The striker returned to Gabon at the end of March to face DR Congo in a qualifying match for the Africa Cup of Nations.
He then returned to England and played Liverpool in the Premier League and Slavia Prague in the first leg of the Europa League quarter-final.
After appearing below his usual form, he then missed Arsenal’s final league game against Sheffield United.
Ahead of his side’s return match against Slavia Prague on Thursday, Aubameyang revealed the reason for his absence on social media.
“I spent a few days in the hospital this week, but I already feel much better every day, thanks to the excellent doctors who detected and treated the virus so quickly.
“I haven’t really felt the last two weeks but I’ll be back stronger than ever! I’m going to watch my boys now, a huge game for us! Let’s go and let’s go.”
The African region had 94% of all malaria cases and deaths in 2019, according to the World Health Organization.
Speaking after the game, Arsenal manager Mikel Arteta confirmed that Aubameyang has returned home and hopes he will be back in good shape soon.
“We will see how he recovers. I think he will need a few days to recover,” said Arteta. “He wants to be back as soon as possible, that’s what he told me.”
Without their captain, Arsenal still managed to beat Slavia Prague 4-0 to qualify for the semi-finals of the Europa League where they will face Villarreal.
Nicolas Pepe opened the scoring ahead of Bukayo Saka and a brace from Alexandre Lacazette ensured a clear victory against the Czech team.
Slavia Prague were 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 happened at the end of the match when Kudela was seen saying something in Kamara’s ear with her hand covering her mouth.
After the game, Rangers manager Steven Gerrard spoke to the media where he confirmed Kamara told him he had been racially abused by Kudela.
Before kick-off, Arsenal players took the knee as Slavia Prague remained standing. Frenchman Lacazette, Arsenal captain for the night, knelt directly in front of the opposition and looked at them directly.
The act of kneeling was picked 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 this initiative and they had the right reasons for it, so the club and I were very supportive.
“Fortunately, the referees and UEFA also gave their support, so I think it was a good gesture.”
Czech President Milos Zeman’s office strongly condemned the 10-match ban against Kudela.
Presidential Chief of Staff Vratislav Mynar wrote an open letter criticizing UEFA’s decision, saying its fight against racism was “the height of hypocrisy, affirmative action and complacency embarrassing in the face of silly tendencies ”.
Mynar also claimed that the verdict united football fans in the Czech Republic.
“I very much appreciate the fact that the Czech public, in all of society, do not identify with your verdict. On the contrary – you have managed to unite old rivals – even temporarily,” he wrote.
“We will not kneel in front of you. No threat will work against a Czech football fan.”
Mynar said Czech President Milos Zeman had been briefed on the situation and expressed sympathy to all those who were disappointed with Wednesday’s decision.
In a statement to CNN Sport, UEFA said “it has 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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