Biotech investors have seen their portfolios take a hit from the government shutdown. Even with today's run, the Nasdaq Biotechnology Index is down about 4% since the shutdown started last week.

And to add insult to injury, the government shutdown has limited biotech investors' ability to do some due diligence. Here are three things you can't do right now:

Get new info on ClinicalTrials.gov
The government-run website is designed for patients to find clinical trials to enroll in, but that hasn't kept investors from checking the website to look up information on the clinical trials that companies are running, including endpoints and inclusion criteria for the trial.

Unfortunately, the website is being "maintained with minimal staffing," with a disclaimer on the top of the page about the potential for information to be out of date.

Clinicaltrialsgov

Source: ClinicalTrials.gov

Changes in enrollment criteria for ARIAD Pharmaceuticals' (NASDAQ:ARIA) EPIC trial, for instance, turned out to be a sign that the drug's cardiovascular issues might be more of an issue than the initial data let on. I don't know if the change would have been considered a "critical update" by the government, but there's no doubt investors believe it was. Shares fell about 70% this week after ARIAD released new data, and suspended enrollment in the EPIC trial.

Watch some advisory committee meetings
Investors in Amarin (NASDAQ:AMRN) don't have to worry about its upcoming advisory committee meeting. It looks like Amarin's attempt to get Vascepa approved for a wider population will go off without any major issues. With Monday being a Federal holiday, expect the briefing documents to come out of Friday.

Merck (NYSE:MRK), ALK, and Stallergenes weren't as lucky. The Allergenic Products Advisory Committee meeting scheduled for November 5 and 6 was cancelled this week. The committee was set to review Merck's grass allergy immunotherapy tablet, which is partnered with ALK and Stallergenes' tablet for the same indication, on another day.

Why did the meeting get nixed? Allergy products aren't covered by PDUFA fees. No money, no people to run the meeting.

With the meeting a month away, it's tempting to see this as a bad sign that the FDA, at least, thinks the shutdown might last that long. But investors should keep in mind that a lot more goes into an advisory committee meeting than putting a few chairs around a table so that the committee of outside experts can discuss the drug. The committee is provided with a detailed report of its review to that point, which the agency should be working on now if it's to be delivered to the committee in a month.

The drug from Stallergenes, Merck, and ALK  will get its day in front of the advisory committee eventually, but not until the division that reviews it gets back to work.

Get an update on the flu season
During the government shutdown, the Centers for Disease Control and Prevention has suspended tracking of the flu season.

For large companies that make flu vaccines, the lack of insight into the severity of the flu season isn't likely to be all that big of a deal. The vaccines that are made specifically for the flu season have already been manufactured and sent out. They're not going to make any more money if the flu season is worse than expected.

But sales of rescue treatments, such as Roche and Gilead Sciences' (NASDAQ:GILD) Tamiflu, that can be stored, are more likely to see benefits from a strong flu season. Investors won't get any indication whether sales will be above or below average until Roche reports sales, or the CDC starts back up again.

Let's hope this ends soon
While most drugs in the queue are still being reviewed, the agency isn't accepting new applications that require user fees. The delay, including any backlog that occurs, could cost companies millions of dollars in sales. It's not like the patent clock stops when the government is shut down.

Fool contributor Brian Orelli has no position in any stocks mentioned. The Motley Fool recommends Gilead Sciences. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.