Identification and Chronological Analysis of Genomic Signatures in Influenza A Viruses

An increase in the availability of data on the influenza A viruses (IAV) has enabled the identification of the potential determinants of IAV host specificity using computational approaches. In this study, we proposed an alternative approach, based on the adjusted Rand index (ARI), for the evaluation of genomic signatures of IAVs and their ability to distinguish hosts they infected. Our experiments showed that the host-specific signatures identified using the ARI were more characteristic of their hosts than those identified using previous measures. Our results provided updates on the host-specific genomic signatures in the internal proteins of the IAV based on the sequence data as of February 2013 in the National Center for Biotechnology Information (NCBI). Unlike other approaches for signature recognition, our approach considered not only the ability of signatures to distinguish hosts (according to the ARI), but also the chronological relationships among proteins. We identified novel signatures that could be mapped to known functional domains, and introduced a chronological analysis to investigate the changes in host-specific genomic signatures over time. Our chronological analytical approach provided results on the adaptive variability of signatures, which correlated with previous studies’ findings, and indicated prospective adaptation trends that warrant further investigation.     

Molecular Basis for the Generation in Pigs of Influenza A Viruses with Pandemic Potential

Genetic and biologic observations suggest that pigs may serve as “mixing vessels” for the generation of human-avian influenza A virus reassortants, similar to those responsible for the 1957 and 1968 pandemics. Here we demonstrate a structural basis for this hypothesis. Cell surface receptors for both human and avian influenza viruses were identified in the pig trachea, providing a milieu conducive to viral replication and genetic reassortment. Surprisingly, with continued replication, some avian-like swine viruses acquired the ability to recognize human virus receptors, raising the possibility of their direct transmission to human populations. These findings help to explain the emergence of pandemic influenza viruses and support the need for continued surveillance of swine for viruses carrying avian virus genes.     

植物病毒沉默抑制因子研究进展

RNA沉默是广泛存在于真菌、动物和植物中的一种特异序列降解机制.在植物中,RNA沉默是一种抵抗外界植物病毒入侵的自然机制.但是,植物病毒通常也会采取编码沉默抑制因子的相应机制来抵抗基因沉默,以便能够入侵植物.论述了主要沉默抑制因子的机制、特点和相关确认沉默抑制因子实验,并对沉默抑制因子的研究前景进行了展望.     

Circulating Avian Influenza Viruses Closely Related to the 1918 Virus Have Pandemic Potential

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末端酶介导的双链DNA病毒核酸组装

病毒是一类非细胞结构的微生物,专性宿主细胞内寄生,以复制方式进行增殖。在病毒复制的过程中,组装是其特有的过程。不同类型病毒之组装的机制有很大差异,目前对双链DNA(dsDNA)病毒的组装机制研究较多,包括位点特异性组装和满头组装两种方式,采用何种方式进行组装与其基因组编码的末端酶有关。该文介绍末端酶介导的dsDNA病毒组装的有关进展。     

流感病毒的裂解气相色谱分析

裂解气相色谱法(Pyrolysis Gas Chromatography,PGC)在微生物学的应用中曾多侧重于细菌的鉴定,Mayer最早用PGC做植物病毒的快速鉴定,80年代国内开始开展了病毒的PGC研究。本文报道用PGC分析流感病毒和新城疫病毒的初步结果。     

Investigation into the Attenuation of Influenza Viruses by Serial Passage

For vaccination live viruses are better than dead ones, but live influenza vaccines are difficult to prepare. One influenza A₂ and two influenza B viruses were passed in series in embryonated eggs. At several stages of their passage they were inoculated into volunteers, and their effects assessed by virus isolations, antibody rises, and clinical reactions. The A₂ virus and one of the influenza B viruses, both of which had grown readily in embryonated eggs on first isolation, continued to induce human infections and clinical reactions after 30 egg passes. The other influenza B virus acquired enhanced human pathogenicity after three passages from man to man. After adaptation to eggs in which it at first grew reluctantly, its human virulence was appreciably reduced. It underwent no further change during a total of 20 egg passes. There was little convincing evidence of an increased incidence of clinical reactions during the winter seasons, but the numbers of volunteers were too small to draw definite conclusions.     

Cooperation between the Hemagglutinin of Avian Viruses and the Matrix Protein of Human Influenza A Viruses

To analyze the compatibility of avian influenza A virus hemagglutinins (HAs) and human influenza A virus matrix (M) proteins M1 and M2, we doubly infected Madin-Darby canine kidney cells with amantadine (1-aminoadamantane hydrochloride)-resistant human viruses and amantadine-sensitive avian strains. By using antisera against the human virus HAs and amantadine, we selected reassortants containing the human virus M gene and the avian virus HA gene. In our system, high virus yields and large, well-defined plaques indicated that the avian HAs and the human M gene products could cooperate effectively; low virus yields and small, turbid plaques indicated that cooperation was poor. The M gene products are among the primary components that determine the species specificities of influenza A viruses. Therefore, our system also indicated whether the avian HA genes effectively reassorted into the genome and replaced the HA gene of the prevailing human influenza A viruses. Most of the avian HAs that we tested efficiently cooperated with the M gene products of the early human A/PR/8/34 (H1N1) virus; however, the avian HAs did not effectively cooperate with the most recently isolated human virus that we tested, A/Nanchang/933/95 (H3N2). Cooperation between the avian HAs and the M proteins of the human A/Singapore/57 (H2N2) virus was moderate. These results suggest that the currently prevailing human influenza A viruses might have lost their ability to undergo antigenic shift and therefore are unable to form new pandemic viruses that contain an avian HA, a finding that is of great interest for pandemic planning.     

Activation of Influenza A Viruses by Host Proteases from Swine Airway Epithelium

Pigs are important natural hosts of influenza A viruses, and due to their susceptibility to swine, avian, and human viruses, they may serve as intermediate hosts supporting adaptation and genetic reassortment. Cleavage of the influenza virus surface glycoprotein hemagglutinin (HA) by host cell proteases is essential for viral infectivity. Most influenza viruses, including human and swine viruses, are activated at a monobasic HA cleavage site, and we previously identified TMPRSS2 and HAT to be relevant proteases present in human airways. We investigated the proteolytic activation of influenza viruses in primary porcine tracheal and bronchial epithelial cells (PTEC and PBEC, respectively). Human H1N1 and H3N2 viruses replicated efficiently in PTECs and PBECs, and viruses containing cleaved HA were released from infected cells. Moreover, the cells supported the proteolytic activation of HA at the stage of entry. We found that swine proteases homologous to TMPRSS2 and HAT, designated swTMPRSS2 and swAT, respectively, were expressed in several parts of the porcine respiratory tract. Both proteases cloned from primary PBECs were shown to activate HA with a monobasic cleavage site upon coexpression and support multicycle replication of influenza viruses. swAT was predominantly localized at the plasma membrane, where it was present as an active protease that mediated activation of incoming virus. In contrast, swTMPRSS2 accumulated in the trans-Golgi network, suggesting that it cleaves HA in this compartment. In conclusion, our data show that HA activation in porcine airways may occur by similar proteases and at similar stages of the viral life cycle as in human airways.     

Genetic Adaptation of Influenza A Viruses in Domestic Animals and Their Potential Role in Interspecies Transmission: A Literature Review

EcoHealth - In December 2011, the European Food Safety Authority awarded a Grant for the implementation of the FLURISK project. The main objective of FLURISK was the development of an...     

Microarray Multiplex Assay for the Simultaneous Detection and Discrimination of Influenza A and Influenza B Viruses

In this study, we present a microarray approach for the typing of influenza A and B viruses, and the subtyping of H1 and H3 subtypes. We designed four pairs of specific multiplex RT-PCR primers and eight specific oligonucleotide probes and prepared microarrays to identify the specific subtype of influenza virus. Through amplification and fluorescent marking of the multiplex RT-PCR products on the M gene of influenza A and B viruses and the HA gene of subtypes H1 and H3, the PCR products were hybridized with the microarray, and the results were analyzed using a microarray scanner. The results demonstrate that the chip developed by our research institute can detect influenza A and B viruses specifically and identify the subtypes H1 and H3 at a minimum concentration of 1 × 10² copies/μL of viral RNA. We tested 35 clinical samples and our results were identical to other fluorescent methods. The microarray approach developed in this study provides a reliable method for the monitoring and testing of seasonal influenza.     

The Potential of Avian H1N1 Influenza A Viruses to Replicate and Cause Disease in Mammalian Models

H1N1 viruses in which all gene segments are of avian origin are the most frequent cause of influenza pandemics in humans; therefore, we examined the disease-causing potential of 31 avian H1N1 isolates of American lineage in DBA/2J mice. Thirty of 31 isolates were very virulent, causing respiratory tract infection; 22 of 31 resulted in fecal shedding; and 10 of 31 were as pathogenic as the pandemic 2009 H1N1 viruses. Preliminary studies in BALB/cJ mice and ferrets showed that 1 of 4 isolates tested was more pathogenic than the pandemic 2009 H1N1 viruses in BALB/cJ mice, and 1 of 2 strains transmitted both by direct and respiratory-droplet contact in ferrets. Preliminary studies of other avian subtypes (H2, H3, H4, H6, H10, H12) in DBA/2J mice showed lower pathogenicity than the avian H1N1 viruses. These findings suggest that avian H1N1 influenza viruses are unique among influenza A viruses in their potential to infect mammals.     

Isolation of Influenza A and B Viruses in HeLa Cells

The HeLa cell line which is one of the most popular cell lines was shown to be suitable for isolation of types A (H₃N₂) and B influenza viruses from throat washings of patients. Sixty-nine and 67 out of 147 throat washings taken from patients during the period from January to April, 1994, were positive for influenza A virus in HeLa cells and MDCK cells, respectively. Seven out of 10 throat washings taken between January and March, 1993, were positive for influenza B virus in MDCK. Of these 7, 4 were also positive for HeLa cells.     

Attenuated Bordetella pertussis Protects against Highly Pathogenic Influenza A Viruses by Dampening the Cytokine Storm

The threat of a pandemic spread of highly virulent influenza A viruses currently represents a top global public health problem. Mass vaccination remains the most effective way to combat influenza virus. However, current vaccination strategies face the challenge to meet the demands in a pandemic situation. In a mouse model of severe influenza virus-induced pneumonitis, we observed that prior nasal administration of an attenuated strain of Bordetella pertussis (BPZE1) provided effective and sustained protection against lethal challenge with two different influenza A virus subtypes. In contrast to most cross-protective effects reported so far, the protective window offered upon nasal treatment with BPZE1 lasted up to at least 12 weeks, suggesting a unique mechanism(s) involved in the protection. No significant differences in viral loads were observed between BPZE1-treated and control mice, indicating that the cross-protective mechanism(s) does not directly target the viral particles and/or infected cells. This was further confirmed by the absence of cross-reactive antibodies and T cells in serum transfer and in vitro restimulation experiments, respectively. Instead, compared to infected control mice, BPZE1-treated animals displayed markedly reduced lung inflammation and tissue damage, decreased neutrophil infiltration, and strong suppression of the production of major proinflammatory mediators in their bronchoalveolar fluids (BALFs). Our findings thus indicate that protection against influenza virus-induced severe pneumonitis can be achieved through attenuation of exaggerated cytokine-mediated inflammation. Furthermore, nasal treatment with live attenuated B. pertussis offers a potential alternative to conventional approaches in the fight against one of the most frightening current global public health threats.Influenza virus pandemics are unpredictable but recurring events that can have severe consequences on societies worldwide. In the 20th century, three novel influenza virus strains emerged, causing the 1918, 1957, and 1968 pandemics, the most devastating being the 1918 Spanish flu that led to an estimated 50 million deaths (47). The recent spread of highly pathogenic avian influenza (HPAI) H5N1 virus across parts of Asia, Europe, and the Middle East, with an overall fatality rate of over 60% for humans, as well as the rapid pandemic spread of a novel influenza A virus of the H1N1 subtype, has caused worldwide concern about a potential remake of the 1918 disaster (8).Severe complications arising from pandemic influenza or HPAI H5N1 viruses are associated with rapid, massive inflammatory cell infiltration, resulting in acute respiratory distress, and reactive hemophagocytosis with multiple organ involvement. Both the 1918 Spanish influenza virus and HPAI H5N1 induce a cytokine storm characterized by an exaggerated production of inflammatory cytokines and chemokines in the serum and lungs caused by uncontrolled activation of the host''s innate immune system. This triggers massive pulmonary edema, primary and/or secondary pneumonia, and alveolar hemorrhage with acute bronchopneumonia (4, 12, 24, 27, 37, 40, 43, 44).The relationship between mortality, viral load, and immunopathology during influenza virus infection remains elusive and somewhat controversial. Some studies suggest that severe lung immunopathology is a direct consequence of a high viral load that the host is unable to resolve (12, 13), whereas others have reported that influenza virus-induced mortality is not a direct function of viral burden but a consequence of immune-mediated pathology (9, 11). Moreover, the picture is further complicated by the fact that different highly virulent influenza A viruses may induce distinct pathological signatures and lead to different courses of acute respiratory distress syndrome, refuting the hypothesis of a single, universal cytokine storm underlying all fatal influenza virus diseases (16).Currently, vaccination remains the cornerstone of influenza virus prevention. However, due to constant antigenic drift and shift of the two major viral surface proteins hemagglutinin (HA) and neuraminidase (NA) (7), influenza virus vaccines must be reformulated each year in order to match the circulating subtypes (41). The potential emergence of an influenza virus pandemic at any time, combined with limited vaccine supplies, has rendered global vaccination strategies difficult. Therefore, a universal influenza virus vaccine that can provide protection against different variants or strains and thus not require frequent updates is highly desirable.Here, we report that nasal administration of a recently developed live attenuated Bordetella pertussis vaccine strain, named BPZE1 (35), provides effective and sustained protection against lethal challenge with mouse-adapted H3N2 or H1N1 (A/PR/8/34) influenza A viruses. We demonstrate that the protective mechanism(s) does not target the viral particles or the infected host cells but controls the influenza virus-mediated inflammation by dampening the cytokine storm. As BPZE1 has recently entered phase I safety trials with humans (http://www.child-innovac.org), our observations support the potential application of this vaccine strain as a universal prophylactic treatment against highly pathogenic influenza A viruses.