1. Department of Molecular Pathology, Armed Forces Institute of Pathology, Rockville, Maryland 20850, USA
2. †Present addresses: Board on Life Sciences, The National Academies, 6th Floor, 500 Fifth Street N.W., Washington DC 20001, USA (A.H.R.); University of Iowa, Roy J. and Lucille A. Carver College of Medicine, 200 CMAB, Iowa City, Iowa 52242, USA (R.M.L.)

Correspondence to: Jeffery K. Taubenberger¹ Correspondence and requests for materials should be addressed to J.K.T. (Email: taubenberger@afip.osd.mil).

Abstract

The influenza A viral heterotrimeric polymerase complex (PA, PB1, PB2) is known to be involved in many aspects of viral replication and to interact with host factors¹, thereby having a role in host specificity^{2, 3}. The polymerase protein sequences from the 1918 human influenza virus differ from avian consensus sequences at only a small number of amino acids, consistent with the hypothesis that they were derived from an avian source shortly before the pandemic. However, when compared to avian sequences, the nucleotide sequences of the 1918 polymerase genes have more synonymous differences than expected, suggesting evolutionary distance from known avian strains. Here we present sequence and phylogenetic analyses of the complete genome of the 1918 influenza virus^{4, 5, 6, 7, 8}, and propose that the 1918 virus was not a reassortant virus (like those of the 1957 and 1968 pandemics^{9, 10}), but more likely an entirely avian-like virus that adapted to humans. These data support prior phylogenetic studies suggesting that the 1918 virus was derived from an avian source¹¹. A total of ten amino acid changes in the polymerase proteins consistently differentiate the 1918 and subsequent human influenza virus sequences from avian virus sequences. Notably, a number of the same changes have been found in recently circulating, highly pathogenic H5N1 viruses that have caused illness and death in humans and are feared to be the precursors of a new influenza pandemic. The sequence changes identified here may be important in the adaptation of influenza viruses to humans.

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