Its researchers have also detected a new virus linked to a rare type of prostate cancer and another virus that causes diarrheal disease in children. In yet another project, they are collecting unusual strains of HIV from Cameroon, Africa.

While at least twenty other labs are studying the genetic structure of the flu virus through conventional sequencing, the San Francisco lab is one of two in the entire nation engaged in viral discovery and “deep sequencing,” seeking mutations that occur at very low frequencies. The other is the Center for Infection and Immunity at Columbia University in New York City. “They’re doing a great job. What they do is very important,” said molecular virologist Paul Luciw of the University of California-Davis. “The technology enables analysis of strain variation. If you find something very different, then you have to pay more attention — isolating that patient and looking at the patient’s contacts.”

More specimens arrive every day.

The technology uses tiny glass slides dotted with thousands of fragments of DNA from 2,500 known viruses. The tool can study an entire genome at once — so experiments that used to be impossible are now being performed in days or hours.

All the viral sequences are stored in a huge computer database.

A flu virus is thought to reproduce about every eight hours. Within one day, it is spawned several generations. As it breeds, it mixes and morphs. By comparing H1N1’s genetic code with other influenzas, scientists have found a new combination of elements of previously known viruses. Three flu strains — from pigs, birds and humans — combined in one animal to create an unusual “triple re-assortment.”

It is not known how, when or where this happened. Then it jumped into humans. Chiu’s team is watching its continued evolution, a gradual accretion of minor mutations called genetic “drift.” “There are changes,” he said. “Not a lot of changes — but there are changes. Now we’re investigating the significance of these changes.”

Krieger writes that what he is worried about is a big change called genetic “shift,” when there is a dramatic re-assortment and exchange of strands of genetic material that trigger hard-to-predict epidemic trajectories. Such a shift could build a virus that is fast-growing, adept at infecting lungs, unfamiliar to the immune system — and highly contagious. “That would be a big deal,” he said. For now, they are waiting and watching, so that a catastrophe like 1918 need never happen again.