A compact microarray for subtyping of influenza a virus

A version of the universal oligonucleotide hybridization microchip with the size of 6 × 5 spots (4 × 4 mm) has been proposed, which operates on the principle of “one spot-one subtype.” This microchip may be the prototype of a biosensor for fixation of influenza A virus and typing of 15 subtypes of hemagglutinin and 9 subtypes of neuraminidase.     

Microarray for diagnostics of human pathogenic influenza A viruses subtypes

An oligonucleotide microchip was developed for diagnostics of human pathogenic Influenza A viruses subtypes. It contains discriminating probes for H1-, H2-, H3-, H5-, H7- and H9-subtypes of hemagglutinin and for N1-, N2-, and N7-subtypes of neuraminidase. The additional set of probes was used for M-gene of Influenza A viruses definition. Microchip was tested on samples pathogenic H5N1 avian influenza viruses, pandemic H1N1 swine influenza viruses and seasonal H1N1 and H3N2 influenza viruses. The microchip can be used for the analysis of both cultured strains and clinical specimens.     

Universal oligonucleotide microarray for sub-typing of Influenza A virus

A universal microchip was developed for genotyping Influenza A viruses. It contains two sets of oligonucleotide probes allowing viruses to be classified by the subtypes of hemagglutinin (H1-H13, H15, H16) and neuraminidase (N1-N9). Additional sets of probes are used to detect H1N1 swine influenza viruses. Selection of probes was done in two steps. Initially, amino acid sequences specific to each subtype were identified, and then the most specific and representative oligonucleotide probes were selected. Overall, between 19 and 24 probes were used to identify each subtype of hemagglutinin (HA) and neuraminidase (NA). Genotyping included preparation of fluorescently labeled PCR amplicons of influenza virus cDNA and their hybridization to microarrays of specific oligonucleotide probes. Out of 40 samples tested, 36 unambiguously identified HA and NA subtypes of Influenza A virus.     

Development of multiplex rt-PCR assays for rapid detection and subtyping of influenza type A viruses from clinical specimens

We developed multiplex RT-PCR assays that can detect and identify 12 hemagglutinin (H1-H12) and 9 neuraminidase (N1-N9) subtypes that are commonly isolated from avian, swine, and human influenza A viruses. RT-PCR products with unique sizes characteristic of each subtype were amplified by multiplex RT-PCRs, and sequence analysis of each amplicon was demonstrated to be specific for each subtype with 24 reference viruses. The specificity was demonstrated further with DNA or cDNA templates from 7 viruses, 5 bacteria, and 50 influenza A virus negative specimens. Furthermore, the assays could detect and subtype up to 105 dilution of each of the reference viruses that had an original infectivity titer of 106 EID50/ml. Of 188 virus isolates, the multiplex RT-PCR results agreed completely with individual RT-PCR subtyping results and with results obtained from virus isolations. Furthermore, the multiplex RT-PCR methods efficiently detected mixed infections with at least two different subtypes of influenza viruses in one host. Therefore, these methods could facilitate rapid and accurate subtyping of influenza A viruses directly from field specimens.     

Reassortment and Insertion-Deletion Are Strategies for the Evolution of Influenza B Viruses in Nature

The evolution of influenza B viruses is poorly understood. Reassortment of influenza B viruses in nature as a means of genetic variation has not been considered to be a major contributor to their evolution. However, the current practice of assigning evolutionary relationships by antigenic analysis of the hemagglutinin of influenza B viruses would fail to detect reassortants. In this study, influenza B viruses isolated within the past 10 years from sites in the United States and China were studied by nucleotide sequencing of the hemagglutinin and neuraminidase genes and construction of phylogenetic trees to assess evolutionary relationships. A group of viruses represented by B/Houston/1/92 possess a hemagglutinin derived from a B/Yamagata/16/88-like strain and a neuraminidase derived from a B/Victoria/2/87-like strain. A second reassortment event between the hemagglutinin of a B/Yamagata/16/88-like virus closely related to the B/Beijing/184/93 strain and the neuraminidase of a B/Victoria/2/87-like strain is represented by a single virus, B/Memphis/3/93. The neuraminidase of the reassortant viruses is most closely related to that of B/Victoria/2/87-like viruses currently circulating in Nanchang, China. A pattern of insertions and deletions in the hemagglutinin and the neuraminidase of different strains of influenza B viruses is observed. Reassortment plays a role in the evolution of influenza B viruses and may necessitate a change in the methods used to assess and identify new influenza viruses.     

Subtyping of influenza virus A hemagglutinin with a hybridization microarray

An oligonucleotide microarray for influenza A hemagglutinin subtyping was presented. The number of probes for the determination of each subtype of hemagglutinin (H1-H13, H15, H16, pandemic flu H1N1) varied from 13 to 28. When testing the microarray using 40 type-A influenza virus isolates, the hemagglutinin subtypes were unambiguously determined for 36 specimens.     

Binding affinity of GM3 lactone for influenza virus

We investigated the interaction of GM3 lactone with influenza virus. The specific bindings of influenza virus and its hemagglutinin to GM3 lactone-containing mixed monolayers were studied by using a quartz-crystal microbalance. It has been known that gangliosides as receptors for influenza virus are also substrates for virus neuraminidase. GM3 lactone, however, was found to bind to influenza virus hemagglutinin, but not to be substrate for virus neuraminidase.     

Antiviral Activity of Antiserum Specific for an Influenza Virus Neuraminidase

Antiserum specific for influenza A(2) neuraminidase was produced by immunization of rabbits with the purified enzyme which had been isolated by electrophoresis from the proteins of a detergent-disrupted A(0)A(2) influenza virus recombinant [X-7 (F1)]. This recombinant contained hemagglutinin of the A(0) subtype and A(2) neuraminidase. Antiserum to the isolated A(2) neuraminidase did not react in any of four serological tests with A(0) or A(2) subtype viruses that lacked the A(2) enzyme. In contrast, the antiserum inhibited the neuraminidase activity only of wild-type and recombinant viruses containing the A(2) enzyme, regardless of the nature of their hemagglutinin proteins. The antiserum caused hemagglutination-inhibition of some, but not all, viruses bearing the A(2) enzyme, and it reduced the plaque size or plaque number of all viruses tested that contained A(2) neuraminidase. In the chick embryo and in cell culture, low dilutions of antiserum reduced the yield of virus. True neutralization of virus in the chick embryo did not occur. We conclude that an antiserum specific for A(2) neuraminidase influenced the yield and release of virus from influenza virus-infected cells.     

Genetic variability of isolates of pandemic influenza A virus H1N1 isolated in Russia in 2009

Complete nucleotide sequence of the genome segments encoding the surface glycoproteins, hemagglutinin, and neuraminidase of influenza A virus H1N1 derived from the patients with influenza in the context of pandemic (H1N1) 2009 was determined out of 14 isolates of pandemic influenza. The philogenetic analysis of these sequences demonstrated their genetic similarity to the corresponding genes of the pandemic influenza virus A (H1N1) 2009 isolates obtained in other countries; each gene homology was greater than 99%. Neuraminidase mutations causing virus resistance to oseltamivir and other neuraminidase inhibitors, known from the literature, were not detected. The hemagglutinin gene mutation D222G was found in 4 isolates from autopsy material. In the hemagglutinin of pandemic A/Salekhard/01/2009(H1N1) isolate a mutation G155E leading to the increase in viral replication in developing chick embryos was detected. The nature and frequency of nucleotides substitutions within HA and NA genes were determined in the current research.     

MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences

Background

High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and subtype of a given strain. This analysis has, to date, required the manual inspection of mass spectra of whole virus and antigen digests.

Results

A computer algorithm, FluTyper, has been designed and implemented to achieve the automated analysis of MALDI mass spectra recorded for proteolytic digests of the whole influenza virus and antigens. FluTyper incorporates the use of established signature peptides and newly developed naïve Bayes classifiers for four common influenza antigens, hemagglutinin, neuraminidase, nucleoprotein, and matrix protein 1, to type and subtype the influenza virus based on their detection within proteolytic peptide mass maps. Theoretical and experimental testing of the classifiers demonstrates their applicability at protein coverage rates normally achievable in mass mapping experiments. The application of FluTyper to whole virus and antigen digests of a range of different strains of the influenza virus is demonstrated.

Conclusions

FluTyper algorithm facilitates the rapid and automated typing and subtyping of the influenza virus from mass spectral data. The newly developed naïve Bayes classifiers increase the confidence of influenza virus subtyping, especially where signature peptides are not detected. FluTyper is expected to popularize the use of mass spectrometry to characterize influenza viruses.     

Virulence factors of influenza A viruses: WSN virus neuraminidase required for plaque production in MDBK cells.

The genetic basis for the distinctive capacity of influenza A/WSN/33 (H0N1) virus (WSN virus) to produce plaques on bovine kidney (MDBK) cells was found to be related to virus neuraminidase. Recombinant viruses that derived only the neuraminidase of WSN virus were capable of producing plaques, whereas recombinant viruses identical to WSN except for neuraminidase did not produce plaques. With viruses that do not contain WSN neuraminidase, infectivity of virus yields from MDBK cells was increased approximately 1,000-fold after in vitro treatment with trypsin. In contrast, no significant increase in infectivity was observed after trypsin treatment of viruses containing WSN neuraminidase. In addition, polyacrylamide gel analysis of proteins of WSN virus obtained after infection of MDBK cells demonstrated that hemagglutinin was present in the cleaved form (HA1 + HA2), whereas only uncleaved hemagglutinin was obtained with a recombinant virus that derived all of its genes from WSN virus except its neuraminidase. These data are in accord with the hypothesis that neuraminidase may facilitate production of infectious particles by removing sialic acid residues and exposing appropriate cleavage sites on hemagglutinin.     

Subtyping of influenza virus A hemagglutinine with hybridization microarray

An oligonucleotide microarray for influenza A hemagglutinine subtyping was presented. The number of probes for determination of each subtype hemagglutinine (H1-H13, H15, H16, pandemic flu H1N1)varied from 13 to 28. When testing of the microarray using 40 type A influenza virus isolates the hemagglutinin subtypes were unambiguously determined for 36 specimens.     

甲型流感病毒流行毒株检测和分型基因芯片的研制

【目的】研制一种可同时对甲型流感病毒H1N1、H1N2、H3N2、H5N1和H9N2等5种流行亚型进行检测和分型的基因芯片。【方法】根据National Center for Biotechnology Information中Influenza Virus Resource数据库,针对H1N1、H1N2、H3N2、H5N1和H9N2等5种亚型甲型流感病毒的HA和NA基因设计46条特异性寡核苷酸探针和1条质控探针,点制成基因芯片。利用通用引物扩增流感病毒HA和NA基因,使用Klenow酶对扩增产物进行荧光标记和片段化,将标记后产物和芯片杂交,清洗、扫描后根据荧光信号判定检测结果。用18株不同种属来源的甲型流感病毒分离毒株和186份咽拭子对芯片特异性、敏感性和临床应用进行初步评价。【结果】所有18株分离毒株均能被芯片准确检测并分型,芯片检测灵敏度能达约1×104个病毒基因拷贝。同时8份咽拭子检测结果为H1N1阳性,4份咽拭子为H3N2阳性。【结论】研究表明该芯片具有较高的特异性和灵敏度,可为甲型流感病毒的监测提供一种有效的方法。     

Fine specificity analysis of human influenza-specific cloned cell lines

Influenza-specific human-T-cell clones, proliferating in the presence of virus-infected cells with restriction by class II molecules and displaying class II-restricted CTL activity or specific helper activity in antibody synthesis, have been analyzed for antigenic specificities. All of them were obtained by in vitro stimulation against influenza A/Texas virus. In all cases the virus specificity appeared identical in cytolytic and proliferative responses. Three of the clones were broadly cross-reactive, recognizing all or almost all type A influenza strains. The three remaining clones were subtype specific when tested with human strains and recognized the surface glycoproteins of influenza virus. One of these lines reacted with an epitope of the neuraminidase N2 while the other two recognized the hemagglutinin H3. By using a large panel of mammalian and avian influenza strains, it can be demonstrated that hemagglutinin-specific human T cells can recognize a cross-reacting determinant shared by H3 and H4 subtypes of hemagglutinin which has never been detected with antibodies.     

Effect of Influenza Virus Proteins Modulate Hemostasis in vitro and in vivo

We studied the effect of influenza virus proteins—hemagglutinin, neuraminidase, nucleoprotein, and membrane protein—on hemostasis in vitro and in vivo. The results demonstrated that envelope proteins hemagglutinin and neuraminidase enhanced the fibrinolytic and anticoagulant activities of blood plasma and the activity of human tissue plasminogen activator. The membrane protein proved to have the highest activity among the core proteins of influenza virus; in contrast to hemagglutinin and neuraminidase, it inhibited fibrinolysis, increased the coagulant activity of blood plasma, and decreased the activity of human tissue plasminogen activator. The combined action of hemagglutinin and neuraminidase increased the plasma fibrinolytic and anticoagulant activities to a greater extent than the individual action of each agent. The combined action of hemagglutinin and membrane protein also increased the plasma fibrinolytic and anticoagulant activities, although to a lesser extent than the action of hemagglutinin alone. These data indicate that viral proteins are physiologically active and can cause influenza-specific disturbances of hemostasis.     

Inhibition of influenza A virus hemagglutinin and induction of interferon by synthetic sialylated glycoconjugates.

Multivalent forms of neoglycoproteins and polyacrylamides containing sialic acid were prepared and shown to be potent inhibitors of influenza A virus (H3N2) hemagglutinin with chick red blood cells. The synthetic sialylated glycoconjugates, although they were neuraminidase substrates, did not suppress viral neuraminidase and did not reduce infectivities in chick embryos. The copolyacrylamide conjugate containing a spacer group of approximately 11 A (1 A = 0.1 nm) between the polymer backbone and the sialic acid residues was the best hemagglutinin inhibitor. Moreover, it exhibited promising interferon-inducing properties.     

Purification of neuraminidase from influenza virus on an immunosorbent

A procedure for isolation of neuraminidase from influenza virus using the nonionic detergent Triton x-100 was developed. To achieve further purification, the protein mixture was passed through a Sepharose column packed with immobilized antibodies against hemagglutinin. The neuraminidase preparation thus obtained fully retained its enzymatic and antigenic properties and during electrophoretic separation under denaturating conditions gave one protein band.     

High-efficiency formation of influenza virus transfectants.

cDNA-derived RNAs were introduced into the genomes of influenza viruses by using an improved ribonucleoprotein (RNP) transfection protocol. Up to 10(5) viral transfectants with a novel neuraminidase gene could be obtained by using a 35-mm dish (10(6) cells) for RNP transfection. In addition to genes coding for surface proteins (hemagglutinin and neuraminidase), we also exchanged a gene coding for nonsurface proteins. The cDNA-derived influenza A/PR/8/34 virus NS gene was introduced into a temperature-sensitive mutant with a defect in this gene. We suggest that the term influenza virus transfectant be used for those viruses which are made by RNP transfection with cDNA-derived RNA.     

Properties of current influenza A (H1N1) virus strains and the characteristics of the epidemics they induce

Three epidemics of influenza A (H1N1) occurring in 1977, 1979 and 1981 were studied. These epidemics were found to be gradually dying down, which was manifested by progressively decreasing morbidity rate, the frequency and intensity of seroconversions, as well as by a decrease in the duration of the epidemic period. Changes in the biological properties of influenza A (H1N1) virus were accompanied by changes in its antigenic properties. The drift of neuraminidase in the influenza A (H1N1) virus of 1981 towards increased relationship with neuraminidase in the virus of 1952 was observed, while hemagglutinin in the strains of each of these two groups retained its individual character.     

Oligonucleotide microarray for subtyping of influenza virus A neuraminidase

Microarray for influenza A neuraminidase subtyping was presented. Selection of oligoprobes proceeded in two steps. First step included selection of peptides specific for each subtype of neuraminidase. At the second step oligoprobes were calculated using found peptides structures with the subsequent additional selection of the most specific and representative probes. From 19 to 24 probes were used for determination of each subtype of neuraminidase. Microchip testing for 19 samples with the most widespread types (N1 and N2) specifies in unequivocal definition 18 of them and only one isolate has not been identified.