280. Sheu, T. G., V. M. Deyde, M. Okomo-Adhiambo, R. J. Garten, X. Xu, R. A. Bright, E. N. Butler, T. R. Wallis, A. I. Klimov, and L. V. Gubareva. 2008. Surveillance for
neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Antimicrob Agents Chemother 52:3284-92.
281. Shinya, K., M. Ebina, S. Yamada, M. Ono, N. Kasai, and Y. Kawaoka. 2006. Avian flu:
influenza virus receptors in the human airway. Nature 440:435-6.
282. Shinya, K., S. Hamm, M. Hatta, H. Ito, T. Ito, and Y. Kawaoka. 2004. PB2 amino acid at
position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice. Virology 320:258-66.
283. Shornick, L. P., A. G. Wells, Y. Zhang, A. C. Patel, G. Huang, K. Takami, M. Sosa, N. A. Shukla, E. Agapov, and M. J. Holtzman. 2008. Airway epithelial versus immune cell Stat1
function for innate defense against respiratory viral infection. J Immunol 180:3319-28. 284. Sims, A. C., R. S. Baric, B. Yount, S. E. Burkett, P. L. Collins, and R. J. Pickles. 2005.
Severe acute respiratory syndrome coronavirus infection of human ciliated airway epithelia: role of ciliated cells in viral spread in the conducting airways of the lungs. J Virol 79:15511- 24.
285. Singhera, G. K., T. S. Chan, J. Y. Cheng, T. Z. Vitalis, K. J. Hamann, and D. R.
Dorscheid. 2006. Apoptosis of viral-infected airway epithelial cells limit viral production and
is altered by corticosteroid exposure. Respir Res 7:78.
286. Sinn, P. L., G. Williams, S. Vongpunsawad, R. Cattaneo, and P. B. McCray, Jr. 2002.
Measles virus preferentially transduces the basolateral surface of well-differentiated human airway epithelia. J Virol 76:2403-9.
287. Skiadopoulos, M. H., A. C. Schmidt, J. M. Riggs, S. R. Surman, W. R. Elkins, M. St Claire, P. L. Collins, and B. R. Murphy. 2003. Determinants of the host range restriction of
replication of bovine parainfluenza virus type 3 in rhesus monkeys are polygenic. J Virol
77:1141-8.
288. Skiadopoulos, M. H., T. Tao, S. R. Surman, P. L. Collins, and B. R. Murphy. 1999.
Generation of a parainfluenza virus type 1 vaccine candidate by replacing the HN and F glycoproteins of the live-attenuated PIV3 cp45 vaccine virus with their PIV1 counterparts. Vaccine 18:503-10.
289. Skiadopoulos, M. H., L. Vogel, J. M. Riggs, S. R. Surman, P. L. Collins, and B. R. Murphy. 2003. The genome length of human parainfluenza virus type 2 follows the rule of
six, and recombinant viruses recovered from non-polyhexameric-length antigenomic cDNAs contain a biased distribution of correcting mutations. J Virol 77:270-9.
290. Smith, C. B., R. H. Purcell, J. A. Bellanti, and R. M. Chanock. 1966. Protective effect of
antibody to parainfluenza type 1 virus. N Engl J Med 275:1145-52.
291. Solomon, T. 2003. Exotic and emerging viral encephalitides. Curr Opin Neurol 16:411-8.
292. Spann, K. M., K. C. Tran, B. Chi, R. L. Rabin, and P. L. Collins. 2004. Suppression of the
induction of alpha, beta, and lambda interferons by the NS1 and NS2 proteins of human respiratory syncytial virus in human epithelial cells and macrophages [corrected]. J Virol
78:4363-9.
293. Spann, K. M., K. C. Tran, and P. L. Collins. 2005. Effects of nonstructural proteins NS1 and
NS2 of human respiratory syncytial virus on interferon regulatory factor 3, NF-kappaB, and proinflammatory cytokines. J Virol 79:5353-62.
294. Spicer, A. P., T. Duhig, B. S. Chilton, and S. J. Gendler. 1995. Analysis of mammalian
MUC1 genes reveals potential functionally important domains. Mamm Genome 6:885-8. 295. Spicer, A. P., G. Parry, S. Patton, and S. J. Gendler. 1991. Molecular cloning and analysis
of the mouse homologue of the tumor-associated mucin, MUC1, reveals conservation of potential O-glycosylation sites, transmembrane, and cytoplasmic domains and a loss of minisatellite-like polymorphism. J Biol Chem 266:15099-109.
296. Spicer, A. P., G. J. Rowse, T. K. Lidner, and S. J. Gendler. 1995. Delayed mammary
tumor progression in Muc-1 null mice. J Biol Chem 270:30093-101.
297. Steel, J., A. C. Lowen, S. Mubareka, and P. Palese. 2009. Transmission of influenza virus
in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. PLoS Pathog
5:e1000252.
298. Stevens, J., O. Blixt, T. M. Tumpey, J. K. Taubenberger, J. C. Paulson, and I. A. Wilson.
2006. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science 312:404-10.
299. Stojdl, D. F., B. D. Lichty, B. R. tenOever, J. M. Paterson, A. T. Power, S. Knowles, R. Marius, J. Reynard, L. Poliquin, H. Atkins, E. G. Brown, R. K. Durbin, J. E. Durbin, J. Hiscott, and J. C. Bell. 2003. VSV strains with defects in their ability to shutdown innate
immunity are potent systemic anti-cancer agents. Cancer Cell 4:263-75.
300. Stonebraker, J. R., D. Wagner, R. W. Lefensty, K. Burns, S. J. Gendler, J. M. Bergelson, R. C. Boucher, W. K. O'Neal, and R. J. Pickles. 2004. Glycocalyx restricts adenoviral vector
access to apical receptors expressed on respiratory epithelium in vitro and in vivo: role for tethered mucins as barriers to lumenal infection. J Virol 78:13755-68.
301. Sturm-Ramirez, K. M., T. Ellis, B. Bousfield, L. Bissett, K. Dyrting, J. E. Rehg, L. Poon, Y. Guan, M. Peiris, and R. G. Webster. 2004. Reemerging H5N1 influenza viruses in Hong
Kong in 2002 are highly pathogenic to ducks. J Virol 78:4892-901.
302. Subbarao, E. K., W. London, and B. R. Murphy. 1993. A single amino acid in the PB2 gene
303. Suzuki, T., A. Portner, R. A. Scroggs, M. Uchikawa, N. Koyama, K. Matsuo, Y. Suzuki, and T. Takimoto. 2001. Receptor specificities of human respiroviruses. J Virol 75:4604-13.
304. Swayne, D. E., and D. L. Suarez. 2000. Highly pathogenic avian influenza. Rev Sci Tech 19:463-82.
305. Takeuchi, K., T. Komatsu, J. Yokoo, A. Kato, T. Shioda, Y. Nagai, and B. Gotoh. 2001.
Sendai virus C protein physically associates with Stat1. Genes Cells 6:545-57. 306. Taniguchi, T., and A. Takaoka. 2002. The interferon-alpha/beta system in antiviral
responses: a multimodal machinery of gene regulation by the IRF family of transcription factors. Curr Opin Immunol 14:111-6.
307. Taubenberger, J. K., and D. M. Morens. 2006. 1918 Influenza: the mother of all pandemics.
Emerg Infect Dis 12:15-22.
308. Taubenberger, J. K., and D. M. Morens. 2008. The pathology of influenza virus infections.
Annu Rev Pathol 3:499-522.
309. Thery, C., M. Boussac, P. Veron, P. Ricciardi-Castagnoli, G. Raposo, J. Garin, and S. Amigorena. 2001. Proteomic analysis of dendritic cell-derived exosomes: a secreted
subcellular compartment distinct from apoptotic vesicles. J Immunol 166:7309-18.
310. Thomas, P. G., P. Dash, J. R. Aldridge, Jr., A. H. Ellebedy, C. Reynolds, A. J. Funk, W. J. Martin, M. Lamkanfi, R. J. Webby, K. L. Boyd, P. C. Doherty, and T. D. Kanneganti.
2009. The intracellular sensor NLRP3 mediates key innate and healing responses to influenza A virus via the regulation of caspase-1. Immunity 30:566-75.
311. Thompson, C. I., W. S. Barclay, and M. C. Zambon. 2004. Changes in in vitro susceptibility
of influenza A H3N2 viruses to a neuraminidase inhibitor drug during evolution in the human host. J Antimicrob Chemother 53:759-65.
312. Thompson, C. I., W. S. Barclay, M. C. Zambon, and R. J. Pickles. 2006. Infection of
human airway epithelium by human and avian strains of influenza a virus. J Virol 80:8060-8. 313. Travis, S. M., B. A. Conway, J. Zabner, J. J. Smith, N. N. Anderson, P. K. Singh, E. P.
Greenberg, and M. J. Welsh. 1999. Activity of abundant antimicrobials of the human airway.
Am J Respir Cell Mol Biol 20:872-9.
314. Tu, J., H. Zhou, T. Jiang, C. Li, A. Zhang, X. Guo, W. Zou, H. Chen, and M. Jin. 2009.
Isolation and molecular characterization of equine H3N8 influenza viruses from pigs in China. Arch Virol 154:887-90.
315. Tugizov, S. M., J. W. Berline, and J. M. Palefsky. 2003. Epstein-Barr virus infection of
polarized tongue and nasopharyngeal epithelial cells. Nat Med 9:307-14.
316. Tumpey, T. M., C. F. Basler, P. V. Aguilar, H. Zeng, A. Solorzano, D. E. Swayne, N. J. Cox, J. M. Katz, J. K. Taubenberger, P. Palese, and A. Garcia-Sastre. 2005.
Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science
310:77-80.
317. Tumpey, T. M., T. R. Maines, N. Van Hoeven, L. Glaser, A. Solorzano, C. Pappas, N. J. Cox, D. E. Swayne, P. Palese, J. M. Katz, and A. Garcia-Sastre. 2007. A two-amino acid
change in the hemagglutinin of the 1918 influenza virus abolishes transmission. Science
318. Tuvim, M. J., S. E. Evans, C. G. Clement, B. F. Dickey, and B. E. Gilbert. 2009.
Augmented lung inflammation protects against influenza A pneumonia. PLoS One 4:e4176. 319. Ueno, K., T. Koga, K. Kato, D. T. Golenbock, S. J. Gendler, H. Kai, and K. C. Kim. 2008.
MUC1 mucin is a negative regulator of toll-like receptor signaling. Am J Respir Cell Mol Biol
38:263-8.
320. Uiprasertkul, M., P. Puthavathana, K. Sangsiriwut, P. Pooruk, K. Srisook, M. Peiris, J. M. Nicholls, K. Chokephaibulkit, N. Vanprapar, and P. Auewarakul. 2005. Influenza A
H5N1 replication sites in humans. Emerg Infect Dis 11:1036-41.
321. Ulane, C. M., A. Kentsis, C. D. Cruz, J. P. Parisien, K. L. Schneider, and C. M. Horvath.
2005. Composition and assembly of STAT-targeting ubiquitin ligase complexes:
paramyxovirus V protein carboxyl terminus is an oligomerization domain. J Virol 79:10180-9. 322. Valadi, H., K. Ekstrom, A. Bossios, M. Sjostrand, J. J. Lee, and J. O. Lotvall. 2007.
Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9:654-9.
323. Valdivia-Arenas, M., A. Amer, L. Henning, M. Wewers, and L. Schlesinger. 2007. Lung
infections and innate host defense. Drug Discov Today Dis Mech 4:73-81.
324. Van Cleve, W., E. Amaro-Carambot, S. R. Surman, J. Bekisz, P. L. Collins, K. C. Zoon, B. R. Murphy, M. H. Skiadopoulos, and E. J. Bartlett. 2006. Attenuating mutations in the
P/C gene of human parainfluenza virus type 1 (HPIV1) vaccine candidates abrogate the inhibition of both induction and signaling of type I interferon (IFN) by wild-type HPIV1. Virology 352:61-73.
325. Van Cleve, W., E. Amaro-Carambot, S. R. Surman, J. Bekisz, P. L. Collins, K. C. Zoon, B. R. Murphy, M. H. Skiadopoulos, and E. J. Bartlett. 2006. Attenuating mutations in the
P/C gene of human parainfluenza virus type 1 (HPIV1) vaccine candidates abrogate the inhibition of both induction and signaling of type I interferon (IFN) by wild-type HPIV1. Virology. 352: 61-73.
326. Van Hoeven, N., C. Pappas, J. A. Belser, T. R. Maines, H. Zeng, A. Garcia-Sastre, R. Sasisekharan, J. M. Katz, and T. M. Tumpey. 2009. Human HA and polymerase subunit
PB2 proteins confer transmission of an avian influenza virus through the air. Proc Natl Acad Sci U S A 106:3366-71.
327. Varkey, J. B., and B. Varkey. 2008. Viral infections in patients with chronic obstructive
pulmonary disease. Curr Opin Pulm Med 14:89-94.
328. Vines, A., K. Wells, M. Matrosovich, M. R. Castrucci, T. Ito, and Y. Kawaoka. 1998. The
role of influenza A virus hemagglutinin residues 226 and 228 in receptor specificity and host range restriction. J Virol 72:7626-31.
329. Wagner, R., M. Matrosovich, and H. D. Klenk. 2002. Functional balance between
haemagglutinin and neuraminidase in influenza virus infections. Rev Med Virol 12:159-66. 330. Walters, R. W., P. Freimuth, T. O. Moninger, I. Ganske, J. Zabner, and M. J. Welsh. 2002.
Adenovirus fiber disrupts CAR-mediated intercellular adhesion allowing virus escape. Cell
110:789-99.
331. Wan, H., and D. R. Perez. 2007. Amino acid 226 in the hemagglutinin of H9N2 influenza
viruses determines cell tropism and replication in human airway epithelial cells. J Virol
332. Wang, H., E. P. Lillehoj, and K. C. Kim. 2003. Identification of four sites of stimulated
tyrosine phosphorylation in the MUC1 cytoplasmic tail. Biochem Biophys Res Commun
310:341-6.
333. Wang, H., E. P. Lillehoj, and K. C. Kim. 2004. MUC1 tyrosine phosphorylation activates the
extracellular signal-regulated kinase. Biochem Biophys Res Commun 321:448-54.
334. Wang, Y. H., Y. C. Huang, L. Y. Chang, H. T. Kao, P. Y. Lin, C. G. Huang, and T. Y. Lin.
2003. Clinical characteristics of children with influenza A virus infection requiring hospitalization. J Microbiol Immunol Infect 36:111-6.
335. Wat, D., C. Gelder, S. Hibbitts, F. Cafferty, I. Bowler, M. Pierrepoint, R. Evans, and I. Doull. 2008. The role of respiratory viruses in cystic fibrosis. J Cyst Fibros. 7: 320-8.
336. Weber, F., G. Kochs, and O. Haller. 2004. Inverse interference: how viruses fight the
interferon system. Viral Immunol 17:498-515.
337. Webster, R. G., W. J. Bean, O. T. Gorman, T. M. Chambers, and Y. Kawaoka. 1992.
Evolution and ecology of influenza A viruses. Microbiol Rev 56:152-79.
338. Weinberg, G. A., C. B. Hall, M. K. Iwane, K. A. Poehling, K. M. Edwards, M. R. Griffin, M. A. Staat, A. T. Curns, D. D. Erdman, and P. G. Szilagyi. 2009. Parainfluenza virus infection
of young children: estimates of the population-based burden of hospitalization. J Pediatr
154:694-9.
339. Weingartl, H. M., R. A. Albrecht, K. M. Lager, S. Babiuk, P. Marszal, J. Neufeld, C. Embury-Hyatt, P. Lekcharoensuk, T. M. Tumpey, A. Garcia-Sastre, and J. A. Richt.
2009. Experimental infection of pigs with the human 1918 pandemic influenza virus. J Virol
83:4287-96.
340. Welliver, R., D. T. Wong, T. S. Choi, and P. L. Ogra. 1982. Natural history of parainfluenza
virus infection in childhood. J Pediatr 101:180-7.
341. Whelan, S. P., J. N. Barr, and G. W. Wertz. 2004. Transcription and replication of
nonsegmented negative-strand RNA viruses. Curr Top Microbiol Immunol 283:61-119. 342. White, M. R., E. J. Helmerhorst, A. Ligtenberg, M. Karpel, T. Tecle, W. L. Siqueira, F. G.
Oppenheim, and K. L. Hartshorn. 2009. Multiple components contribute to ability of saliva
to inhibit influenza viruses. Oral Microbiol Immunol 24:18-24.
343. Whiteley A, M. D., Legastelois I, Campitelle L, Donatelli I, et al. 2007. Generation of
candidate human influenza vaccine strains in cell culture--rehearsing the European response to an H7N1 pandemic threat. Influenza and Other Respiratory Viruses 1:157-166.
344. WHO, posting date. Cumulative Number of Confirmed Human Cases of Avian Influenza
A/(H5N1) Reported to WHO, 2 June 2009. [Online.] 345. WHO. 2008. The global burden of disease: 2004 update.
346. WHO. 2009. Influenza A (H1N1) update 48.
347. Wright, K. E., G. A. Wilson, D. Novosad, C. Dimock, D. Tan, and J. M. Weber. 1995.
Typing and subtyping of influenza viruses in clinical samples by PCR. J Clin Microbiol
348. Wright, P. F., M. R. Ikizler, R. A. Gonzales, K. N. Carroll, J. E. Johnson, and J. A. Werkhaven. 2005. Growth of respiratory syncytial virus in primary epithelial cells from the
human respiratory tract. J Virol 79:8651-4.
349. Wright, P. I., M.; Carroll, K.N.; and Endo, Y. 1996. Interactions of viruses with respiratory
epithelial cells. Seminars in Virology 7:227-35.
350. Xu, L. G., Y. Y. Wang, K. J. Han, L. Y. Li, Z. Zhai, and H. B. Shu. 2005. VISA is an adapter
protein required for virus-triggered IFN-beta signaling. Mol Cell 19:727-40.
351. Yao, Y., L. J. Mingay, J. W. McCauley, and W. S. Barclay. 2001. Sequences in influenza A
virus PB2 protein that determine productive infection for an avian influenza virus in mouse and human cell lines. J Virol 75:5410-5.
352. Yen, H. L., L. M. Herlocher, E. Hoffmann, M. N. Matrosovich, A. S. Monto, R. G. Webster, and E. A. Govorkova. 2005. Neuraminidase inhibitor-resistant influenza viruses may differ
substantially in fitness and transmissibility. Antimicrob Agents Chemother 49:4075-84. 353. Yen, H. L., A. S. Lipatov, N. A. Ilyushina, E. A. Govorkova, J. Franks, N. Yilmaz, A.
Douglas, A. Hay, S. Krauss, J. E. Rehg, E. Hoffmann, and R. G. Webster. 2007.
Inefficient transmission of H5N1 influenza viruses in a ferret contact model. J Virol 81:6890-8. 354. Yeow, W. S., W. C. Au, W. J. Lowther, and P. M. Pitha. 2001. Downregulation of IRF-3
levels by ribozyme modulates the profile of IFNA subtypes expressed in infected human cells. J Virol 75:3021-7.
355. Yie, J., K. Senger, and D. Thanos. 1999. Mechanism by which the IFN-beta enhanceosome
activates transcription. Proc Natl Acad Sci U S A 96:13108-13.
356. Yoneyama, M., M. Kikuchi, T. Natsukawa, N. Shinobu, T. Imaizumi, M. Miyagishi, K. Taira, S. Akira, and T. Fujita. 2004. The RNA helicase RIG-I has an essential function in
double-stranded RNA-induced innate antiviral responses. Nat Immunol 5:730-7.
357. Yuta, A., W. J. Doyle, E. Gaumond, M. Ali, L. Tamarkin, J. N. Baraniuk, M. Van Deusen, S. Cohen, and D. P. Skoner. 1998. Rhinovirus infection induces mucus hypersecretion. Am
J Physiol 274:L1017-23.
358. Zambon, M. C., J. D. Stockton, J. P. Clewley, and D. M. Fleming. 2001. Contribution of
influenza and respiratory syncytial virus to community cases of influenza-like illness: an observational study. Lancet 358:1410-6.
359. Zhang, L., A. Bukreyev, C. I. Thompson, B. Watson, M. E. Peeples, P. L. Collins, and R. J. Pickles. 2005. Infection of ciliated cells by human parainfluenza virus type 3 in an in vitro
model of human airway epithelium. J Virol 79:1113-24.
360. Zhang, L., M. E. Peeples, R. C. Boucher, P. L. Collins, and R. J. Pickles. 2002.
Respiratory syncytial virus infection of human airway epithelial cells is polarized, specific to ciliated cells, and without obvious cytopathology. J Virol 76:5654-66.
361. Zhang, Z., J. Zhang, K. Huang, K. S. Li, K. Y. Yuen, Y. Guan, H. Chen, and W. F. Ng.
2009. Systemic infection of avian influenza A virus H5N1 subtype in humans. Hum Pathol