PHILADELPHIA (GenomeWeb News) – Researchers at the US Centers for Disease Control and Prevention have sequenced ten or more complete swine flu viral genomes and hope to have a potential vaccine candidate in about a month, according to Joe Miller, the chief laboratory preparedness officer for the CDC's influenza division.
Speaking by phone to attendees at the American Society for Microbiology annual meeting here yesterday, Miller said that as of Tuesday morning the CDC had sequenced roughly 600 genes — about eight complete swine flu genomes — from 149 viral American swine flu viruses. The isolates were obtained from about 80 to 90 US swine flu cases.
The team has also sequenced viral isolates from about a dozen-and-a-half Mexican swine flu cases (roughly two complete genome sequences) as well as additional samples from El Salvador.
All of the sequences are being submitted to GenBank as soon as they are generated, Miller added. That database also contains sequencing information from several other labs around the world.
So far, Miller said, researchers have not seen a huge amount of genetic or antigenic variation in the H1N1 viruses sequenced. He said the CDC and other labs are currently preparing vaccine candidates and hope to have a viable candidate within three to four weeks.
Miller also outlined the CDC's role in developing an rRT-PCR-based swine flu test. The team had a set of swine reagents on hand in case of a swine flu outbreak, he explained. Those reagents included three primer sets: one set for detecting influenza A, another for detecting swine influenza A, and a third for distinguishing the H1 subtype of swine flu A.
After tweaking and re-validating the primer design, Miller said, the agency sent the primer set to the oligonucleotide synthesis company Biosearch Technologies, which is manufacturing the primers. The CDC subsequently applied for — and was granted — emergency use authorization for the rRT-PCR test from the US Food and Drug Administration. Miller said the CDC has now shipped the test to 245 labs in about 136 countries.
Miller's comments were part of a late-breaking session on laboratory responses to H1N1 swine flu at the ASM annual meeting. The session was added because organizers deemed the topic too pressing to wait until next year's meeting.
To date, there have been nearly 5,500 confirmed swine flu cases in the US, including 229 hospitalizations and seven deaths. Experts say the actual number of infected individuals is likely far higher, since extensive testing is often limited to those who are very ill.
Unlike the typical seasonal flu, which predominantly affects older individuals, Miller noted that some 64 percent of confirmed US cases have been in individuals who are five to 24 years old.