Influenza A viruses are significant human pathogens causing yearly epidemics and occasional pandemics. Past pandemics have resulted in significant morbidity and mortality. The 1918 influenza pandemic was thought to have resulted in the death of at least 675,000 people in the U.S., and 50 million people worldwide. Pandemics in 1957 and 1968, while less severe, were also of major public health importance. In 2009, a novel pandemic emerged and caused up to 18,000 deaths in the U.S. and up to 575,000 deaths globally. Understanding the molecular basis for the formation of pandemic influenza strains is critical. The 1957 and 1968 pandemics were human-avian reassortant viruses in which two or three influenza gene segments from the then circulating human influenza viruses were replaced with genes from an avian source. The 2009 pandemic virus arose via reassortment between two swine-adapted influenza viruses. Sequence and phylogenetic analysis of the 1918 pandemic virus suggested that it was derived from an avian-like virus possibly via an intermediate host in the decade before the pandemic. The 1918 pandemic virus caused several epidemiologically distinct waves. The so-called first wave, in the summer months of 1918, may have represented an early form of the more virulent second wave. To understand how this pandemic virus emerged and to model its virulence, it is important to place this virus in the context of human influenza viruses circulating before 1918 and to follow the early evolution of human H1N1 viruses after 1918. Because human influenza isolates are not available earlier than 1933, the only way to characterize these viruses is by identification of influenza RNA fragments preserved in formalin-fixed, paraffin-embedded autopsy tissues. Efforts to identify pre-1918 influenza virus RNA-positive autopsy material are continuing. Possible fatal influenza pneumonia cases from 1907-1917 have been identified in tissue archives and anonymized materials are being screened for host and viral RNA by RT-PCR. In a related effort, a method has been developed allowing high-throughput deep sequencing of host, viral, and bacterial RNA from archival tissue samples. This method significantly reduces ribosomal RNA allowing sequence analysis of viral and host mRNA expression and identification of secondary bacterial infections. Lastly, new techniques to positively enrich for influenza virus RNA sequences have been developed utilizing oligonucleotide probes designed by downloading all influenza A and B virus sequences in GenBank prior to construction of cDNA libraries for next generation sequencing. Validation of this technique using cloacal swabs samples from wild birds is on-going.

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