In regard to the swine flu infections going on, here are some Open Access PLoS papers articles about flu. In total they provide some useful background reading on flu that anyone can get access to. I have updated the list after prodding from @bpb on Twitter …
- PLoS Medicine – Modeling the Worldwide Spread of Pandemic …
- PLoS Pathogens: Influenza Virus Transmission Is Dependent on …
- PLoS Biology – Whole-Genome Analysis of Human Influenza A Virus …
- PLoS Biology – Pandemic Influenza: The Inside Story
- PLoS Pathogens: H5N1 and 1918 Pandemic Influenza Virus Infection …
- PLoS ONE: Replication and Transmission of H9N2 Influenza Viruses …
- PLoS ONE: Estimation of Influenza Vaccine Effectiveness from …
- PLoS Medicine – Reducing the Impact of the Next Influenza Pandemic …
- PLoS Medicine – A Systematic Analytic Approach to Pandemic …
More from PLoS Pathogens (click here for a link to a title search for “influenza”)
- Cellular Proteins in Influenza Virus Particles
- Evolutionary Dynamics and Emergence of Panzootic H5N1 Influenza Viruses
- Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature
- Changing Selective Pressure during Antigenic Changes in Human Influenza H3
- Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus
- Spatial, Temporal, and Species Variation in Prevalence of Influenza A Viruses in Wild Migratory Birds
- Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918
- Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia
- Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
- Influenza in Migratory Birds and Evidence of Limited Intercontinental Virus Exchange
- The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds
- Phylogenetic Analysis Reveals the Global Migration of Seasonal Influenza A Viruses
- Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
- Estimation of Transmission Parameters of H5N1 Avian Influenza Virus in Chickens
- Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
- Evidence of Infection by H5N2 Highly Pathogenic Avian Influenza Viruses in Healthy Wild Waterfowl
- Superior Immunogenicity of Inactivated Whole Virus H5N1 Influenza Vaccine is Primarily Controlled by Toll-like Receptor Signalling
- Genetic Compatibility and Virulence of Reassortants Derived from Contemporary Avian H5N1 and Human H3N2 Influenza A Viruses
- Domestic Pigs Have Low Susceptibility to H5N1 Highly Pathogenic Avian Influenza Viruses
More from PLoS Medicine
- Influenza in Tropical Regions
- A Comparative Analysis of Influenza Vaccination Programs
- Influenza-Associated Hospitalization in a Subtropical City
- Delaying the International Spread of Pandemic Influenza
- Antiviral Resistance and the Control of Pandemic Influenza
- Influenza-Associated Hospitalization in a Subtropical City
- Health Benefits of Universal Influenza Vaccination Strategy
- Influenza Pandemic Vaccines: Spread Them Thin?
- Mapping Antibody Epitopes of the Avian H5N1 Influenza Virus
- Air Travel and the Spread of Influenza: Authors’ Reply
- Test Your Knowledge: Ten Questions about Influenza
- A Step Closer to Meeting the Threat of Avian Influenza
- Sharing H5N1 Viruses to Stop a Global Influenza Pandemic
- Air Travel and the Spread of Influenza: Important Caveats
- Correction: Air Travel and the Spread of Influenza: Important Caveats
- A Systematic Analytic Approach to Pandemic Influenza Preparedness Planning
- Can Immunity Induced by the Human Influenza Virus N1 Neuraminidase Provide Some Protection from Avian Influenza H5N1 Viruses?
- Optimizing the Dose of Pre-Pandemic Influenza Vaccines to Reduce the Infection Attack Rate
- Pandemic Influenza: Risk of Multiple Introductions and the Need to Prepare for Them
- The Effect of Universal Influenza Immunization on Mortality and Health Care Use
- Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and Containment Interventions
- Priority Setting for Pandemic Influenza: An Analysis of National Preparedness Plans
- Prophylactic and Therapeutic Efficacy of Human Monoclonal Antibodies against H5N1 Influenza
- Monitoring the Impact of Influenza by Age: Emergency Department Fever and Respiratory Complaint Surveillance in New York City
- Antigenic Fingerprinting of H5N1 Avian Influenza Using Convalescent Sera and Monoclonal Antibodies Reveals Potential Vaccine and Diagnostic Targets
- Empirical Evidence for the Effect of Airline Travel on Inter-Regional Influenza Spread in the United States
- Neuraminidase Antibodies and H5N1: Geographic-Dependent Influenza Epidemiology Could Determine Cross-Protection against Emerging Strains
- Live, Attenuated Influenza A H5N1 Candidate Vaccines Provide Broad Cross-Protection in Mice and Ferrets
- The Effects of Influenza Vaccination of Health Care Workers in Nursing Homes: Insights from a Mathematical Model
- Reducing the Impact of the Next Influenza Pandemic Using Household-Based Public Health Interventions
More from PLoS Computational Biology
- Can Influenza Epidemics Be Prevented by Voluntary Vaccination?
- The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics
- Neuraminidase Inhibitor Resistance in Influenza: Assessing the Danger of Its Generation and Spread
- Risk Maps for the Spread of Highly Pathogenic Avian Influenza in Poultry
- Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin
- Detecting Emerging Transmissibility of Avian Influenza Virus in Human Households
- On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
More from PLoS One (see even more here)
- Transmissibility of the Influenza Virus in the 1918 Pandemic
- Synchrony of Clinical and Laboratory Surveillance for Influenza in Hong Kong
- Transdermal Influenza Immunization with Vaccine-Coated Microneedle Arrays
- The Impact of the Unstructured Contacts Component in Influenza Pandemic Modeling
- Influenza Virus in Human Exhaled Breath: An Observational Study
- Panorama Phylogenetic Diversity and Distribution of Type A Influenza Virus
- The Waiting Time for Inter-Country Spread of Pandemic Influenza
- Is Exercise Protective Against Influenza-Associated Mortality?
- Augmented Lung Inflammation Protects against Influenza A Pneumonia
- Predicting Pneumonia and Influenza Mortality from Morbidity Data
- Cross-Clade Protective Immune Responses to Influenza Viruses with H5N1 HA and NA Elicited by an Influenza Virus-Like Particle
- Baseline Levels of Influenza-Specific CD4 Memory T-Cells Affect T-Cell Responses to Influenza Vaccines
- A Biological Model for Influenza Transmission: Pandemic Planning Implications of Asymptomatic Infection and Immunity
- Estimation of Influenza Vaccine Effectiveness from Routine Surveillance Data
- Evolutionarily Conserved Protein Sequences of Influenza A Viruses, Avian and Human, as Vaccine Targets
- Activation of Interleukin-32 Pro-Inflammatory Pathway in Response to Influenza A Virus Infection
- Host Genetic Background Strongly Influences the Response to Influenza A Virus Infections
- Influenza A H5N1 Immigration Is Filtered Out at Some International Borders
- Environmental Factors Contributing to the Spread of H5N1 Avian Influenza in Mainland China
- Population-Wide Emergence of Antiviral Resistance during Pandemic Influenza
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Jonathan Eisen's Lab 
Is the sequence of the latest swine strain available, or would it be considered “classified info?” It’s interesting to see how stable the new mutant is and how it behaves with the human receptors…
I also found this PLoS ONE paper
< HREF="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004566" REL="nofollow"> Development of Epitope-Blocking ELISA for Universal Detection of Antibodies to Human H5N1 Influenza Viruses<>Ramy Aziz
CU, NMPDR- U Chicago, and
AE PLoS ONE
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Thanks a lot for the compilation!
I join the last comment… I’m in Mexico City and think it would be pretty useful to get a hand on those 6 genome sequences they’ve sequenced from California’s patients…
They’re supposed to be available at GISAID database (http://platform.gisaid.org/dante-cms/live/struktur.jdante?aid=1131) after registration (which is running slow) and they can’t be shared…
anyone knows where else can we find them?
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The sequences are in GenBank now (http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html).
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Thank you both…
I was curious to see the mutation, but I hope someone with expertise in modeling can predict an inhibitor soon…
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Even more appeared at GenBank today; they are also at GISAID but with restrictions (it’s not an open database).
Jonathan, thanks for the long list of PLoS reports on flu! But the real question: does this mean I have to give up bacon?
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You should have given up bacon long ago.
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I still can't get on the scared band wagon of swine flu! We have excellent health care– we should not be concerned about this!
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