We're on schedule for the expected increase in novel H1N1 flu cases from the swine flu pandemic coincident with school starting up. The red line is this year's flu season, and the peak at week 35 represents influenza like illness (ILI), defined as fever of 100 and cough or sore throat, as seen by sentinel doctors' offices throughout the US. You can find your region here.

The good news is about vaccine.

A single shot of swine flu vaccine protected healthy adults within eight to 10 days, according to a U.S. study that doubles anticipated stockpiles and may help people get immunized faster.

The bad is that vaccine may be too late to stop the peak.

The epidemiologists said Friday that they expected the peak to come as early as next month, long before enough vaccine to protect all 159 million Americans who need it most will be ready. "It would be bizarre for it to peak in January or February, the way seasonal flu does," said Dr. Marc Lipsitch, an epidemiologist at the Harvard School of Public Health and a consultant on flu epidemics to the President's Council of Advisers on Science and Technology. He noted that the pandemics of 1918 and 1957, which were also caused by new viral strains, had both peaked early. Influenza cases are usually near zero at this time of year, but Friday's weekly report from the Centers for Disease Control and Prevention rated flu activity as "widespread" in 11 states, mostly in the Southeast but also in Arizona, Alaska and Oklahoma. ("Widespread" is the highest of five levels.) According to Dr. Anne Schuchat, the agency's chief of immunization and respiratory diseases, 98 percent of those flu cases are the new swine flu.

More than half of all surveyed colleges, and all 50 states and DC have reported cases. It's much more prevalent in the southeast, presumably because school started a couple of weeks early. Here's the southeast ILI tracking, one of the hardest hit regions:

The referenced PCAST report can be found here. Many of PCAST's specific recommendations have already been implemented, although the laudable suggestion to accelerate vaccine production is not easily carried out.

Most people who get this virus are ill but recover relatively quickly; a few who get ill become very ill, and certain high risk groups including pregnant women, children under 5, caretakers of infants, and school age kids with asthma and diabetes are candidates for the first batch of vaccine when it is available in a few weeks. Health care workers are also a target for vaccination so as to not deplete the work force.

The spread of virus and the roll-out of vaccine will keep this story in the news a while longer. And there are still preparations you can take now, including making continuity plans to function with 30% less staff, or on a personal level stocking up on medicine (if you're on it), and some extra food and items so that if you are ill, you needn't go out and infect others. And while schools are planning to be open, some are going to close, so if that involves you, have a back-up plan for child care.

The latest CDC situation update can be found here; guidance on flu prep can be found here and here; home care is here; news is here.

For the wonks who like to get down to detail, there's an excellent review from Lancet Infectious Disease (.pdf) entitled Closure of schools during an influenza pandemic that goes through the plusses and minuses of school closure [see also H1N1: Why Do Schools Close, And When Do They Open? from May 2009.]

The decision to close schools must be made on the basis of the severity of the pandemic. This is illustrated by the recommendations that have been made by the US Centres for Disease Control and Prevention (CDC) which contrast with earlier recommendations.39,40 On the basis of information that many cases in the Mexican epidemic had severe illness, the CDC initially recommended school closure as an option to lessen the risk of infection from a potentially severe disease. However, as estimates of severity were revised downward, recommendations were changed and the early identification and isolation of ill students and staff became the primary method to reduce the spread of influenza in schools.40 The use of stringent and costly measures such as school closure should indeed be based on age-specific estimates of severity and local morbidity indicators. It is important to emphasise again that the WHO phases are not an indication of severity (phase six only means that there is a sustained spread of the virus in different continents); WHO now makes parallel statements on severity and geographical spread.41,42

You really don't want this virus; it's nasty at best and deadly at worst. Cover your cough, wash your hands, and roll up your sleeve when you have the chance. It isn't often that you experience a pandemic, and making this the mildest one on record should be everyone's goal. Recognize that some (but not most) schools will close, and balancing proper concern with prudent action without going overboard is tougher than it looks, hence calls for transparency in communication are key.