Pathogenetix, a Woburn, MA-based company formerly named U.S. Genomics, has raised $4 million of an equity offering that could total $9.5 million, an SEC filing shows. Last November, the firm, which develops biodefense and diagnostic technologies, raised $900,000 of a debt-based round and $1.3 million in an equity financing—the latter of which was bumped up to $1.5 million a month later, according to SEC documents.

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Woburn, MA-based biotech Pathogenetix, formerly known as U.S. Genomics, has raised $1.3 million in equity-based funding, and $900,000 of a planned $1.2 million debt-based offering, according to filings with the SEC. U.S. Genomics developed biodefense and diagnostic technologies, and raised $4.5 million in private equity funding from Becton, Dickinson & Co in 2008, as part of a strategic partnership for pursuing diagnostics for infectious diseases. Pathogenetix has not yet returned a call seeking comment on the newest funding and the company name change.

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AVI Biopharma, the Bothell, WA-based developer of RNA-based therapies, said today it has won an expanded $11.5 million contract from the U.S. Defense Department to develop its drug candidate for Junin virus infection. The new contract means AVI has received $45 million in combined contracts to develop treatments for Ebola, Marburg, and now Junin viral infections. AVI (NASDAQ: AVII) said the cash comes from the Defense Threat Reduction Agency’s Transformational Medical Technologies Initiative for a therapy called AVI-7012. Shares of AVI climbed 28 percent to $2.01 at 9:46 am Eastern time on the news.

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AVI Biopharma has got Ebola virus on its mind. This horrifying bug from central Africa would only have to infect a few people in the U.S. to cause a real bioterror scare, because it’s so deadly and there’s no cure. The federal government would like to get an effective treatment stockpiled just in case a terrorist gets his hands on Ebola virus, and now Portland, OR-based AVI thinks it might have the inside track on the federal contract to deliver an effective treatment.

AVI (NASDAQ: AVII) has been reinventing itself over the past year as a developer of RNA-based drugs. I got an update recently from CEO Leslie Hudson about the latest on the Ebola treatment program.

This month, the U.S. Department of Defense plans to conclude a public solicitation for business opportunities to get a contract to make RNA-based drugs for Ebola and Marburg viruses, Hudson says. The contract specifically states that it must be an RNA therapeutic ready for clinical trials, not a different kind of treatment like a vaccine or a monoclonal antibody, Hudson says. RNA-based therapies, sometimes known as next-generation antisense or gene-silencing drugs, are thought to hold great potential to block the underlying mechanisms of disease in ways that previous therapies can’t. Cambridge, MA-based Alnylam Pharmaceuticals, a leader in RNA-based therapies, has said it is operating a biodefense program that includes Ebola, although it hasn’t said the Ebola treatment is ready for clinical trials like AVI has.

If AVI can secure this contract, which is expected to be awarded later this year, possibly as soon as the summer, it would bring in a total of $50 million, Hudson says. This would be a significant boon to the company, which had $11.5 million in cash entering 2009 year and raised another $16.5 million from Eastbourne Capital and other institutional investors in late January.

“Thus far, we have the only therapeutic approach with sufficient data to be allowed into man,” Hudson says.

As a reminder, AVI got to this point after showing that 100 percent of monkeys who were exposed to Ebola or Marburg lived if they were taking the company’s experimental drugs, AVI-6002 and AVI-6003, respectively.

Of course, that’s a really compelling way to design an experiment, but not ethical to do in people. So what AVI needs to do in a clinical trial is just give healthy volunteers the drug and see if it’s safe, without exposing anybody to Ebola or Marburg. The combination of effectiveness in animals and a pair of safety studies in humans could lead the federal government to purchase bulk stockpiles of the drug for use in case of a scare, Hudson says. He didn’t say how long it would take to get enough convincing data for the Department of Defense to buy a stockpile.

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Torrey Pines Therapeutics said today that it has sold worldwide rights for three drug candidates to Cenomed Biosciences, a subsidiary of Abraxis Bioscience. Cenomed, based in Irvine, CA, will get rights to phenserine, Posiphen, and bisnorcymcerine for chemical defense and biodefense. La Jolla, CA-based Torrey Pines (NASDAQ: TPTX) stands to receive milestone and royalty payments from progress made with the compounds.

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Woburn, MA-based U.S. Genomics, a maker of single-molecule technologies for biodefense and diagnostics, announced today it has raised $4.5 million in private equity funding from Becton, Dickinson & Co. The deal marks the start of a strategic partnership between the firms to develop an infectious-disease diagnostic platform.

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Alnylam Pharmaceuticals (NASDAQ: ALNY) said today that the National Institutes of Health has committed $7.5 million to continue funding another year of its program to develop RNA interference technology against hemorrhagic fever virus, including the deadly Ebola virus. The Cambridge, MA-based company originally got the contract in September 2006, and has received $14.2 million for work over the first two years. The company’s experimental treatment, which uses a lipid-particle delivery method, has been shown to decrease Ebola virus in infected mice, the company said.

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