Once the NA nucleic acid sequences were obtained, they were aligned, in-frame for protein coding, and converted to amino acids using the built-in function in BIOEDIT. The presence or absence of the established NAI resistance-associated mutations, R292K and E119V, was then determined by inspection of the resulting amino acid alignment, with reference to the influenza A/Syd/5/ 97 (H3N2) NA sequence, which was isolated before the licensing and widespread use of neuraminidase inhibitors that began after 1999/2000. Table S1 The 315 downloaded TIGR(JCVI) influenza A(H3N2) HA and NA sequences used to construct the multi-country HA and NA phylogenetic trees shown in Figures S3 and S4 . MS Excel file containing the GenBank Accession numbers of the 315 downloaded TIGR(JCVI) influenza A(H3N2) HA and NA sequences which were used to construct the multi-country HA and NA phylogenetic trees shown in Figures S3 and S4 Author Contributions H5N1 and 1918 Pandemic Influenza Virus Infection Results in Early and Excessive Infiltration of Macrophages and Neutrophils in the Lungs of Mice Fatal human respiratory disease associated with the 1918 pandemic influenza virus and potentially pandemic H5N1 viruses is characterized by severe lung pathology, including pulmonary edema and extensive inflammatory infiltrate. Here, we quantified the cellular immune response to infection in the mouse lung by flow cytometry and demonstrate that mice infected with highly pathogenic (HP) H1N1 and H5N1 influenza viruses exhibit significantly high numbers of macrophages and neutrophils in the lungs compared to mice infected with low pathogenic (LP) viruses. Mice infected with the 1918 pandemic virus and a recent H5N1 human isolate show considerable similarities in overall lung cellularity, lung immune cell sub-population composition and cellular immune temporal dynamics. Interestingly, while these similarities were observed, the HP H5N1 virus consistently elicited significantly higher levels of pro-inflammatory cytokines in whole lungs and primary human macrophages, revealing a potentially critical difference in the pathogenesis of H5N1 infections. These results together show that infection with HP influenza viruses such as H5N1 and the 1918 pandemic virus leads to a rapid cell recruitment of macrophages and neutrophils into the lungs, suggesting that these cells play a role in acute lung inflammation associated with HP influenza virus infection. In addition, primary macrophages and dendritic cells were also susceptible to 1918 and H5N1 influenza virus infection in vitro and in infected mouse lung tissue. The influenza pandemic from 1918 to 1919 was the most devastating infectious disease pandemic ever documented in such a short period of time, killing nearly 50 million people worldwide [1] . Unlike the epidemiological profiles of most influenza infections, young adults aged 18-35 yrs old had the highest mortality rate, so much so that the average life expectancy during those years was lowered by 10 years [2] . In 1918, severe destruction of lung tissue observed by pathologists at autopsy was unlike that typically seen in cases of pneumonia [3] and histopathological analysis of lung tissue showed severe tissue consolidation with unique destruction of the lung architecture [3, 4] . Human infections with highly pathogenic avian influenza (HPAI) strains of subtype H5N1 since the first outbreak in 1997 have also been particularly severe for children and young adults [5] [6] [7] . Assessing pulmonary infiltrates in response to influenza H5N1 virus infection has been difficult due to the lack of autopsy material. The basis for the high morbidity and mortality associated with the 1918 virus and recent H5N1 viruses remains inconclusive based on viral genetic analysis alone and accounts of patient lung pathology provide only qualitative information about the host factors contributing to disease [4, 8, 9] . Great concern about a pandemic caused by a novel avian H5 subtype virus warrants comparative studies to better understand the cellular pathology caused by a pandemic virus and potentially pandemic viruses. Identification and quantification of the inflammatory cell types associated with highly pathogenic respiratory infections represent prospective targets for modulation of host innate immune responses.