Research policy

The Initiative on Genomics & Public Health

Genomics in WHO

Global Influenza Programme

  • Surveillance and epidemiology: GIP uses molecular epidemiology, including evaluation of phylogenic trees and sequence/homology assessments, to answer a variety of questions around seasonal, pandemic, and zoonotic influenza viruses. Whole genome sequencing is an important tool to identify the linage of novel viruses as it may indicate the potential origin of the virus. Molecular information has been used as evidence for human to human transmission of HPAI H5N1 virus and to screen for antiviral resistance markers e.g. H275Y in NA for oseltamivir resistance. During the influenza pandemic in 2009, genomic analysis provided the best evidence of effectiveness of school closures in breaking the disease transmission in Japan.
  • Diagnostics: GIP continually evaluates molecular genetic data from around the world to look for nucleotide changes that might affect or signal impacts to the effectiveness of influenza testing protocols and reagents (including PCR primers), and to update them as necessary.
  • Vaccine development: GIP analyses phylogenetic data on seasonal, pandemic, and zoonotic influenza viruses (as supplementary to antigenic characteristics) to select those viruses that are most appropriate to include in seasonal or pandemic influenza vaccines. Reverse genetics are used to develop and prepare available high-growth reassortants as candidate vaccine viruses.
  • Risk assessment: GIP analyses molecular characteristics in order to identify mutations and markers of concern, such as those associated with increased pathogenicity, transmissibility, and antiviral resistance in humans. As well, newly identified mutations and markers are linked to associated epidemiological and clinical characteristics to evaluate their public health risk, and conversely, viruses associated with severe disease and other clinical characteristics if concern are evaluated in order to identify commonalities in the molecular characteristics.

On an ongoing basis, GIP is involved in global monitoring of human seasonal, pandemic, and zoonotic influenza viruses through the Global Influenza Surveillance Network, comprised by WHO Collaborating Centres and National Influenza Centres. In response to specific virological events of concern, ad-hoc teleconferences with relevant GISN members and external partners are held. Activities to inform the twice yearly selection of influenza vaccine viruses, including collaboration with ERLs and reassortant developing laboratories, are coordinated by GIP. GIP also coordinates a variety of working groups, including a PCR working group to evaluate on an ongoing basis any sequence changes potentially affecting PCR test results and to provide guidance to GISN on different PCR methods. Through collaboration with the animal health sector, primarily the OIE/FAO network of expertise on animal influenza (OFFLU), GIP receives information on influenza viruses circulating in animal populations. Virological information from strains isolated from humans and animals are assessed in the context of epidemiological and clinical information during monthly integrated risk assessments.


GIP works with many partners inside and outside WHO, including WHO Collaborating Centres, National Influenza Centres, H5 Reference Laboratories, OFFLU and OFFLU institutions, OIE, FAO, WHO IVR, and a variety of academic and research institutions.