Influenza Infection

Systems Medicine       

of Infectious Diseases

Research and Consulting Group

Influenza Infection

Implications to Coinfections and the Elderly

Overview: The recent outbreaks of H1N1 (swine flu), H5N1 (bird flu), and H7N9 virus infections have underlined the impact of influenza A virus infections and have shown that influenza A virus is a major threat to human health.  For example, the Mexican Institute for social security reported in 2009 a total of 117,626 people with influenza-like illness. CDC reports also showed that seasonal influenza infections account for annual hospitalization of 226,000 individuals in the USA


State  of the art: The high degree of variability of the influenza virus due to  mutations  and secondary bacterial infections (Streptococcus pneumoniae and Staphylococcus aureus) are the leading cause of illness and death during influenza infection. Furthermore, the consequences of influenza virus infection are generally more severe in individuals over 65 years of age (the elderly).

Our research in Influenza Virus infection aims to:


  • identify clinical markers that are missing to indicate the course of the disease and potential complications


  • provide quantitative understanding of  influenza virus pathogenesis and its shift in the elderly


  • dissect the mechanisms that impair Streptococcus pneumoniae clearance after acute influenza infection

Machine Learning for Multiscale Analysis of Biomedical Data

Relevant Publications in this Field:



  • C. Parra-Rojas, V.K. Nguyen, G. Hernandez-Mejia, E.A. Hernandez-Vargas. Neuraminidase inhibitors in influenza treatment and prevention– Is it time to call it a day?. Viruses.  10(9): 1-13, 2018    - [Link]


  • S. Duvigneau, N. Sharma-Chawla,      A. Boianelli,   S. Stegemann-Koniszewski, V. K. Nguyen,  D. Bruder, and E. A. Hernandez-Vargas. Hierarchical effects of pro-inflammatory cytokines on the post-influenza susceptibility to pneumococcal coinfection. Scientific Reports. Vol. 6(37045):1-11,        2016   [PDF]


  • A.E.S. Almocera, C. Parra-Rojas, G. Hernandez-Mejia, E.A. Hernandez-Vargas. The trichotomy of pneumococcal infection outcomes in the host. Communications in Nonlinear Science and Numerical Simulation. Vol. 73:1-13, 2019 [Link]


  • A. Boianelli,  N. Sharma-Chawla,  D. Bruder, and E.A. Hernandez-Vargas. Oseltamivir PK/PD Modeling and Simulation to Evaluate Treatment Strategies against Influenza-Pneumococcus Coinfection. Frontiers in Cellular and Infection Microbioly. Vol.  6(60):1-11, 2016   [PDF]


  • E.A. Hernandez-Vargas, E. Wilk, L. Canini, F. Toapanta, S. Binder, A. Uvarovskii, T. Ross, C.A. Guzman, A.S. Perelson,  and M. Meyer-Hermann. Effects of aging on influenza virus infection dynamics. Journal of Virology, Vol.88 (8), 2014 [PDF]


  • A. Boianelli, K. Nguyen, T. Ebensen, K. Schulze, E. Wilk, N. Sharma, S. Stegemann-Koniszewski, D. Bruder, F. Toapanta, C. A. Guzman, M. Meyer-Hermann and E. A. Hernandez-Vargas. Modeling Influenza Virus Infection: A Roadmap for Influenza Research. Viruses. 7:5274-5304, 2015   [PDF]