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The IUML strongman won by 171,023 votes. He got 515,330 lakh votes, the highest anyone has secured in the constituency.
A beaming Kunhalikutty told reporters that this was a huge margin of victory in a by-election.
"The BJP has turned out to be the biggest loser. Personally for us, the IUML, we have been able to come back strongly in two assembly segments -- Perinthalmanna and Mankada."
In the 2016 assembly polls, the IUML only scraped through in these two constituencies.
Kunhalikutty said: "This time we have dramatically increased our lead there. This clearly shows that the Left has performed very poorly."
In the 2014 Lok Sabha election, however, then IUML candidate E. Ahamed, whose death led to the by-election, was above 1.94 lakh.
The CPI-M's M. B. Faisal got 344,307 votes and the Bharatiya Janata Party candidate N. Sreeprakash was a distant third with 65,675 votes.
Kunhalikutty secured 55.04 per cent of all votes, compared to Ahamed's 51.28 per cent.
The Left's vote share went up from 28.47 per cent in 2014 to 36.77 per cent. The Bharatiya Janata Party's vote share dipped from 7.59 per cent to 7.01 per cent.
The turnout in the Malappuram by-election on April 12 was 71.33 per cent.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)