Complete Genome Sequence of a Variant Porcine Epidemic Diarrhea Virus Strain Isolated in China

Since October 2010, an outbreak of porcine epidemic diarrhea (PED) has been observed in some provinces of China. Here we report the complete genome sequence of porcine epidemic diarrhea virus (PEDV) strain LC, which was recently isolated from sucking piglets that suffered from severe watery diarrhea in Guangdong. It will help in understanding the epidemiological and molecular characteristics of PEDV in China.     

Complete Genome Sequence of Porcine Epidemic Diarrhea Virus Strain AJ1102 Isolated from a Suckling Piglet with Acute Diarrhea in China

A diarrhea outbreak caused by porcine epidemic diarrhea virus (PEDV) has been observed in China since December 2010. We report here the complete genome sequence of PEDV strain AJ1102 isolated from a suckling piglet with acute diarrhea, which will help toward understanding the molecular and evolutionary characteristics of the epidemic PEDV in China.     

Complete Genome Sequence of a Novel Porcine Sapelovirus Strain YC2011 Isolated from Piglets with Diarrhea

Sapelovirus is a member of the family Picornaviridae and is emerging as an enteric porcine, simian, and avian pathogen. Here, we report the genome sequence of a novel porcine sapelovirus strain YC2011 isolated from piglets with severe diarrhea. The availability of the genome sequence is helpful to further investigations of molecular characteristics and epidemiology of porcine sapelovirus.     

Protective Effects of Cell-Free Supernatant and Live Lactic Acid Bacteria Isolated from Thai Pigs Against a Pandemic Strain of Porcine Epidemic Diarrhea Virus

Probiotics and Antimicrobial Proteins - Porcine epidemic diarrhea virus (PEDV) is a coronavirus which causes severe diarrhea and fatal dehydration in piglets. In general, probiotic supplements...     

Molecular Characterization and Phylogenetic Analysis of Porcine Epidemic Diarrhea Viruses Associated with Outbreaks of Severe Diarrhea in Piglets in Jiangxi,China 2013

Porcine epidemic diarrhea (PED), caused by porcine epidemic diarrhea virus (PEDV), is a highly contagious, acute enteric viral disease of swine characterized by vomiting, watery diarrhea, dehydration and death. To identify and characterize the field PEDVs associated with the outbreaks of severe diarrhea in piglets in Jiangxi, 2013, the complete genome sequences of two representative strains of PEDV, designated CH/JX-1/2013 and CH/JX-2/2013, were determined and analyzed. The genome sequences of both emergent Jiangxi PEDV strains, CH/JX-1/2013 and CH/JX-2/2013, were 28,038 nucleotides in length excluding 3’ poly (A) tail. Compared to the PEDV CV777 strain, CH/JX-1/2013 and CH/JX-2/2013 had some unique genetic characteristics in the proximal region of the 5´-UTRs. Phylogenetic analysis of the complete genomes and the structural proteins revealed that CH/JX-1/2013 and CH/JX-2/2013 had a close relationship with post-2010 Chinese PEDV strains and US strains identified in 2013. The nucleotide identity between the two Jiangxi strains (CH/JX-1/2013 and CH/JX-2/2013) and 30 strains of PEDV identified ante-2010 and post-2010 ranged from 96.3–97.0% and 97.3–99.7%, respectively. Multiple nucleotide and deduced amino acid mutations were observed in the ORF1a/b, S, ORF3, E, M and N genes among the current field PEDV strains when compared to the CV777 strain. Some of the mutations altered the amino acid charge and hydrophilicity, and notably, there was an amino acid substitution in the middle of one neutralizing epitope (L1371I) of the S gene of both CH/JX-1/2013 and CH/JX-2/2013. Taken together, the accumulated genetic variations of the current field PEDV strains might have led to antigenic changes of the viruses, which might confer the less effectiveness or failure of the CV777-based vaccines currently being widely used in Jiangxi, China.     

Biology of a Novel Mycobacteriophage, SWU1, Isolated from Chinese Soil as Revealed by Genomic Characteristics

Mycobacteriophage SWU1 is a newly isolated phage from a soil sample collected at Gongping village, Pingchang County, Sichuan Province, China, using Mycobacterium smegmatis mc(2)155 as a host. Plaques of SWU1 appear as a unique bull's-eye on an M. smegmatis lawn. In this paper, we report the complete genome sequence of SWU1 and some major findings from the analysis result.     

Complete Genome Sequence of a Vero Cell-Adapted Isolate of Porcine Epidemic Diarrhea Virus in Eastern China

In early 2012, a widespread porcine epidemic diarrhea virus (PEDV) occurred in eastern China. A cell-adapted isolate, SD-M, was at the four-passage level of virulent field strain SD, which was isolated from a 2-day-old dead suckling piglet that had suffered from severe diarrhea in Shandong Province, China. We report here the complete genome sequence of SD-M. This sequence will promote a better understanding of the molecular pathogenesis of PEDV.     

Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World

The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses.     

来自猪肠道芽胞杆菌培养液中氨基酸成分分析

从动物肠道分离得到112株芽胞杆菌,采用氨基酸全自动分析仪对分离得到的芽胞杆菌的上清进行氨基酸分析。结果表明,不同芽胞杆菌菌株上清中各氨基酸水平相差较大。其中,动物的几种限制性必需氨基酸中,赖氨酸的含量分布在0.18~0.32g·L~(-1)之间,蛋氨酸的含量分布在0.05~0.09g·L~(-1)之间。精氨酸的含量分布在0.004~0.02g·L~(-1)之间。所有氨基酸种类中,赖氨酸、亮氨酸、苯丙氨酸、异亮氨酸含量较为丰富,超过了0.1g·L~(-1),而天冬氨酸、苏氨酸、丝氨酸含量较少,不到0.01g·L~(-1)。这些结果为开发提高饲料氮利用效率的饲用益生菌提供参考。     

Evaluation on the Efficacy and Immunogenicity of Recombinant DNA Plasmids Expressing Spike Genes from Porcine Transmissible Gastroenteritis Virus and Porcine Epidemic Diarrhea Virus

Porcine transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PDEV) can cause severe diarrhea in pigs. Development of effective vaccines against TGEV and PEDV is one of important prevention measures. The spike (S) protein is the surface glycoprotein of TGEV and PEDV, which can induce specific neutralization antibodies and is a candidate antigen for vaccination attempts. In this study, the open reading frames of the TGEV S1 protein and in addition of the S or S1 proteins of PEDV were inserted into the eukaryotic expression vector, pIRES, resulting in recombinant plasmids, pIRES-(TGEV-S1-PEDV-S1) and pIRES-(TGEV-S1-PEDV-S). Subsequently, 6–8 weeks old Kunming mice were inoculated with both DNA plasmids. Lymphocyte proliferation assay, virus neutralization assay, IFN-γ assay and CTL activity assay were performed. TGEV/PEDV specific antibody responses as well as kinetic changes of T lymphocyte subgroups of the immunized mice were analyzed. The results showed that the recombinant DNA plasmids increased the proliferation of T lymphocytes and the number of CD4+ and CD8+ T lymphocyte subgroups. In addition, the DNA vaccines induced a high level of IFN-γ in the immunized mice. The specific CTL activity in the pIRES-(TGEV-S1-PEDV-S) group became significant at 42 days post-immunization. At 35 days post-immunization, the recombinant DNA plasmids bearing full-length S genes of TGEV and PEDV stimulated higher levels of specific antibodies and neutralizing antibodies in immunized mice.     

湖北省不同地区汉坦病毒M片段的分析研究

参考汉坦病毒（ＨＶ）的基因文库软件设计Ｍ片段Ｇ－１区型特异性引物,以ＨＶ　７６／１１８、Ｈ－１１４、Ａ－９及Ｒ－｛２２｝株ＲＮＡ为阳性模板,建立ＨＶ的分型方法──逆转录一半巢式聚合酶链反应（ＲＴ－ｈｅｍｉｎｅｓｔｅｄ　ＰＣＲ）,对湖北省不同地区分离的３０株ＨＶ进行分　型。结果显示：（１）建立的ＲＴ－ｈｅｍｉｎｅｓｔｅｄ　ＰＣＲ分型方法对ＨＶ两型的代表株７６／１１８（ＨＴＮ）、Ａ－９（ＨＴＮ）、Ｈ－１１４（ＨＴＮ）及Ｒ－｛２２｝（ＳＥＯ）ＲＮＡ进行了特异性扩增,其大小与理论值一致;此　法只能检测ＨＶ　ＲＮＡ,不能检测其它病毒ＲＮＡ。（２）分离于湖北省不同地区的３０株ＨＶ的分型结果　为汉滩型２１株、汉城型９株,其中长江以南汉滩型１２株、汉城型２株;长江以北汉滩型９株、　汉城型７株。这表明建立的ＲＴ－ｈｅｍｉｎｅｓｔｅｄ　ＰＣＲ用于ＨＶ的检测特异性好;分析湖北省不同　地区分离的３０株ＨＶ,显示湖北省ＨＦＲＳ流行为混合疫区;且在湖北地区具有一定的地理聚集性。     

湖北省不同地区汉坦病毒M片段的分析研究

参考汉坦病毒(HV)的基因文库软件设计M片段G1区型特异性引物,以HV 76/118、H-114、A9及R22株RNA为阳性模板,建立HV的分型方法--逆转录一半巢式聚合酶链反应(RT-heminested PCR),对湖北省不同地区分离的30株HV进行分型.结果显示(1)建立的RT-heminested PCR分型方法对HV两型的代表株76/118(HTN)、A9(HTN)、H-114(HTN)及R22(SEO)RNA进行了特异性扩增,其大小与理论值一致;此法只能检测HVRNA,不能检测其它病毒RNA.(2)分离于湖北省不同地区的30株HV的分型结果为汉滩型21株、汉城型9株,其中长江以南汉滩型12株、汉城型2株;长江以北汉滩型9株、汉城型7株.这表明建立的RT-heminested PCR用于HV的检测特异性好;分析湖北省不同地区分离的30株HV,显示湖北省HFRS流行为混合疫区;且在湖北地区具有一定的地理聚集性.     

Comparative Genomic Analysis of Two Novel Sporadic Shiga Toxin-Producing Escherichia coli O104:H4 Strains Isolated 2011 in Germany

A large outbreak of gastrointestinal disease occurred in 2011 in Germany which resulted in almost 4000 patients with acute gastroenteritis or hemorrhagic colitis, 855 cases of a hemolytic uremic syndrome and 53 deaths. The pathogen was an uncommon, multiresistant Escherichia coli strain of serotype O104:H4 which expressed a Shiga toxin characteristic of enterohemorrhagic E. coli and in addition virulence factors common to enteroaggregative E. coli. During post-epidemic surveillance of Shiga toxin-producing E. coli (STEC) all but two of O104:H4 isolates were indistinguishable from the epidemic strain. Here we describe two novel STEC O104:H4 strains isolated in close spatiotemporal proximity to the outbreak which show a virulence gene panel, a Shiga toxin-mediated cytotoxicity towards Vero cells and aggregative adherence to Hep-2 cells comparable to the outbreak strain. They differ however both from the epidemic strain and from each other, by their antibiotic resistance phenotypes and some other features as determined by routine epidemiological subtyping methods. Whole genome sequencing of these two strains, of ten outbreak strain isolates originating from different time points of the outbreak and of one historical sporadic EHEC O104:H4 isolate was performed. Sequence analysis revealed a clear phylogenetic distance between the two variant strains and the outbreak strain finally identifying them as epidemiologically unrelated isolates from sporadic cases. These findings add to the knowledge about this emerging pathogen, illustrating a certain diversity within the bacterial core genome as well as loss and gain of accessory elements. Our results do also support the view that distinct new variants of STEC O104:H4 repeatedly might originate from yet unknown reservoirs, rather than that there would be a continuous diversification of a single epidemic strain established and circulating in Germany after the large outbreak in 2011.     

海洋赤潮生物与厦门海域几种细菌的生态关系研究

选择我国沿海易发有毒赤潮藻——塔马亚历山大藻 [Alexandrium tamarense (Lebour) Balech,1 985 ]和从厦门海域筛选的海洋细菌作为实验材料 ,研究在实验生态条件下 A.tamarense的生理生态特征 ,及其与 3株从厦门海域筛选的海洋细菌 S5,S7,S10 与 A.tamarense共同培养表现的生态关系的差异性。结果表明 :在实验室条件下 ,A.tamarense可以较好地生长并保持自然状态下的若干特性 ,其生长曲线与微型生物的生长曲线相似 ;分别在藻细胞生长的延滞期和指数期加入细菌过滤液 ,发现 3种海洋细菌的过滤液对 A.tamarense生长有不同的抑制作用效果。三者的抑藻能力大小依次为 S10 >S5>S7。本文对海洋细菌抑藻作用机理、赤潮的生物防治可能性进行了讨论。     

Genomic Characterization of Japanese Macaque Rhadinovirus,a Novel Herpesvirus Isolated from a Nonhuman Primate with a Spontaneous Inflammatory Demyelinating Disease

Japanese macaque rhadinovirus (JMRV) is a novel gamma-2 herpesvirus that was isolated from a Japanese macaque (JM) with an inflammatory demyelinating encephalomyelitis referred to as Japanese macaque encephalomyelitis, a disease that possesses clinical and histopathological features resembling multiple sclerosis in humans. Genomic DNA sequence analysis reveals that JMRV is a gammaherpesvirus closely related to rhesus macaque rhadinovirus (RRV) and human herpesvirus 8. We describe here the complete nucleotide sequence and structure of the JMRV genome, as well as the sequence of two plaque isolates of this virus. Analysis of the JMRV genome not only demonstrates that this virus shares a number of genes with RRV that may be involved in pathogenesis but also indicates the presence of unique JMRV genes that could potentially contribute to disease development. The knowledge of the genomic sequence of JMRV, and the ability to easily propagate the virus in vitro, make JMRV infection of JM an attractive model for examining the potential role of an infectious viral agent in the development of demyelinating encephalomyelitis disease in vivo.     

Physiological and Genomic Features of a Novel Sulfur-Oxidizing Gammaproteobacterium Belonging to a Previously Uncultivated Symbiotic Lineage Isolated from a Hydrothermal Vent

Strain Hiromi 1, a sulfur-oxidizing gammaproteobacterium was isolated from a hydrothermal vent chimney in the Okinawa Trough and represents a novel genus that may include a phylogenetic group found as endosymbionts of deep-sea gastropods. The SSU rRNA gene sequence similarity between strain Hiromi 1 and the gastropod endosymbionts was approximately 97%. The strain was shown to grow both chemolithoautotrophically and chemolithoheterotrophically with an energy metabolism of sulfur oxidation and O₂ or nitrate reduction. Under chemolithoheterotrophic growth conditions, the strain utilized organic acids and proteinaceous compounds as the carbon and/or nitrogen sources but not the energy source. Various sugars did not support growth as a sole carbon source. The observation of chemolithoheterotrophy in this strain is in line with metagenomic analyses of endosymbionts suggesting the occurrence of chemolithoheterotrophy in gammaproteobacterial symbionts. Chemolithoheterotrophy and the presence of homologous genes for virulence- and quorum sensing-related functions suggest that the sulfur-oxidizing chomolithotrophic microbes seek animal bodies and microbial biofilm formation to obtain supplemental organic carbons in hydrothermal ecosystems.     

Variations in Strains of Streptomyces griseus Isolated from a Degenerating Streptomycin-Producing Culture

Streptomycin-resistant strains were isolated from a degenerated streptomycin-producing culture of Streptomyces griseus. From 250 resistant strains, 3 low, 2 intermediate, and 2 high potency strains were selected; these were compared in their morphological, cultural, physiological, and streptomycin-producing properties. Though no definite correlation between streptomycin production and the other properties could be obtained, the following correlations were considered as distinct differences among the low, intermediate, and high potency strains. (i) When streptomycin-producing ability degenerates, more submerged spore formation or fragmentation of mycelium into shorter filaments appears to occur. (ii) On agar medium, low and intermediate potency strains often show finely wrinkled growth; high potency strains do not show such characteristics. (iii) High potency strains excrete a distinct yellow soluble pigment on synthetic agar medium and on glucose-yeast extract agar, but low and intermediate potency strains show little or no ability to form this soluble pigment. (iv) In low and intermediate potency strains, inositol and arginine did not stimulate streptomycin production as they did in high potency strains. Streptamine showed some stimulating effect in the high potency strains and, in contrast, a depressive effect in intermediate potency strains, though streptidine showed a distinctly stimulating effect in all groups of strains employed.