Genetic stability and linkage analysis of the 2009 Influenza A(H1N1) virus based on sequence homology.

State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
Archives of Virology (Impact Factor: 2.39). 10/2009; 154(12):1883-90. DOI: 10.1007/s00705-009-0526-2
Source: PubMed


The 2009 swine-origin Influenza A virus subtype H1N1 (S-OIV) is generally believed to be a mixture of human, bird and swine viruses, resulting from multiple reassortments. The evolutionary origin of the S-OIV is of high interest but still remains obscure. In order to understand the evolution of the new virus, we performed sequence homology, segment stability and segment linkage analysis, as well as analysis of the host and geographic distribution of the evolutionarily related viruses. Stability analysis demonstrated that segment 6 (NA) was the most unstable one, followed by segment 4 (HA), while the other 6 segments were relatively stable. Host and geographic distribution analysis indicated that all 8 segments of the new virus were closely related to those of swine influenza viruses circulating either in North America or in Eurasia. Segment linkage analysis showed that segments 1 (PB2), 2 (PB1), 3 (PA), 4 (HA), 5 (NP), and 8 (NS) are in linkage disequilibrium exclusively with North American swine influenza viruses, and segments 6 (NA) and 7 (M) are evolutionarily linked solely with Eurasian swine influenza viruses. Two North American swine strains and 2 Eurasian swine strains were identified as possible ancestors of S-OIV 2009. Based on the most recent linkage analysis with the updated influenza sequences, South Dakota avian strains were found to be the closest known relatives of S-OIV 2009.

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Available from: Liu Dabin, Nov 22, 2014
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    • "The novel H1N1/2009, triple-reassortant swine-origin influenza A virus, shows a strong ability to transmit from human to human and has caused influenza A pandemic worldwide since its first emergence in Mexico in March 2009 (MMWR Morb Mortal Weekly Report, 2009). This novel virus contains 8 gene segments encoding haemagglutinin (HA), nucleoprotein (NP), and nonstructural protein (NS) from classic swine influenza A virus of North American lineage, the polymerase basic 2 (PB2) and the polymerase acidic (PA) from avian influenza of North American lineage, the polymerase basic 1 (PB1) from human seasonal influenza A H3N2, and neuraminidase (NA) and matrix protein (MP) from swine influenza A of Eurasian lineage (Babakir-Mina et al., 2009; Dawood et al., 2009; Garten et al., 2009; Lu et al., 2009). The reassortment of swine lineages may have occurred years before emergence in humans. "
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    ABSTRACT: Evolutionary process of swine-origin H1N1 influenza A viruses that infected humans from sporadic to pandemic is of high epidemiological significance but still remains obscure. To understand this process, we performed phylogenetic, bootscan, and adaptive evolution analyses using the sequences of the 8 gene segments from swine-origin H1N1 influenza A viruses that infected humans and the reference viruses. Classic swine H1N1 viruses occasionally infected humans before 1998. Sporadic human infection with the triple-reassortant swine-origin H1N1 viruses was firstly identified in 1998 and has become increasingly frequent since 2005. Except genes encoding the neuraminidase and matrix protein of swine influenza viruses of Eurasian lineage, other 6 genes of A/H1N1/2009 pandemic strain were most closely linked to those of A/Iowa/CEID23/2005(H1N1), a representative swine-origin triple-reassortant virus that infected humans sporadically. Potential positive selections acting on the haemagglutinin gene evolved from classic swine H1N1 viruses to the triple-reassortant H1N1 viruses and on the neuraminidase gene evolved from Eurasian swine viruses to A/H1N1/2009 pandemic viruses might play a role in cross-species transmission and human infection. Surveillance of genetic evolution of influenza A viruses in swine workers might provide useful clues of influenza pandemic.
    Full-text · Article · Jul 2011
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    • "This process of antigenic shift is hypothesized to be the generating event for the 2009 H1N1 virus. Amazingly, the 2009 H1N1 virus was the result of multiple rounds of reassortment that actually combined portions of avian, swine and human influenza viruses, ultimately yielding the virus strain which spread rapidly across the globe [9]. By combining segments from three progenitor strains, the resulting 2009 H1N1 virus was highly variable, allowing for rapid transmission among immunologically na¨ıve human-hosts [10]. "
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    ABSTRACT: Given the interconnected nature of our world today, emerging pathogens and pandemic outbreaks are an ever-growing threat to the health and economic stability of the global community. This is evident by the recent 2009 Influenza A (H1N1) pandemic, the SARS outbreak, as well as the ever-present threat of global bioterrorism. Fortunately, the biomedical community has been able to rapidly generate sequence data so these pathogens can be readily identified. To date, however, the utilization of this sequence data to rapidly produce relevant experimental results or actionable treatments is lagging in spite of obtained sequence data. Thus, a pathogenic threat that has emerged and/or developed into a pandemic can be rapidly identified; however, translating this identification into a targeted therapeutic or treatment that is rapidly available has not yet materialized. This commentary suggests that the growing technology of DNA synthesis should be fully implemented as a means to rapidly generate in vivo data and possibly actionable therapeutics soon after sequence data becomes available.
    Full-text · Article · Mar 2011
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    • "During April 2009, a new influenza A virus outbreak occurred in North America that originated from Mexico and the southwestern United States (Dawood et al., 2009; Peiris et al., 2009). The virus was identified as an H1N1 virus and genetic analysis revealed a unique reassortment of genes that were of swine origin (Garten et al., 2009; Lu et al., 2009; Trifonov et al., 2009). This new pathogen spread faster than any previous virus and was distributed worldwide in only few months (Naffakh and van der Werf, 2009; Smith et al., 2009). "
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    ABSTRACT: Hemagglutinin (HA) is an important influenza virus surface antigen that is highly topical in influenza research. In the present study, the genes encoding the HA1 and HA2 proteins from the 2009 pandemic influenza virus H1N1 (A/California/04/2009(H1N1)) were cloned into a prokaryotic expression plasmid pCold-TF, and soluble fusion proteins containing H1N1 HA1 and HA2 were produced by transformed Escherichia coli. Western blot assays were used to examine the immunoreactivity of the recombinant proteins using polyclonal and monoclonal antibodies derived against the whole virus A/California/04/2009(H1N1). Recombinant protein immunoreactivity was also analyzed qualitatively by ELISA and hemagglutination inhibition using human serum samples. These results will aid future immunological and serological studies of the 2009 pandemic H1N1 virus HA.
    Full-text · Article · Mar 2011 · Journal of virological methods
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