Genomic Signatures of Influenza A Pandemic (H1N1) 2009 Virus

DOI: 10.3201/eid1512.090845
Suggested citation for this article: Chen G-W, Shih S-R. Genomic signatures of influenza A pandemic (H1N1) 2009 virus. Emerg Infect Dis. 2009 Dec; [Epub ahead of print]

Genomic Signatures of Influenza A Pandemic (H1N1) 2009 Virus
Guang-Wu Chen and Shin-Ru Shih

Author affiliation: Chang Gung University, Taoyuan, Taiwan, Republic of China
Adaptive mutations that have contributed to the emergence of influenza A pandemic (H1N1) 2009 virus, which can replicate and transmit among humans, remain unknown. We conducted a large-scale scanning of influenza protein sequences and identified amino acid–conserving positions that are specific to host species, called signatures. Of 47 signatures that separate avian viruses from human viruses by their nonglycoproteins, 8 were human-like in the pandemic (H1N1) 2009 virus. Close examination of their amino acid residues in the recent ancestral swine viruses of pandemic (H1N1) 2009 virus showed that 7 had already transitioned to human-like residues and only PA 356 retained an avian-like K; in pandemic (H1N1) 2009 virus, this residue changed into a human-like R. Signatures that separate swine viruses from human viruses were also present. Continuous monitoring of these signatures in nonhuman species will help with influenza surveillance and with evaluation of the likelihood of further adaptation to humans.

A recent outbreak of pandemic (H1N1) 2009, previously known as the swine-origin influenza A, has infected >296,000 persons worldwide; 3,486 deaths have been reported (1). An increased number of infected humans can potentially alter virulence in the human population. The genomic sequences of many of the new strains of pandemic (H1N1) 2009 virus have revealed important information for promoting medical diagnosis, drug-resistance monitoring, clinical and basic research, and vaccine development. Nevertheless, analyzing adaptive mutation of the new pandemic (H1N1) 2009 virus is a priority so that researchers can evaluate the likelihood that viruses from other nonhuman species will further adapt to humans.

Pandemic (H1N1) 2009 virus consists of multiple reassorted virus genes from different origins. Of its 8 segmented genomic RNAs, 2 polymerase genes, PB2 and PA, were from the avian...

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