Orisin and future distribution of the new A （H 1N1 ） influenza virus emerging in North America in 2009

The origin of the new A （H1N1） influenza virus recently emerging in North America is a hot controversial topic of significance in disease control and risk assessment. Some experts claimed that it was an unusually mongrelized mix of human, avian and swine influenza viruses, while some others concluded that it was totally a simple re-assortment hybrid of two lineages of swine influenza viruses. Here the phylogenetic diversity of the viral PB1, PA and PB2 gene sequences using online web servers, and the results suggest that all the 8 genetic segments of the new virus were possibly from two lineages of swine influenza viruses, and one of the lineage was a mongrelized mix of human, avian and swine influenza viruses emerging in the world approximately 10 years ago. Considering the recent epidemiological trends of the new virus, we believe it will spread more widely in the world and persist long in human populations. It also could spread among swine populations. The future wide spreading of the new virus may coincide the disappearance of a subtype of previous human influenza A virus.     

Rapid genome evolution in Pms 1 region of rice revealed by comparative sequence analysis

Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted com-parative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11, for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra- and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.     

The mutation network for the hemagglutinin gene from the novel influenza A （H1N1 ） virus

A mutation network for the hemagglutinin gene （HA） of the novel type A （H1N1） influenza virus was constructed. Sequence homology analysis indicated that one HA sequence type from the viruses mainly isolated from Mexico was likely the original type in this epidemic. Based on the 658A and 1408T mutations in HA, the viruses evolving into this epidemic were divided into three categories, the Mexico, the transitional and the New York type. The three groups of viruses presented distinctive clustering features in their geographic distributions.     

Urban structure and the risk of influenza A （H1N1） outbreaks in municipal districts

Changsha was one of the most affected areas during the 2009 A （H 1N 1） influenza pandemic in China. Here, we analyze the spatial-temporal dynamics of the 2009 pan- demic across Changsha municipal districts, evaluate the relationship between case incidence and the local urban spatial structure and predict high-risk areas of influenza A （H1NI）. We obtained epidemiological data on all cases of influenza A （H1NI） reported across municipal districts in Changsha dur- ing period May 2009-December 2010 and data on population density and basic geographic characteristics for 239 primary schools, 97 middle schools, 347 universities, 96 mails and markets, 674 business districts and 121 hospitals. Spatial- temporal K functions, proximity models and logistic regres- sion were used to analyze the spatial distribution pattern of influenza A （H1N1） incidence and the association between influenza A （HINI） cases and spatial risk factors and predict the infection risks. We found that the 2009 influenza A （H 1N 1 ） was driven by a transmission wave from the center of the study area to surrounding areas and reported cases increased significantly after September 2009. We also found that the distribution of influenza A （H 1N1） cases was associ- ated with population density and the presence of nearest public places, especially universities （OR = 10.166）. The final pre- dictive risk map based on the multivariate logistic analysis showed high-risk areas concentrated in the center areas of the study area associated with high population density. Our find- ings support the identification of spatial risk factors and high- risk areas to guide the prioritization of preventive and miti- gation efforts against future influenza pandemics.     

Molecular evolution of connective tissue growth factor in Cyprinidae （Teleostei： Cypriniformes）

Connective tissue growth factor （CTGF） plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining （NJ）, maximum parsimony （MP）, maximum likelihood （ML） and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution （dN/dS） for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 bp indel （insertion/deletion） was found at the 5＇ end of CTGF gene of Cyprinidae, and this 6 bp deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity.     

流感（H1N1）大流行，人、猪与禽，谁是根源？

2009年初，当人们还在谈论人感染禽流感的病例频发与人流感病毒大流行之间的关系时，4月初突然传出“猪流感”在墨西哥暴发的消息，一时间人们的注意力又转向了猪。虽然此次流感其时尚未传播开，但人们已对猪有了防范之心。尽管世界卫生组织（WHO）强调食用健康猪的肉不会感染“猪流感”，但是该消息仍然对猪肉的消费产生了很大影响，埃及甚至为防范“猪流感”的传播，扑杀了25万头生猪。     

H5N1亚型禽流感毒株A/Duck/HuBei/3/2005的分子特征及致病性研究

采用分子生物学方法,对1株2005年从湖北省某县分离获得的禽流感病毒株(A/Duck/HuBei/3/2005)进行全基因组序列测定.序列分析显示,该分离株为H5N1亚型.HA蛋白在HA1和HA2连接处,含有连续多碱性氨基酸模体(-RRKKR-).根据进化分析结果,分离株A/Duck/HuBei/3/2005的7个基因来源于2004～2005年湖南地区流行株(CK/HN/999/05,DK/HN303/04),但是PA基因片段发生了重排,来源于野禽.动物实验显示DK/HB/3/05对鸡和鸭均具有高致病性;对小鼠有较低致病性.     

A theoretical study of the proton transfer process in the spin-forbidden reaction ^1HNO（^1A＇） ＋ OH^-→^ 3NO^-（^3∑^-） ＋ H2O

The spin-forbidden reaction 1HNO（^1A＋OH^-→3NO^-（^3∑^-）＋H2O has been extensively explored using vari- ous CASSCF active spaces with MP2 corrections in several basis sets. Natural bond orbital （NBO） analysis, together with the NBO energetic （deletion） analysis, indicates that the two isomers have nearly equal total energy and could compete with each other in the title reaction. More significantly, the singlet/triplet surface crossing regions have been examined and the spin-orbit coupling （SOC） and energetics have been computed. The computational results indicate that the SOC is very large at the crossing point T1/S0 trans （ca. 40.9 cm^-1）. Moreover, the T1/S0 trans has a low energy of 10.67 kcal/mol relative to that of trans-So. Therefore, the surface crossing to the triplet state seems much more efficient at the T1/S0 trans region along the minimum energy path （MEP）, However, The values of single （P1^ISC） and double （P2^ISC） passes estimated at T1/S0 trans show that the ISC occurs with a little probability.     

Molecular characterization of H1N1 influenza A viruses from human cases in North America

Subtypes of H1N1 influenza virus can be found in humans in North America, while they are also associated with the infection of swine. Characterization of the genotypes of viral strains in human populations is important to understand the source and distribution of viral strains. Genomic and protein sequences of 10 isolates of the 2009 outbreak of influenza A （H1N1） virus in North America were obtained from GenBank database. To characterize the genotypes of these viruses, phylogenetic trees of genes PB2, PB1, PA, HA, NP, NA, NS and M were constructed by Phylip3.67 program and N-Linked glycosylation sites of HA, NA, PB2, NS1 and M2 proteins were analyzed online by NetNGlyc1.0 program. Phylogenetic analysis indicated that these isolates are virtually identical but may be recombinant viruses because their genomic fragments come from different viruses. The isolates also contain a characteristic lowly pathogenic amino acid motif at their HA cleavage sites （IPSIQSR↓GL）, and an E residue at position 627 of the PB2 protein which shows its high affinity to humans. The homologous model of M proteins showed that the viruses had obtained the ability of anti-amantadine due to the mutation at the drug-sensitive site, while sequence analysis of NA proteins indicated that the viruses are still susceptible to the neuraminidase inhibitor drug （i.e. oseltamivir and zanamivir） because no mutations have been observed. Our results strongly suggested that the viruses responsible for the 2009 outbreaks of influenza A （H1N1） virus have the ability to cross species barriers to infect human and mammalian animals based on molecular analysis. These findings may further facilitate the therapy and prevention of possible transmission from North America to other countries.     

Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus

In recent months, a novel influenza virus H1N1 broke out around the world. With bioinformatics technology, the 3D structure of HA protein was obtained, and the epitope residues were predicted with the method developed in our group for this novel flu virus. 58 amino acids were identified as potential epitope residues, the majority of which clustered at the surface of the globular head of HA protein. Although it is located at the similar position, the epitope of HA protein for the novel H1N1 flu virus has obvious differences in the electrostatic potential compared to that of HA proteins from previous flu viruses.     

Molecular patterns of avian influenza A viruses

Avian influenza A viruses could get across the species barrier and be fatal to humans. Highly pathogenic avian influenza H5N1 virus was an example. The mechanism of interspecies transmission is not clear as yet. In this research, the protein sequences of 237 influenza A viruses with different subtypes were transformed into pseudo-signals. The energy features were extracted by the method of wavelet packet decomposition and used for virus classification by the method of hierarchical clustering. The clustering results showed that five patterns existed in avian influenza A viruses, which associated with the phenotype of interspecies transmission, and that avian viruses with patterns C and E could across species barrier and those with patterns A, B and D might not have the abilities. The results could be used to construct an early warning system to predict the transmissibility of avian influenza A viruses to humans.     

无血清微载体培养MDCK细胞和甲型流感病毒H1N1的条件优化

 血清微载体培养MDCK细胞,并接种流感病毒H1N1,优化培养条件,为细胞流感疫苗的工艺研发奠定基础.采用不同的细胞接种量在50mL无血清微载体搅拌瓶中培养MDCK细胞,并接种甲型流感病毒H1N1,检测不同pH值和TPCK-胰酶含量的病毒培养液,不同病毒接种量,补加TPCK-胰酶,以及不同收毒时间对血凝效价的影响.以1.0×10⁵mL^-1的MDCK细胞数量接种到无血清微载体上,病毒培养液pH值为7.2~7.4范围内,TPCK-胰酶质量浓度为1.0μg/mL,接种后不补加胰酶,病毒接种量MOI=1.0,并在72h收获,最高血凝效价达到512.由此获得了在无血清为载体上培养MDCK细胞和甲型流感病毒H1N1的适宜条件.     

H5N1亚型禽流感病毒血凝素基因的克隆与表达

 根据已知H5N1亚型禽流感病毒血凝素(HA)基因序列设计、合成克隆引物.自灭活的云南地方H5N1亚型病毒阳性临床组织样品中提取总RNA,反转录后采用高可信度DNA聚合酶(Pyobest^TMDNA Polymerase)扩增HA基因,采用Invitrogen定向表达系统(Champion^TMpET directional TOPO expression system)进行克隆表达,纯化获得N末端携带多聚组氨酸标签的重组HA,分子质量约78ku.采用阳性血清经免疫印迹及ELISA分析重组HA的免疫反应性,结果表明重组HA能与H5N1亚型病毒抗血清发生特异性结合,具有良好的免疫反应性.     

甲型H1N1流感超敏感诊断方法的建立及优化

利用几种助沉剂和核酸纯化方法富集病毒RNA,建立甲型H1N1流感超敏感诊断方法。收集31份甲型H1N1流感确诊病人提取的病毒RNA,稀释至1000分之一倍后分别应用酵母tRNA、糖原、AcrylCarrier助沉剂和磁珠、硅胶颗粒和离心柱的9种组合进行病毒RNA的富集,富集后分别进行RealtimePCR检测。并对检测结果进行统计学分析。利用几种助沉剂和核酸纯化方法的组合时,发现磁珠+AcrylCarrier助沉剂方法是最佳的核酸富集方法,能够大大提高病毒核酸的检出效率。建立了甲型H1N1流感超敏感诊断方法,该方法能够大大提高甲型H1N1流感的检出率。     

Molecular characterization of avian influenza virus (H7N8) isolated from poultry in Central China in the mid-1980s

The molecular and pathogenic properties of avian influenza virus (A/duck/Hubei/216/1985/H7N8) isolated from Hubei Province of China in 1985 were characterized.The hemagglutinin gene (HA) of Dk/Hb/216/85/H7N8 had the multiple amino acid se-quences (-PEIPKGRG-) at the connecting peptide between HA1 and HA2, which is considered to be a distinguishing molecular characteristic of low pathogenicity.The key sites of host markers among the genes (M, NP, NS, PA and PB2) of Dk/Hb/ 216/85/H7N8 were similar to those of...