Molecular characterization of avian reovirus causing tenosynovitis outbreaks in broiler flocks,Iran

ABSTRACT

Avian reoviruses (ARVs) cause arthritis, tenosynovitis, retarded growth, and malabsorption syndrome. After a long time of effective prevention and low rates of viral arthritis/ tenosynovitis in Iran, outbreaks of tenosynovitis in broiler flocks have increased in recent years. Lameness, splay legs, high rate of cull birds, poor performance, uneven birds at harvest, and condemnation at processing cause huge economic losses. In this study, ARVs from the tendons of birds from 23 broiler flocks with marked tenosynovitis were characterized, and their genetic relationship was examined. Analysis of the amino acid sequence of Sigma C protein revealed that all ARVs detected in affected broiler flocks shared genetic homogeneity and this suggests that a single genotype is involved in recent outbreaks. This genotype, so-called “Ardehal strain”, is grouped in cluster I with vaccine strains. The amino acid sequence similarity between Ardehal and vaccine strains, including S1133, 1733, and 2408 was less than 80%. As the outbreaks have occurred in progenies of vaccinated flocks, it is proposed here that the difference between vaccine and field strains might contribute to the failure of currently available vaccines to induce protective immunity against Ardehal strain and this led to widespread viral tenosynovitis in Iran.     

Genetic characterization of an H5N1 avian influenza virus from a vaccinated duck flock in Vietnam

This study reports the genetic characterization of a highly pathogenic avian influenza virus subtype H5N1 isolated from a moribund domestic duck in central Vietnam during 2012. In the moribund duck’s flock, within 6 days after vaccination with a commercial H5N1 vaccine (Re-5) to 59-day-old birds, 120 out of 2,000 ducks died. Genetic analysis revealed a substantial number of mutations in the HA gene of the isolate in comparison with the vaccine strains, Re-1 and Re-5. Similar mutations were also found in selected Vietnamese H5N1 strains isolated since 2009. Mutations in the HA gene involved positions at antigenic sites associated with antibody binding and also neutralizing epitopes, with some of the mutations resulting in the modification of N-linked glycosylation of the HA. Those mutations may be related to the escape of virus from antibody binding and the infection of poultry, interpretations which may be confirmed through a reverse genetics approach. The virus also carried an amino acid substitution in the M2, which conferred a reduced susceptibility to amantadine, but no neuraminidase inhibitor resistance markers were found in the viral NA gene. Additional information including vaccination history in the farm and the surrounding area is needed to fully understand the background of this outbreak. Such understanding and expanded monitoring of the H5N1 influenza viruses circulating in Vietnam is an urgent need to provide updated information to improve effective vaccine strain selection and vaccination protocols, aiding disease control, and biosecurity to prevent H5N1 infection in both poultry and humans.     

Pathogenicity of a variant goose parvovirus,from short beak and dwarfism syndrome of Pekin ducks,in goose embryos and goslings

The pathogenicity of a variant goose parvovirus (GPV), isolated from short beak and dwarfism syndrome of Pekin ducks (strain Cherry Valley), was investigated in embryonating goose eggs and goslings. The virus was easily grown in GPV antibody-free goose embryos and caused high mortality and severe lesions of goose embryos, indicating that the variant GPV has good adaptation and high pathogenicity to embryonated goose eggs similar to the classical GPV. Like the third egg-passage virus (strain H) of a classical GPV, the third egg-passage virus (strain JS1) of the variant GPV caused Derzsy’s disease in 2-day-old goslings with high mortality. The findings suggest that the variant GPV strain, which had specifically adapted to Pekin ducks, still retained high pathogenicity for its original host. The mortality (73.3–80%) caused by the first and third egg-passages of the variant GPV was somewhat lower than that (93.3%) caused by the third passage virus of the classical GPV, reflecting the higher pathogenicity of the classical GPV for its original host. These findings are likely to reinforce the importance of surveillance for parvoviruses in different waterfowl species and stimulate further study to elucidate the impact of mutations in the GPV genome on its pathogenicity to goslings and ducks.     

Identification and characterization of a novel natural recombinant avian leucosis virus from Chinese indigenous chicken flock

Virus Genes - Avian leukosis virus (ALV) caused tremendous economic losses to poultry industry all over the world, especially in China. One natural recombinant ALV strain, designated as HB2015032,...     

Genetic characterization of avian influenza viruses isolated from waterfowl in southern part of South Korea in 2006

Aquatic birds are a reservoir of all known influenza A viruses. Avian influenza viruses have played a major role in the creation of pandemic influenza viruses in humans. In this study, we genetically characterized genes of nine isolates from waterfowl in Eulsukdo, a congregating place for migratory birds on the flyway of migration from Siberia, which is located in the southern part of South Korea. Phylogenic analysis showed that HA and NA genes of isolates belonged to Eurasian lineage, and lineage analysis showed that NS, PB1, PA, NP, and M genes of isolates clustered with Eurasian lineage, and PB2 genes of isolates belonged to North American or Eurasian lineage. Results suggest that the interregional transmission of genes of avian influenza viruses may occur in the migratory birds.     

一种新的FR4剪切变异体的确认和鉴定

目的 确认并鉴定一个新发现的小鼠FR4剪切变异体,并在mRNA水平检测其在小鼠脾淋巴细胞亚群中的表达.方法 PCR克隆FR4 CDS区时发现存在一个新的剪切变异体,酶切和测序予以鉴定,Western blot检测脾细胞中变异体的表达,流式分选脾细胞中CD8+、CD4+CD25-、CD4+CD25+T淋巴细胞,RT-PCR检测新的变异体在各细胞亚群中的表达.结果 凝胶电泳显示存在一个CDS区碱基数大于野生型FR4的条带,测序表明此条带在野生型外显子基础上包含一个内含子成分,Westernblotting证实新发现的剪切体在蛋白水平也存在,脾细胞中不同T细胞亚群均表达此新型变异体.结论 mRNA和蛋白水平均证实存在一种新型FR4剪切变异体,不同T细胞亚群均表达此变异体暗示其在淋巴细胞摄取叶酸功能上不可或缺.     

一例重型Cornelia de Lange综合征患者的NIPBL基因变异分析

目的分析1例重型Cornelia de Lange综合征(Cornelia de Lange syndrome,CdLS)患儿的NIPBL基因变异,明确其遗传学病因。方法提取患儿及其父母外周血中DNA物质,应用全外显子基因组测序法检测相关基因变异,应用Sanger测序法验证变异。对可疑变异进行生物信息学预测。结果经全外显子基因组测序分析并经Sanger测序验证,发现患儿NIPBL基因第9外显子存在c.1507A>G(p.Lys503Glu)杂合错义变异,该变异为新发变异,且为未报道过的新变异。经PolyPhen-2、Mutation Taster、SIFT预测软件预测c.1507A>G(p.Lys503Glu)变异为可能有害变异,并经HomoloGene系统分析NIPBL蛋白第503位Lys在各种属间均高度保守,该位点氨基酸改变可导致编码的NIPBL原有蛋白功能发生障碍。而经过PubMed BLAST系统进一步分析发现该位点氨基酸的改变可通过影响Neuromodulin_N superfamily结构域的形成来导致NIPBL蛋白功能发生障碍的。结论NIPBL基因c.1507A>G(p.Lys503Glu)错义变异可能为该患儿罹患重型CdLS的致病原因,基因变异检测结果可以为家系的遗传咨询和产前诊断提供依据。     

Serological and genomic characterization of human rotaviruses detected in China

A total of 1,385 stool specimens were collected from children with diarrhea at two hospitals in Wuhan, Hubei Province, China, in 1994 and 1995, and screened for rotavirus by polyacrylamide gel electrophoresis of viral RNA. Group A rotavirus was detected with high frequency; 56.5% (87/154) and 40.8% (502/1,231) of the specimens collected in 1994 and 1995, respectively, were positive for rotavirus. Assignment of G serotype and P type (VP4 genotype) of group A rotavirus by ELISA with monoclonal antibodies and/or PCR, respectively, showed that strains of G2-P[4] and G1-P[8] specificity were predominant in 1994 and in 1995, respectively. In contrast, a single strain was found to have a P[9] type specificity, and no G4 strain was detected. Unusual combinations of RNA pattern-subgroup-G serotype-P type, such as long pattern-subgroup I-G1-P[8], short pattern-subgroup II-G3-P[4] and short pattern-subgroup I-G1-P[4], were detected in four specimens. Nucleotide sequences of the VP8* and/or NSP5 genes from two Chinese P[8] strains 470 and 582 and one Chinese P[9] strain 512 as well as five Japanese P[9] strains (K8, AU1, M318, O264, and O265) were determined and compared with the published sequences of the corresponding gene. In the phylogenetic tree of VP8* sequences of P[9] strains, which formed two clusters each having strain K8 or AU-1 as the representative strain, the Chinese P[9] strain was found in the cluster represented by AU-1, although it was most distantly related to other strains. While NSP5 sequences of human strains with P[9] specificity were related to simian and bovine strains, that of Chinese P[8] strains was most closely related to those of porcine strains. A single group C rotavirus (No. 208) was detected. Nucleotide sequences of its VP4, VP6, VP7, and NSP4 genes were very similar to those of group C human rotaviruses detected worldwide. J. Med. Virol. 55:168–176, 1998. © 1998 Wiley-Liss, Inc.     

Identification and sequence characterization of a novel HLA-A11 serological variant (HLA-A*1108)

In this report we describe the identification of a novel HLA-A*11 allele, HLA-A*1108, found in two individuals of a Spanish family. This new allele was detected during routine HLA typing by an atypical serological reactivity pattern and by inconclusive patterns obtained in DNA-based typing methods. The nucleotide sequence of exons 2 and 3 of HLA-A*1108 was identical to HLA-A*11011 except for two nucleotide substitutions at codons 152 (GCG-->GAG) and 156 (CAG-->CGG). These mutations change the non-charged amino acid alanine, at codon 152, to negative glutamic acid, and also non-charged glutamine, at codon 156, to positive arginine, which may explain its anomalous serological reactivity.     

一个Chediak-Higashi综合征家系CHS1/LYST基因新变异

目的对1个旁系血亲婚配的Chediak-Higashi综合征家系的CHS1/LYST基因进行变异检测,探讨LYST基因变异与临床表型的关系。方法收集临床资料及家系调查,分析2例患者的临床资料和实验室检查结果。提取患者外周血DNA及父母等16名亲属指甲的DNA,采用外显子组测序分析患者的致病基因,根据基因变异点对亲属相应位点做Sanger测序,确认携带者。结果该家系中2例患者临床均有皮肤部分白化及免疫缺陷,表现为反复严重感染、出血倾向且发生嗜血现象,骨髓细胞及血涂片检查均出现粗大的嗜酸性包涵体颗粒。LYST基因第34外显子存在c.8782C>T(p.Gln2928*)纯合无义变异,与其表型相关,且该变异为新变异点。确认6名表型正常的家系成员的LYST基因存在与先证者相同的杂合变异,另10名表型正常的家系成员则均未检测到该变异。结论基因变异分析结果丰富了Chediak-Higashi综合征致病基因的变异谱,为临床明确病因提供了重要依据,并为家系遗传咨询和产前诊断提供了参考依据。     

一个线粒体DNA耗竭综合征家系临床及DGUOK基因分析

目的对一个线粒体DNA耗竭综合征家系进行遗传基因变异分析,探讨其分子发病机制。方法提取家系中患者及其父母外周血基因组DNA,采用高通量测序技术检测致病基因变异,并对变异进行Sanger测序验证。结果发现患者DGUOK基因存在c.505_508delTATC的纯合变异,父母都是该位点的杂合变异携带者。c.505_508delTATC为未见报道的新变异位点,造成169位氨基酸由酪氨酸(Y)变异为精氨酸(R),随后编码框改变,在199位翻译提前终止,理论上产生截短蛋白p.Y169Rfs31X。结论c.505_508delTATC为DGUOK基因致病性变异,扩展了DGUOK基因变异谱。     

Functional characterization of a novel PRRT2 variant found in a Portuguese patient with hemiplegic migraine

Familial hemiplegic migraine (FHM) is a rare autosomal-dominant form of migraine with aura. Three disease-causing genes have been identified for FHM: CACNA1A, ATP1A2 and SCN1A. However, not all families are linked to one of these three genes.PRRT2 variants were also commonly associated with HM symptoms; therefore, PRRT2 is hypothesized as the fourth gene causing FHM. PRRT2 plays an important role in neuronal migration, spinogenesis, and synapse mechanisms during development and calcium-dependent neurotransmitter release. We performed exome sequencing to unravel the genetic cause of migraine in one family, and a novel PRRT2 variant (c.938C > T;p.Ala313Val) was identified with further functional studies to confirm its pathogenicity. PRRT2-A313V reduced protein stability, led to protein premature degradation by the proteasome and altered the subcellular localization of PRRT2 from the plasma membrane (PM) to the cytoplasm. We identified and characterized for the first time in a Portuguese patient, a novel heterozygous missense variant in PRRT2 associated with HM symptoms. We suggest that PRRT2 should be included in the diagnosis of HM.     

Phylogenetic analysis of clinical mumps virus isolates from vaccinated and non-vaccinated patients with mumps during an outbreak, Switzerland 1998-2000

During the past decade mumps outbreaks have occurred in several European countries with universal vaccination programs probably due to poor efficacy of the Rubini vaccine strain. However, the evolution of vaccine escape mutants has also been considered. A phylogenetic analysis was undertaken on 69 clinical mumps isolates obtained from 39 vaccinated and 22 non-vaccinated mumps cases (and six cases with unknown vaccination status) during an outbreak in 1998-2000. Two major strain clusters (SWI-H, SWI-C) with two subgroups each (SWI-H1/2, SWI-C1/2) were identified, which belonged to genotypes C and H. No association between viral clusters and vaccination status or a specific vaccine strain (Jeryl-Lynn or Rubini) was found. Cluster SWI-C1 occurred more frequently in the Western part of Switzerland (P < 0.001). Isolates causing complicated disease tended to cluster more frequently with SWI-H1 (P = 0.11). Wild-type strains homologous or similar to the Rubini vaccine strain (isolated in Switzerland in 1974) were no longer circulating. Therefore, there was no evidence for vaccine escape mutants. Strain redistribution may have occurred during the past decades. Continuous monitoring of circulating mumps virus populations is needed.     

Molecular characterization of a novel monopartite begomovirus isolated from Pouzolzia zeylanica in China

The complete genome sequence of a monopartite begomovirus isolate TY01 was obtained from diseased Pouzolzia zeylanica plants exhibiting golden mosaic symptoms in Baise, Guangxi Province, China. It consisted of 2723 nucleotides (nt) and encoded two ORFs (CP and AV2) in the virion-sense DNA and five ORFs (AC1-AC5) in the complementary-sense DNA. Compared with the DNA-A sequences of other begomoviruses, it has the highest (78.5 %) nucleotide sequence identity with ageratum yellow vein virus (AYVV) isolate AFSP6D from Thailand, which is less than the 89 % identity in the complete genome that has been defined as the threshold value for demarcation of species in the genus Begomovirus, family Geminiviridae. Phylogenetic analysis showed that TY01 was grouped in a separate clade from the other 28 begomovirus isolates. These results indicate that isolate TY01 is a member of a novel Begomovirus species, for which the name “Pouzolzia golden mosaic virus” (PGMV) is proposed.     

一例视网膜色素变性患者 C2ORF71基因的变异分析

目的:分析1例视网膜色素变性(retinitis pigmentosa, RP)患者的基因变异,明确其可能的遗传学病因。方法:应用全外显子测序技术对先证者进行致病基因筛查,结合临床表型确定可疑变异,应用Sanger测序法验证检出的变异,分析双亲携带变异位点的情况。采用多种软件对所检出的变异进行致病性分析。结果:全外显子...