The striker had returned to Gabon at the end of March to play DR Congo in an Africa Cup of Nations qualification game.
He then returned to England and played against Liverpool in the Premier League and Slavia Prague in the first leg of the Europa League quarterfinal.
After looking short of his usual form, he then missed Arsenal’s last league game against Sheffield United.
Ahead of his side’s return fixture against Slavia Prague on Thursday, Aubameyang revealed the reason for his absence on social media.
“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.”
The African region was home to 94% of all malaria cases and deaths in 2019, according to the World Health Organization.
Speaking after the match, Arsenal manager Mikel Arteta confirmed Aubameyang had returned to his home and hoped he would be back to full fitness soon.
“We’ll see how he recovers. I think he’ll need a few days to recover from that,” Arteta said. “He wants to be back as soon as possible, that’s what he said to me.”
Without its captain, Arsenal still managed to beat Slavia Prague 4-0 to progress into the Europa League semifinals where it will play Villarreal.
Nicolas Pepe opened the scoring before Bukayo Saka and a brace from Alexandre Lacazette secured an emphatic victory against the Czech side.
Slavia Prague was without Ondrej Kudela after UEFA banned the defender for 10 games for racist behavior towards Rangers’ midfielder Glen Kamara in the previous round.
The incident occurred late in the match when Kudela was seen saying something into Kamara’s ear with his hand covering his mouth.
After the game, Rangers manager Steven Gerrard spoke to the media where he confirmed that Kamara told him that he was racially abused by Kudela.
Ahead of kick-off, Arsenal players took the knee as Slavia Prague remained standing. Frenchman Lacazette, Arsenal’s captain for the night, knelt directly in front of the opposition and gazed directly at them.
The act of kneeling was taken up by the Premier League last season in solidarity with Black Lives Matter.
“The players asked me and the club,” Arteta said after the game. “They wanted to take that initiative and they had the right reasons for it, so the club and I were very supportive.
“Thankfully the referees and UEFA have been supportive as well, so I think it was a good gesture.”
The office of Czech President Milos Zeman strongly condemned the 10-match ban handed down to Kudela.
The Head of the Office of President of the Republic, Vratislav Mynar, penned an open letter that criticized UEFA’s decision, claiming its fight against racism was “the pinnacle of hypocrisy, positive discrimination, and embarrassing pandering to silly trends.”
Mynar also claimed that the verdict united football fans in the Czech Republic.
“I very much appreciate the fact that the Czech public, across the whole society, does not identify with your verdict. On the contrary — you managed to unite old rivals — even temporarily,” he wrote.
“We will not kneel down in front of you. No threats work against a Czech football fan.”
Mynar said Czech President Milos Zeman had been informed of the situation and expressed his sympathy with all those who were disappointed by Wednesday’s decision.
In a statement to CNN Sport, UEFA said “it has a zero tolerance against racism and any player who wants to take the knee is allowed to do so in our competitions.”
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