Scientists at the J Craig Venter Institute (JCVI), along with researchers at the National Centre for Biotechnology Information (NCBI) and 44 academic institutions have sequenced and published more than 10,000 influenza virus genomes as part of the Influenza Virus Genome Sequencing Project (IGSP) of the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH). This important milestone was reached on January 3, 2013 with the 10,000th influenza virus genome deposited into the NCBI’s data repository, GenBank.

The JCVI virology group, led by David Wentworth, Ph.D., has been responsible for sequencing approximately 75 percent of the influenza virus genomes available in GenBank.

The World Health Organization estimates that each year, between two and five million people are severely affected with influenza and between 200,000 and 500,000 people die from annual influenza virus epidemics. In the United States, epidemic influenza virus strains annually infect five to 20 per cent of the population, resulting in more than 200,000 hospitalizations and between 3,000 and 49,000 fatalities each year, with an average of about 23,000 deaths. According to the US Centres for Disease Control, this year influenza virus is emerging as an important health threat as 41 states have already reported widespread influenza activity. The morbidity and mortality caused by influenza A viruses can escalate dramatically when novel strains emerge from animal sources and periodically cause pandemics.

In 2005 NIH/NIAID launched the IGSP to combat influenza viruses because there were only about 200 complete influenza genomes publicly available. Influenza viruses represent significant scientific and public health challenges because they are highly transmissible pathogens that are continually evolving to evade the hosts’ immune response. The segmented RNA genome of influenza viruses, which allows two viruses to reassort during co-infections to create progeny very different from either parent, further complicates efforts to combat this pathogen.  The project was designed to help researchers understand how influenza viruses evolve, spread and cause disease.

JCVI scientists pioneered dynamic, large-scale, high-throughput sequencing, and bioinformatics pipelines designed to sequence whole- influenza virus genomes. This work continues to be funded through the NIAID’s Genome Sequencing Centre contract. Data generated has been crucial in furthering understanding of influenza molecular epidemiology, evolution, transmission, and pathogenesis. This project has far exceeded its initial goals and the methods developed and data collected have directly resulted in more than 30 publications from JCVI authors and their collaborators. Additionally, virtually all phylogenetic analyses on influenza virus use the data generated by the NIAID-sponsored genome sequencing centre.

The IGSP has facilitated the development of other NIH-sponsored resources including the NCBI Influenza Virus Resource and the Influenza Research Database, which have tools for sequence analysis and integrating genomic data with other research data. The influenza genomic data is also mined by basic researchers, vaccine producers and anti-viral drug developers with the goal of developing new vaccines and antivirals to combat future pandemics.

According to Dr Wentworth, our team is proud to be a part of such an important project, which will continue to benefit human and animal health. Dr Wentworth added, “We are now using next generation, deep sequencing technologies to understand the molecular mechanisms central to influenza evolution, to better identify mixed infections in humans, and to reveal genetic determinants responsible for virulence. We believe that through continued work such as this, strains for vaccine production can be identified and more rapidly developed.”

The 2009 H1N1 influenza pandemic was an example of the kind of worldwide threat society faces with influenza. JCVI researchers, as part of the IVGSP, played a vital role during the H1N1 influenza pandemic. Emergency sequencing capabilities were used to rapidly sequence and publically release the complete genome of two strains from this emerging pandemic within 48 hours of receiving amplified genomic material from the Wadsworth Center at the New York State Department of Health.  JCVI’s scientists efficiently collaborated with virologists worldwide as the pandemic unfolded and this has resulted in deposition of > 85% of H1N1pdm genomes into publicly available databases. Analyses of these genomes have allowed for an increased understanding of human influenza evolution, phylogeography and pandemic preparedness.

J Craig Venter, Ph.D., JCVI founder and CEO stated, “Now more than ever enhanced understanding of influenza virus genomics is of global importance. Sequence-based tracking of emerging new strains of influenza is one of the most important steps in limiting future pandemics. I am pleased that JCVI is a significant contributor to this ongoing research effort.”

The JCVI is a not-for-profit research institute dedicated to the advancement of the science of genomics; the understanding of its implications for society; and communication of those results to the scientific community, the public, and policymakers.