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The India Meteorological Department (IMD) has issued a yellow alert in three districts-Pathanamthitta, Alappuzha and Ernakulam.
A yellow alert predicts heavy rainfall between 6 cm and 11 cm.
The IMD has predicted rains till October 5.
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The Kerala State Disaster Management Authority (KSDMA) said in the last 24 hours, the most affected places were in Pathanamthitta, Alappuzha, Kottayam, Ernakulam and Kozhikode districts.
It said on Sunday, two camps each were opened at Alappuzha and Kotayam districts.
A total of 26 persons were affected in various rain-related incidents in the last 24 hours, SDMA added.
The heavy downpour had earlier submerged hundreds of acres of paddy fields at Edathua, a tiny hamlet in the Kuttanad region in Alappuzha district.
The Disaster Management Authority has urged people living in high ranges to maintain extra vigil in view of the incessant rains.