The 45 deaths include two pediatric deaths and the majority of the 45 deaths were of unvaccinated people, said Dr. Gil Chavez, deputy director and state epidemiologist with the Department of Public Health's Center for Infectious Diseases.
There have been at least 21 flu deaths in the Bay Area as of Wednesday, according to local health departments.
That number is higher than the 14 confirmed in the region so far by the state Department of Public Health.
Chavez said county public health departments are on the front lines regarding flu deaths and are the first to report them to the community.
"There will be a lag before they report them to us," Chavez said.
The California Department of Public Health is also not required to report flu deaths of people over age 65, Chavez said.
There were 106 flu deaths in California during the 2012-2013 season, Chavez said. He said the 2013-2014 flu season has not yet peaked.
The H1N1 "swine flu" strain is predominant this season, according to Chavez.
"We are clearly in the midst of what appears to be an earlier peaking, severe flu season, and I encourage everyone who has not yet gotten a flu vaccination to do so," California Department of Public Health director Dr. Ron Chapman said.
Public health officials did not have a regional breakdown of where the flu is hitting hardest.
They said the flu has been reported statewide.
Dr. James Watt, chief of the state's Division of Communicable Disease Control, said there won't be data on the proportion of California's population that has been vaccinated until after the current flu season.
A predominant number of those under 65 who have died of the flu had underlying health conditions that put them more at risk, Watt said. Those conditions typically include heart and lung disease, HIV, cancer and obesity, Watt said.
Pregnant women also appear to be at risk of contracting the H1N1 virus, he said. This season's flu also is affecting young adults.
In Sonoma County, Matthew Walker, 23, of Santa Rosa succumbed to the flu. Public health officials said there is plenty of influenza vaccine.
The state public health department has purchased 50,000 doses for local health departments.
There are also 290,000 federally purchased doses via the Vaccines for Children program, with the doses available for local health departments or private providers, according to the Department of Public Health.
There also is no known widespread shortage of anti-viral medication to treat the influenza, public health officials said.
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