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The Arsenal captain contracted the disease while on international duty with Gabon last month.
Aubameyang has spent the last few days in hospital and did not travel with the Arsenal squad for the second leg of their Europa League quarter-final with Slavia Prague on Thursday.
Since returning from international duty last month, Aubameyang has not seemed fully fit and his performance against Liverpool was criticised before he was dropped for the first leg against Slavia.
It is unclear how long Aubameyang will out but the striker has vowed to “be back stronger than ever soon”.
In an Instagram post from his hospital bed minutes before Arsenal kicked off against Slavia, Aubameyang said: “Hey guys, thanks for all the messages and calls. Unfortunately I contracted malaria whilst being on national team duty in Gabon a few weeks ago.
“I’ve spent a few days in hospital this week but I’m already feeling much better every day, thanks to the great doctors that detected and treated the virus so quickly.
“I wasn’t really feeling myself the last couple weeks but will be back stronger than ever soon!
“Will be watching my boys now, huge game for us! Let‘s go and get it Arsenal.”
Aubameyang played one game for Gabon while he was on international duty, scoring in their 3-0 Africa Cup of Nations qualifying win over DR Congo on March 25.
He did not travel with the Gabon squad for a match in Angola on March 29 because it is on the UK Government’s list of coronavirus ‘red list’ countries.