pairwise comparisons of complete VP1, VP0, and VP3 nucleotide and amino acid sequences and the partial 3D nucleotide sequence, DHVs of the same genotype were clearly distinguished from those of heterologous genotypes. Analysis of the amino acid sequences of the three capsid proteins demonstrated the presence of conserved elements that form the eight-stranded beta-barrel structures, as well as intervening domains that vary in sequence between strains of different genotypes as seen in other picorna viruses.

BackgroundPorcine astrovirus (PoAstV) is widely distributed worldwide, and is highly prevalent among piglets with or without diarrhea, existing as at least five distinct lineages (PoAstV1–PoAstV5) within the genus Mamastrovirus. However, our knowledge of the diversity and epidemiology of PoAstV in China is limited.ResultsIn this study, fecal samples from 21/120 (17.5 %) domestic pigs, including 18/100 (18 %) diarrheic and 3/20 (15 %) healthy pigs, and from 1/9 (11.1 %) healthy wild boars tested in Sichuan Province were positive for PoAstV on reverse transcription–PCR. Of the 22 positive samples, 13.6 % were positive for PoAstV only, whereas 40.9 % also contained Porcine epidemic diarrhea virus (PEDV), 22.7 % also contained porcine group A rotavirus (PRoVA), and 22.7 % also contained PEDV and PRoVA. A phylogenetic analysis of the RdRp gene revealed genetic heterogeneity among the PoAstV sequences and two lineages were detected in this study, with PoAstV-2 predominant. PoAstV-5 was detected in wild boars for the first time.ConclusionsPoAstV infections exist in Sichuan Province regardless of the disease status in the pig population, either alone or in combination with other enteric viruses, and may be associated with diarrhea.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-015-0462-6) contains supplementary material, which is available to authorized users.

In this study, we investigated the diversity of diatrypaceous fungi from six regions in China based on morpho-molecular analyses of combined ITS and tub2 gene regions. We accept 23 genera in Diatrypaceae with 18 genera involved in the phylogram, and the other five genera are lacking living materials with sequences data. Eleven species included in four genera (viz. Allocryptovalsa, Diatrype, Diatrypella, and Eutypella) have been isolated from seven host species, of which nine novel species (viz. Allocryptovalsa castaneae, A. castaneicola, Diatrype betulae, D. castaneicola, D. quercicola, Diatrypella betulae, Da. betulicola, Da. hubeiensis, and Da. shennongensis), a known species of Diatrypella favacea, and a new record of Eutypella citricola from the host genus Morus are included. Current results show the high diversity of Diatrypaceae which are wood-inhabiting fungi in China.

Hazelnut (Corylus heterophylla Fisch.) is an important nut crop in China but has been declining owing to the destructive effects of fungal branch canker and dieback. The identification and management of these pathogens are difficult because of the lack of attention to branch canker, insufficient understanding of phylogenetic, and overlapping morphological characteristics of the pathogens. In total, 51 strains were isolated from Chinese wild hazelnut in this study, and three species of Cytospora and two of Diaporthe were identified through morphological observation and multi-locus phylogenetic analyses (ITS, act, rpb2, tef1-α, and tub2 for Cytospora; ITS, cal, his3, tef1-α, and tub2 for Diaporthe). Three new species, Cytospora corylina, C. curvispora, and Diaporthe corylicola, and two known species, Cytospora leucostoma and Diaporthe eres, grew at 5–30°C and a pH of 3.0–11.0, with optimum growth at approximately 25°C and pH 4.0–7.0. Additionally, the effects of six carbon sources on mycelial growth were investigated. This study explored the main pathogenic fungi species of Corylus heterophylla, completed the corresponding database of pathogenic fungi information, and clarified their biological characteristics. Moreover, the results of this study provided a theoretical basis for Corylus heterophylla disease management and prevention in China.

Sequence analysis of duck hepatitis virus type 1 (DHV-1) led to its classification as the only member of a new genus, Avihepatovirus, of the family Picornaviridae, and so was renamed duck hepatitis A virus (DHAV). The 5= untranslated region (5= UTR) plays an important role in translation initiation and RNA synthesis of the picornavirus. Here, we provide evidence that the 651-nucleotide (nt)-long 5= UTR of DHAV genome contains an internal ribosome entry site (IRES) element that functions efficiently in vitro and within BHK cells. Comparative sequence analysis showed that the 3= part of the DHAV 5= UTR is similar to the porcine teschovirus 1 (PTV-1) IRES in sequence and predicted secondary structure. Further mutational analyses of the predicted domain IIId, domain IIIe, and pseudoknot structure at the 3= end of the DHAV IRES support our predicted secondary structure. However, unlike the case for the PTV-1 IRES element, analysis of various deletion mutants demonstrated that the optimally functional DHAV IRES element with a size of approximately 420 nt is larger than that of PTV-1 and contains other peripheral domains (Id and Ie) that do not exist within the type IV IRES elements. The domain Ie, however, could be removed without significant loss of activity. Surprisingly, like the hepatitis A virus (HAV) IRES element, the activity of DHAV IRES could be eliminated by expression of enterovirus 2A protease. These findings indicate that the DHAV IRES shares common features with type IV picornavirus IRES elements, whereas it exhibits significant differences from type IV IRESs. Therefore, we propose that DHAV possesses a distinct type IV IRES element of picornavirus.T he internal ribosome entry site (IRES) elements have the function to direct cap-independent internal initiation of protein synthesis, which is mechanistically quite different from the canonical cap-dependent mechanism for the translation initiation of the majority of cellular mRNAs (3). Earlier studies have indicated that all cytoplasmic cellular mRNAs possess a 5= terminal cap structure (m7GpppG. . .) that is recognized by the translation initiation factor complex-eukaryotic initiation factor 4 (eIF4F), which contains three proteins including eIF4E (cap-binding protein); eIF4A (ATP-dependent RNA helicase); and eIF4G, which acts as a protein scaffold. This complex of proteins acts as a bridge between the mRNA and the 40S ribosomal subunit via its interaction with eIF3 by multiple protein-protein interactions (23). In contrast to the cellular mRNAs, no cap structure exists at the 5= terminus of some viral mRNAs, such as those of picornaviruses and relevant viruses like hepatitis C virus (HCV). Initiation of protein synthesis for these viruses which rely on cap structure is termed internal initiation; in this case, the IRES element located within the 5= untranslated region (5= UTR) of the viral genome can exert the function to direct translation initiation (4, 19). Previous studies have showed that these IRES elements contain diverse secondary structures with ...

Cytospora canker is a destructive disease of numerous hosts and causes serious economic losses with a worldwide distribution. Identification of Cytospora species is difficult due to insufficient phylogenetic understanding and overlapped morphological characteristics. In this study, we provide an assessment of 23 Cytospora spp., which covered nine genera of Rosaceae, and focus on 13 species associated with symptomatic branch or twig canker and dieback disease in China. Through morphological observation and multilocus phylogeny of internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (LSU), actin ( act ), RNA polymerase II subunit ( rpb2 ), translation elongation factor 1-α ( tef1- α), and beta-tubulin ( tub2 ) gene regions, the results indicate 13 distinct lineages with high branch support. These include 10 new Cytospora species, i.e., C. cinnamomea , C. cotoneastricola , C. mali-spectabilis , C. ochracea , C. olivacea , C. pruni-mume , C. rosicola , C. sorbina , C. tibetensis , and C. xinjiangensis and three known taxa including Cytospora erumpens , C. leucostoma , and C. parasitica . This study provides an initial understanding of the taxonomy of Cytospora associated with canker and dieback disease of Rosaceae in China.