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The 19-year-old midfielder suffered sprained and partially torn ligaments in his right knee after a challenge with Dortmund defender Sokratis Papastathopoulos as Wolfsburg fell to a 2-0 defeat at Signal Iduna Park in the DFB-Pokal semi-final.
Malanda could now face two months on the sidelines, meaning that he will play no part in Wolfsburg's Bundesliga run-in as they seek a top-four finish.
"He's been lucky in that it's not the cruciate, which we feared, but it's still unfortunate for him," Wolfsburg coach Dieter Hecking told the club's official website.
Article continues below"It's a pity but at least he will be fighting fit for the start of pre-season.
"He was one of our most active players (against Dortmund). He's a young lad but he showed that he's already capable of assuming the responsibility."
He had been tipped to be a surprise inclusion in Marc Wilmots' Belgium squad for the FIFA World Cup in Brazil later this year, but this setback is likely to scupper those hopes.
