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VIRAL EVOLUTON
1. Pomeroy
LW, Bjornstad ON, Holmes EC. The Evolutionary and Epidemiological
Dynamics of the Paramyxoviridae. J Mol Evol. 2008 Jan 24;66:98-106.
2. Duffy S, Holmes EC. Phylogenetic Evidence for Rapid Rates of
Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato
Yellow Leaf Curl Virus. Journal of Virology 2008 Jan;82(2):957-65.
3. Duffy S, Shackleton LA, Holmes EC. Rates of evolutionary change
in viruses: patterns and determinants. Nat Rev Genet. 2008 Apr;9(4):267-76.
Epub 2008 Mar 4.
4. Jarman RG, Holmes EC, Rodpradit P, Klungthong C, Gibbons RV,
Nisalak A, Rothman AL, Libraty DH, Ennis FA, Mammen MP Jr, Endy
TP. Microevolution of Dengue Viruses Circulating Among Primary
School Children in Kamphaeng Phet, Thailand. Journal of Virology
2008 Mar 26 [Epub ahead of print]
5. Pardini MI, Jamal LF, Durigon EL, Massad E, Perez JF, Pinho
JR, Holmes EC, de Andrade Zanotto PM. Boosting Virology in Brazil.
PLoS Biology. 2008 Mar 11;6(3):e57.
6. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK,
Holmes EC. The genomic and epidemiological dynamics of human influenza
A virus. Epub April 16 2008.
INFLUENZA
Disease
burden studies in the tropics and temperate climates
1. Alonso, WJ, Viboud C, Simonsen L, Hirano EW, Daufenbach LZ,
Miller MA. Seasonal Patterns of Influenza in Brazil: traveling
wave from the Amazon to the Sub-Tropics. Am J Epidemiol. 2007
Jun 15; 165(12):1434-42. Epub 2007 Mar 16. (see also Tropical
flu spreads the 'wrong way' (News@nature) (alternative
link))
2. Rizzo C, Bella A, Viboud C, Simonsen L, Miller MA, Rota MC,
Salmaso S, Ciofi Degli Atti ML. Trends for Influenza related deaths
during Pandemic and Epidemic Seasons, Italy, 1969-2001. 2007 May
EID 13(5):694-699.
3. Dushoff J, Plotkin JB, Viboud C, Earn DJ, Simonsen L. Mortality
due to influenza in the United States--an annualized regression
approach using multiple-cause mortality data. Am J Epidemiol.
2006 Jan 15;163(2):181-7. Epub 2005 Nov 30.
4. Rizzo C, Viboud C, Montomoli E, Simonsen L, Miller MA. Influenza-related
mortality in the Italian elderly: No decline associated with increasing
vaccination coverage. Vaccine. 2006 Oct 30;24(42-43):6468-75.
Epub 2006 Jul 7.
5. Viboud C, Alonso WJ, Simonsen L. Influenza in Tropical Regions.
Plos Med. March 2006. 3:4:e89.
6. Simonsen, L., Taylor, R., Viboud, C., Dushoff, J., Miller,
M. 2006. US flu mortality estimates are based on solid science.
Bmj 332(7534): 177-8.
7. Dushoff J. Assessing influenza-related mortality: Comment on
Zucs et al. Emerg. Themes Epidemiol., 2:7, 2005.
8. Dushoff J, J. B. Plotkin, S. A. Levin, and D. J. D. Earn. Dynamical
resonance can account for seasonality of influenza epidemics. Proc Natl. Acad. Sci. USA, 101:1691516916, 2004.
9. Reichert TA, Simonsen L, Sharma A, Pardo SA, Fedson DS, Miller
MA. Influenza and the winter increase in mortality in the United
States, 1959-1999. Am J Epidemiol. 2004 Sep 1;160(5):492-502.
10. Viboud C, Pakdaman K., Boëlle P-Y., Myers M., Wilson
M. L., Valleron A-J., Flahault A. Association of influenza epidemics
with global climate variability 2004. Eur J Epidemiol 19(11):
1055-9.
11. Simonsen L, Blackwelder WC, Reichert TA, Miller MA. Estimating
deaths due to influenza and respiratory syncytial virus. JAMA.
2003 May 21;289(19):2499-500
Transmission
dynamics of influenza virus and disease
1. Viboud C, Tam T, Fleming D, Handel A, Miller M, Simonsen L.
Transmissibility and mortality impact of epidemic and pandemic
influenza, with emphasis on the unusually deadly 1951 epidemic.
Vaccine. 2006 Nov 10;24(44-46):6701-7. Epub 2006 Jun 9.
2. Viboud C, Tam T, Fleming D, Miller M, Simonsen L. 1951 influenza
epidemic, England and Wales, Canada and the United States. Emerg
Infect Dis 2006 Apr;12(4):661-8
3. Viboud C, Bjørnstad O, Smith DL, Simonsen L, Miller
MA, Grenfell B. Synchrony, waves, and spatial hierarchies in the
spread of influenza. Science Apr 21;312(5772):447-51. Epub 2006
Mar 30.
4. Viboud C, Miller MA, Grenfell B, Bjørnstad O, Simonsen
L. Air travel and the spread of influenza: Important Caveats.
PLos Med Nov 2006;3(11):e503.
5. Viboud C, Boëlle PY, Cauchemez S, Lavenu A, Valleron AJ,
Flahault A., Carrat F. Risk factors of influenza transmission
in households. Br J Gen Pract 2004;54(506): 684-9.
6. Viboud C, Boëlle P-Y., Pakdaman KP., Carrat F, Valleron
A-J., Flahault A. Correlations over time and space of influenza
epidemics in the USA, France and Australia: 1972-97. Emerging
Infectious Diseases. Emerg Infect Dis 2004;10(1): 32-9.
7. Cauchemez S, Carrat F, Viboud C, Valleron AJ, Boëlle PY.
A Bayesian MCMC approach to study transmission of influenza: application
to household longitudinal data. Stat Med 2004; 23(22): 3469-87.
8. Viboud C, Boëlle P-Y., Carrat F., Valleron A-J., Flahault
A. Prediction of the spread of influenza epidemics by the method
of analogues. American Journal of Epidemiology 2003. 158:10; 996-1006.
Vaccine
impact and control studies on various target populations including
indirect effects
1. Le Menach A, Vergu E, Grais RF, Smith DL, Flahault A. Key strategies
for reducing spread of avian influenza among commercial poultry
holdings: lessons for transmission to humans. Proceedings of the
Royal Society of London, B, Biological Sciences. DOI: 10.1098/rspb.2006.3609.
2. Goodwin K, Viboud C, Simonsen L. Antibody response to influenza
vaccination in the elderly: A quantitative review. Vaccine. 2006
Feb 20;24(8):1159-69. Epub 2005 Sep 19.
3. Simonsen L, Reichert TA, Viboud C, Blackwelder WC, Taylor RJ,
Miller MA. Impact of Influenza Vaccination on Seasonal Mortality
in the US Elderly Population. Archives of Internal Medicine 2005;165(3):265-72.
4. Simonsen L, Viboud C, Blackwelder WC, Taylor RJ, Miller MA.
Researchers defend influenza vaccine study.Infectious Diseases
News, Aug 2005 (Guest Editorial)
5. Reichert TA. The Japanese program of vaccination of schoolchildren
against influenza:implications for control of the disease. Semin
Pediatr Infect Dis. 2002 Apr;13(2):104-11.
6. Reichert TA, Sugaya, N, Fedson DS, Glezen WP, Simonsen L, Tashiro
M. The Japanese Experience with Vaccinating School Children Against
Influenza. 2001 March NEJM 344(12):889-96.
Influenza
virus evolutionary patterns
1. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic
analysis reveals the global migration of seasonal influenza A
viruses. PLoS Pathog. 2007 Sep 14;3(9):1220-8.
2. Nelson MI, Holmes EC. The evolution of epidemic influenza.
2007 March Nature 8:196-205.
3. Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution
shapes the phylodynamics of interpandemic influenza A (H3N2) in
humans. Science. 2006 Dec 22;314(5807):1898-903
4. Holmes EC, Lipman DJ, Zamarin D & Yewdell JW. Comment on
"Large Scale Sequence Analysis of Avian Influenza Isolates".
Science 15 Sept 2006; 313:1573b.
5. Chen R & Holmes EC. Avian influenza virus exhibits rapid
evolutionary dynamics. Molecular Biology and Evolution 2006 Dec;23(12):2336-41.
6. Kuiken T, Holmes EC, McCauley J, Rimmelzwaan GF, Williams CS
& Grenfell BT. Host species barriers to influenza virus infections.
Science 2006 312: 394-397.
7. Wolf YL, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long Intervals
of Stasis Punctuated by Bursts of Positive Selection in the Seasonal
Evolution of Influenza A Virus. Biology Direct, October 26, 2006.
8. S. A. Levin, Dushoff J, and J. B. Plotkin. Evolution and persistence
of influenza A and other diseases. Math. Bioscience, 188:1728,
2004.
9. J. B. Plotkin and Dushoff J. Codon bias and frequency-dependent
selection on the hemagglutinin epitopes of influenza A virus.
Proc. Natl. Acad. Sci. USA, 100:71527157, 2003.
10. D. J. D. Earn, Dushoff J, and S. A. Levin. Ecology and evolution
of the flu. 2002. Trends Ecol. Evol. 17:334-40, 2002.
11. J. B. Plotkin, Dushoff J, and S. A. Levin. Hemagglutinin sequence
clusters and the antigenic evolution of influenza A virus. 2002.
Proc. Natl. Acad. Sci. USA, 99:6263-68.
Pandemic
influenza and other topics
1. Chowell G, Bettencourt LM, Johnson N, Alonso WJ, Viboud C.
The 1918-1919 influenza pandemic in England and Wales: spatial
patterns in transmissibility and mortality impact. Proc Biol Sci.
2008 Mar 7;275(1634):501-509.
2. Andreasen V, Viboud C, Simonsen L. Epidemiologic characterization
of the 1918 influenza pandemic summer wave in Copenhagen: implications
for pandemic control strategies. J Infect Dis. 2008 Jan 15;197(2):270-8.
3. Gottfredsson M, Halldórsson BV, Jónsson S, Kristjánsson
M, Kristjánsson K, Kristinsson KG, Löve A, Blöndal
T, Viboud C, Thorvaldsson S, Helgason A, Gulcher JR, Stefánsson
K, Jónsdóttir I. Lessons from the past: Familial
aggregation analysis of fatal pandemic influenza (Spanish flu)
in Iceland in 1918.Proc Natl Acad Sci U S A. 2008 Jan 23; [Epub
ahead of print]
4. Reichert TA. Preparing for the next influenza pandemic: lessons
from multinational data. Pediatr Infect Dis J. 2005 Nov;24(11
Suppl):S228-31. Review.
5. Viboud C, Grais RF, Lafont BA, Miller MA, et al. Multinational
impact of the 1968 Hong Kong influenza pandemic: evidence for
a smoldering pandemic. J Infect Dis. 2005; 192(2): 233-48.
6. Simonsen L, Viboud C, Taylor R. Influenza vaccination in elderly
people. Lancet. 2005 Dec 17;366(9503):2086.
7. Simonsen L, Olson DR, Viboud C, Heiman E, Miller MA, Reichert
TA. Pandemic influenza and mortality: past evidence and projections
for the future. In: Institute of Medicine's Pandemic Influenza:
Assessing Capabilities for Prevention and Response. Forum on Microbial
Threats series, (2004). 1-26-46.
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