In April 2009, the first human cases of the 2009 H1N1 influenza virus in the U.S. were reported by the Centers for Disease Control and Prevention (CDC). This strain, which continues to circulate, is a unique combination of influenza genes not previously identified in humans.

By April 2009, multiple countries reported an ongoing spread of the virus later confirmed to be H1N1. Hospitalizations and deaths associated with children and young adults infected with H1N1 were higher than known circulating influenzas. A means to rapidly identify, track, and treat emerging infections was critical to slow the epidemic.

The CDC influenza team sequenced the H1N1 strain, developed a real-time reverse transcription polymerase chain reaction (rRT-PCR) test by designing primer and probe sets for identifying and distinguishing the novel strain from other circulating influenzas, and then published the sequences and protocols for public health laboratory use on an influenza database. The CDC then manufactured diagnostic test kits to enable health care professionals to quickly identify the 2009 H1N1 virus in patient samples.

By April 2009, multiple countries reported an ongoing spread of the virus later confirmed to be H1N1. Hospitalizations and deaths associated with children and young adults infected with H1N1 were higher than known circulating influenzas.

The rRT-PCR test developed by the CDC was authorized for use by the Food and Drug Administration (FDA) under an Emergency Use Authorization (EUA) on April 28, 2009, less than two weeks after the new pandemic virus was identified. Three days later, CDC test kits began shipping to domestic and international public health laboratories. These transfer needs were immediate and critical as H1N1 virus infections were confirmed worldwide.

An increasing demand compelled the CDC to outsource purified primer and probe production. By November 2009, the first commercial license agreements were negotiated with Life Technologies, Inc. and Biosearch Technologies. The commercial agreements were for production of diagnostic oligonucleotide primer and probe sets for H1N1 and for patented influenza panel test kits for the universal detection of all influenza type A and B viruses, and the identification of strains with specificity to human H1 and H3, Asian avian H5, Eurasian H7, North American H7, and Asian H9 viruses.

To address the overwhelming volume of requests for testing procedures and technical support, the CDC Laboratory Support for Influenza Surveillance (CLSIS) website was created and eventually upgraded to a SharePoint site. The CLSIS SharePoint site was instrumental in facilitating rapid sharing of testing procedures for additional outbreaks of novel influenzas such as avian A/H7N9 in China in 2013. CLSIS currently supports over 200 domestic and international users by providing the latest information on CDC influenza rRT-PCR testing procedures.