Dr. Allison Arwady said about 90 pharmacies have gotten the bivalent vaccine and about 170 will have gotten them by the end of the week.
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WATCH: Mayor Lightfoot, Dr. Arwady give update on COVID booster rollout
Lightfoot, Dr. Arwady update COVID vaccine booster rollout plan
CVS and Walgreens are gearing up for the new COVID vaccine. Half of the city's supply delivered this week will go to Chicago pharmacies. Anyone over 12 years old who has received their primary vaccine series is eligible for the new shot two months after your last one.
"This is not the flu, it's much more serious, much more contagious and unfortunately much more deadly, so we have got to get people vaccinated," Mayor Lori Lightfoot said.
Lightfoot and Arwady are begging Chicagoans to get the tweaked vaccine that Arwady says is a perfect match against the omicron BA.4 and BA.5 subvariants, the strains that account for almost all of the current COVID cases.
Arwady said in the past six weeks, 36% of reinfections are people who had earlier Omicron subvariants.
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"Getting vaccinated right now is not just about me and my protection, it's about making it harder for new variants to emerge," Arwady said.
New, possibly more dangerous variants is the fear if not enough people get the new vaccine soon. Seventy-seven percent of Chicagoans are eligible.
Besides pharmacies, the updated booster will go to health care settings, senior centers, city family vaccination cites, Chicago Public Schools, mobile clinics and Sunday Swap-a-Ramas.
The vaccine will also be made available at clinics, including family vaccine clinics at City Colleges as well as through CDPH's at-home vaccine program, Mayor Lightfoot said.
"No matter where you live in Chicago, there is a vaccine available for you, near your home and we can bring it to your home," Arwady said.
Pfizer's tweaked vaccine was authorized for those 12 and older, and Moderna was authorized for adults 18 and older. It should be taken at least two months after the last shot.
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WATCH: Who should be getting updated COVID vaccine booster shots?
Who should be getting updated COVID vaccine booster shots?
The city's been allocated 150,000 initial doses in addition to the 580,000 doses the state is expecting to get in the first week. This updated vaccine will replace current boosters.
For more information, visit chicago.gov/covidvax.