Toll-like receptors (TLRs) are key molecules of the innate immune systems, which detect conserved structures found in a broad range of pathogens and triggers innate immune responses. A subset of TLRs recognize viral components and induce antiviral responses by producing type I interferons. Whereas TLR2 and TLR4 recognize viral components at the cell surface, TLR3, TLR7, TLR8 and TLR9 are exclusively expressed in endosomal compartments. After phagocytes internalize viruses or virus-infected apoptotic cells, viral nucleic acids are released in phagolysosomes and are recognized by these TLRs. Recent reports have shown that hosts also have a mechanism to detect replicating viruses in the cytoplasm in a TLR-independent manner. In this review, we focus on the viral recognition by innate immunity and the signaling pathways.

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Yeast is often considered to be a model eukaryotic organism, in a manner analogous to E. coli as a model prokaryotic organism. Yeast has been extensively characterized and the genomes completely sequenced. Despite the small genome size, yeast displays most of features of higher eukaryotes. The facts that most of cellular machinery is conserved among different eukaryotes and that the powerful technologies of genetics and molecular biology are available have made yeast model eukaryotic cells in biological and biomedical sciences including virology. Cumulative data indicate that yeast can be a host for animal viruses. I briefly describe yeast gene expression and review viral replication in yeast. Great discovery include complete replication of animal viruses and production of virus-like particle vaccines in yeast. Current studies on yeast focus on identification of host factors and machinery used for viral replication. The studies are based on traditional yeast genetics and genome-wide identification using a complete set of yeast deletion strains.

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Human polyomavirus JC (JCV) is a causative agent for progressive multifocal leukoencephalopathy, a fatal demyelinating disorder. The viruses form intranuclear viral inclusions in infected oligodendrocytes. The outer capsid of JCV is thought to be composed of 360 molecules of major capsid protein VP1, and minor capsid proteins VP2 and VP3 in an appropriate ratio. However, the regulatory mechanisms of gene expression for the capsid proteins, their nuclear transport, and formation of viral inclusions are not well understood. We have recently clarified the following regarding the mechanism underlying JCV virion assembly; (i) major and minor capsid proteins are synthesized from messenger RNAs, the expression ratio of which is determined by alternative splicing, (ii) messenger RNAs for the major and minor capsid proteins are polycistronic, and their translation occurs downstream of the regulatory protein, agnoprotein, (iii) major and minor capsid proteins are translocated to the nucleus in a cooperative manner and accumulate at the dot-shaped intranuclear structures called promyelocytic leukemia nuclear bodies (PML-NBs), (iv) efficient viral replication can occur at the PML-NBs, where capsid assembly is likely to be associated with viral DNA replication. PML-NBs are the sites for expression of important nuclear functions for the host cells. The finding that the target of JCV infection is the PML-NB may contribute greatly to our understanding of the mechanism underlying cellular degeneration, which occurs after the formation of intranuclear viral inclusions.

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Measles virus (MV) is a member of the genus Morbillivirus in the family Paramyxoviridae. Clinical isolates of MV use signaling lymphocyte activating molecule (SLAM) as a cellular receptor. SLAM is mainly expressed on immune cells such as immature thymocytes, activated lymphocytes and mature dendritic cells. This distribution of SLAM can account for the lymphotropism of MV. On the other hand, laboratory strains of MV use CD46 as an alternative receptor, through amino acid change(s) in the receptor binding hemagglutinin protein. Recently, several reports imply the existence of the cellular receptor(s) other than SLAM and CD46. In this review, we discuss the receptor usage of MV and its adaptation to cultured cells.

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The replication of eukaryotic positive-strand RNA virus genomes occurs in membrane-bound replication complexes. Currently, little is known about the process of replication complex formation and the molecular structure of the replication complexes. We are trying to understand how eukaryotic positive-strand RNA viruses replicate using tobamoviruses as models. Here, I describe our approaches to this end.

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An interplay or battle between virus and its host has been observed within a single cell. Upon an infection with retroviruses including human immunodeficiency virus type 1 (HIV-1), the viral genome is subjected to several processes that include uncoating, reverse transcription of the viral genomic RNA into a cDNA copy, transport of this cDNA into the nucleus, and integration of the cDNA into the host chromosome. Antiretroviral restriction factors such as TRIM5α and APOBEC3G have been recently identified. In addition, nuclear membrane protect host chromosomal DNA against incoming viral genome. For successful retroviral infection, viral genome must overcome these cellular barriers to establish proviral state, in which viral cDNA was stably integrated into host chromosomal DNA. In this review, I would summarize the host factors that regulate the intercellular dynamics of HIV-1 genome during the early phase of infection, especially focusing on factors interacting with HIV-1 integrase and the preintegration complex.

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It is considered there are two main pathways for poliovirus dissemination towards the central nervous system in humans. One is the pathway through the blood brain barrier. The orally ingested virus invades into the blood circulation, and then the virus permeates into the central nervous system through the blood brain barrier. The other is the neural pathway. In this pathway, the intramuscularly-inoculated virus is transported through the axons from the synapse to the cell body in the central nervous system. We have developed the oral infection system using the mouse models. Moreover, we proposed the possibility that PV is transcytosed through the brain capillary epithelia in a specific manner. As for the neural pathway, we have proved that PV is endocytosed into CD155 containing vesicles and the vesicles are retrogradely transported in the axon of rat primary motor neuron. We have also shown that the cytoplasmic dynein takes part in the transport.

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Poliovirus is the causative agent of poliomyelitis. It replicates efficiently in the neurons in the central nervous system and produces severe pathological lesions. It cannot replicate well in the non-neural tissues. In spite of this strict neurotropism in vivo, however, it can replicate in cells of monolayer cultures derived from almost any tissues of primates as Enders and colleagues initially shown. It was supposed that cellular changes during the process of cultivation were required for acquisition of susceptibility. This question remained unsolved for a long time. We have recently shown that cells in culture acquire poliovirus susceptibility by loosing rapid and robust interferon response that has been normally maintained in tissues in vivo.

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We analyzed the seasonal influenza activity in 2004/05 and 2005/06 seasons. In 2004/05 season, the prevalence of influenza started lately. The arrival of a peak of influenzal prevalence was the ninth week, and was late in comparison with an average year. The prevalence scale was very large, and the estimation number of patients was 17700000. Since the start of the 2004/05 season, influenza activity has mainly been associated with influenza B viruses. The start of prevalence of 2005/06 season was 50th week and was comparatively early. The peak of the prevalence was the 4th week, same as an average year. Since the start of the 2005/06 season, influenza activity has mainly been associated with influenza A/H3 viruses.
H5N1 highly pathogenic avian influenza virus have spread through Africa and Europe from Asia. For purpose such as inhibition of the outbreak of new variant influenza, the prevention of human to human infection and expansion, early containment, the public health organization has to do unified epidemiological investigation immediately nationwide. By doing epidemiological investigation, the prevention of infection expansion, specification of the source of infection, assessment of the risk of infection, and early detection of new variant influenza virus and containment, are expected.

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Since the end of 2003, simultaneous outbreaks caused by H5N1 highly pathogenic avian influenza viruses (H5N1-HPAIV) occurred in poultries and in wild birds in the East Asia. The outbreaks are spreading now at least 48 countries in the Middle Eastern, African and European countries in addition to the East Asia. During the outbreaks, over 200 human infection cases with 55% fatality are confirmed at the moment and some human-to-human transmission in family clusters have been observed. The outbreaks are no more out of control and pandemic potential caused by H5N1-HPAIV is major concern. Therefore, it is urgently necessary to develop new diagnostic kits and effective vaccines and to stockpile anti-influenza drugs before pandemic alert period phase 4 defined by WHO. Furthermore, international supports to the affected countries for development and improvement of diagnostic system are required in the public health aspect.

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Avian influenza A (H5N1) virus infections have resulted in more than 100 human deaths; yet, human-to-human transmission is rare. We demonstrated that the epithelial cells in the upper respiratory tract of humans mainly possess sialic acid linked to galactose by α 2,6 linkages (SAα 2,6Gal), a molecule preferentially recognized by human viruses. However, many cells in the respiratory bronchioles and alveoli possess SAα 2,3Gal, which is preferentially recognized by avian viruses. These facts are consistent with the observation that H5N1 viruses can be directly transmitted from birds to humans and cause serious lower respiratory tract damage in humans. Furthermore, this anatomical difference in receptor prevalence may explain why the spread of H5N1 viruses among humans is limited. However, since some H5N1 viruses isolated from humans recognize human virus receptors, additional changes must be required for these viruses to acquire the ability for efficient human-to-human transmission.

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During protein evolution the amino acid substitutions accumulate with time. However, the effect of accumulation of the amino acid substitutions to structural changes has not been estimated well. We will propose that the discordance of amino acid substitution on the HA protein of influenza A virus is useful for the assessment of structural changes during evolution. Discordance value can be obtained from the experimental data of tolerance or intolerance by introducing site directed mutagenesis at the homologous positions of two HA proteins holding the same amino acid residues. The value of discordance correlated to the number of amino acid differences among proteins. In the H3HA discordance rate was calculated to be 0.45% per one amino acid change. Furthermore, discordance of amino acid substitutions suggests that tolerable amino acid substitutions in different order have a probability of promoting irreversible divergence of the HA protein to different subtypes.

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The genome of influenza A virus is a set of eight segmented- and single-stranded RNAs. A basic transcription and replication unit is the genome complexed with viral RNA-dependent RNA polymerases and nucleoprotein (NP). For the efficient transcription and replication of the genome, not only viral factors but also host cell-derived factors are required. Although receptor and protease molecules play important roles in infection and pathogenicity, it is also possible that host factors involved in the virus genome function determine these. PB2, for instance, is reported to be a possible candidate for determination of the host range of avian influenza viruses. Here we summarize recent progresses in the molecular mechanism of the influenza virus genome transcription and replication and discuss the involvement of host factors in these processes.

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Children with influenza usually shed viruses from the several days before onset of clinical symptoms, and viruses are isolated for one or two weeks after onset. Point-of-care rapid diagnostic tests are useful to guide use of antiviral agents, appears over 90% sensitivity and specificity for influenza A with nasopharyngeal specimens compared with cell culture. The detection limits of these test kits are 103 pfu or over, so it is necessary to consider viral load in clinical specimens for diagnosis with these kits. Viral load are decreased after the start of antiviral agents, but influenza viruses are isolated in more than half of pediatric patients when fever get down, and resistant viruses are detected in some of these patients. It is very important for influenza control to investigate on viral shedding and resistant viruses.

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In central and west Africa, Ebola virus, a member of the filovirus group, has produced sporadic outbreaks of lethal disease. This virus causes hemorrhagic fever in humans and nonhuman primates, resulting in mortality rates of up to 90%. Although there are no satisfactory biologic explanations for this extreme virulence, it has been suggested that functions of the envelope glycoprotein are likely to play important roles in the pathogenicity of Ebola virus.

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