As part of the Influenza Genome Sequencing Project, JCVI will be sequencing a large number of high yield influenza reassortants created in the lab of Dr. Doris Bucher at New York Medical College. Dr. Bucher’s lab has prepared the type A H3N2 high yield reassortants (hyrs) for the influenza vaccine for the past several years, both within the US and world wide.
The Bucher lab continues the tradition of preparing the hyrs as developed by preeminent influenza virologist Dr. Edwin D. Kilbourne (1920-2011). Dr Kilbourne developed and applied the technology to produce the first genetically engineered influenza vaccines; these vaccines, which typically change yearly, have been in use for over 40 years.
JCVI will be sequencing approximately 46 hyrs from Dr. Kilbourne’s collection which was assembled as part of the Kilbourne/New York Medical College Archive of Influenza Virus Reassortants, Mutants, and Antisera. Detailed information is provided for every virus stored in the archive with information at the archive website (www.flu-archive.org). The assembly of the archive was sponsored by the NIAID and viruses in the archive are available through BEI Resources (www.beiresources.org). All sequence data and meta data associated with the hyrs sequenced at JCVI will be made publically available in the Influenza Research Database (www.fludb.org).
Dr. Kilbourne passed away on February 21, 2001 at the age of 90. A eulogy in remembrance of Dr. Kilbourne and his pioneering work in the field of influenza virology can be found at: http://jid.oxfordjournals.org/content/204/2/185.full
Posts by Rebecca Halpin
The advent of large amounts of influenza genomic sequence data produced by the Influenza Genome Sequencing Project (IGSP) has led to new concepts regarding influenza viral diversity. It was previously believed that a single influenza lineage entered a human population at the start of an influenza season and gradually spread over time; however, recent analyses of influenza genomes revealed that multiple viral lineages co-circulate within individual populations throughout an influenza season. These different lineages appear to be continuously introduced which provides the opportunity for frequent intra-subtype reassortment. Interestingly, similar levels of influenza diversity exist within populations of both large metropolitan cities and small towns (E.C. Holmes, 2009). Multiple, diverse viral lineages of the same subtype have been observed co-circulating in urban locations comprised of expansive travel networks and rural locations that are geographically isolated.
Additional analyses of complete influenza genomes have led to a ‘source-sink’ model of influenza seasonality. In this model, a global, human ‘source’ population of influenza viruses is thought to be responsible for the antigenic variants that ignite seasonal epidemics in the ‘sink’ populations of the Northern and Southern hemispheres (A. Rambaut, 2008; E. C. Holmes, 2009). The geographic regions of East and Southeast Asia have been hypothesized as potential sources of influenza due to the large, dense human populations which would allow influenza viruses to antigenically evolve with maximum efficiency. These locales may be the focus of future surveillance efforts aimed at identifying emergent influenza viruses that have evolved mechanisms to evade current vaccines.
Studies using whole genomic influenza sequence data produced by the Influenza Genome Sequencing Project (IGSP) have focused mainly on influenza evolution and epidemiology. For instance, IGSP data has provided important insight into the frequency of intrasubtype reassortment (in which reassortment occurs between different segments of the Influenza genome). The data suggests that reassortment occurs frequently, leading to viruses with altered antigenic properties that may evade current vaccines. Thus, it is useful to study not only the HA and NA segments that produce the hemagglutinin and neuraminidase proteins that sit on the surface of the virion and interact with host cells, but the whole viral genome, as this provides a complete picture of the emergence of the virus (E.C. Holmes, 2009).
The significance of intrasubtype reassortment for strain emergence was shown by the appearance of the new strain of Influenza H1N1 in 2009, which is a reassortant virus containing multiple swine influenza lineages.
In the October 2010 publication by Ilyushina et al, they show that despite the lack of detection thus far in humans, viable seasonal/pandemic Influenza virus reassortants can be generated in a laboratory setting. Their study showed that intrasubtype reassortment is able to occur between seasonal H3N2 and pandemic H1N1 viruses, potentially leading to the emergence of a strain with higher virulence.
Since 2004, the JCVI Influenza Genome Sequencing Project, funded by the National Institute of Allergy and Infectious Diseases (NIAID), has sequenced thousands of human, swine, and avian influenza isolates from collections around the world to provide researchers with a better understanding of the evolution of this important pathogen and to enable the development of new therapeutics, diagnostics, and vaccines.
JCVI has been collaborating with groups worldwide to monitor the evolution of the pandemic H1N1 Influenza virus (also known as H1N1pdm) that entered the human population in the spring of 2009 and has been responsible for at least 16,226 deaths worldwide. Genomic sequence information and epidemiological data are being used to address critical scientific questions of virus adaptation.
Some of the questions we are trying to answer with our current H1N1pdm studies include:
- How do pandemic viruses collected during the first wave of the pandemic compare to those collected in the later phases? We have ongoing studies in New York, Texas, Wisconsin, and California which address this question.
- How will the presence of a new pandemic influenza virus affect the evolution of seasonal H1N1 and H3N2 viruses? Will the seasonal viruses become extinct? Will we identify novel reassortants between the H1N1pdm and seasonal human viruses?
- Will the pandemic virus acquire resistance to neuraminidase inhibitors such as Tamiflu?
- How does H1N1pdm isolated in the tropics differ from isolates collected in temperate regions? What is the relationship between strains present in the tropics and epidemic strains in temperate regions? We have collections in Nicaragua, Hong Kong, and Brazil which will help answer these questions.
- What are the evolutionary dynamics of H1N1pdm in a situation of intense viral transmission such as between students in a university setting?
- Influenza samples have never been collected during the summer months. Thus the collection of pandemic influenza samples during the summer gives us a glimpse of viral persistence and transmission during the off peak months. How do circulating influenza strains collected during the southern hemisphere’s influenza season compare to those collected during the US summer and which strains persist into the next northern hemisphere flu season?
For more information please visit http://gsc.jcvi.org/projects/msc/influenza/
