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Authorities have declared a state of emergency in five regions
Journalist Juan Carlos Barahona told the BBC that San Vicente had almost been completely cut off by landslides and collapsed bridges.
Mr Barahona, of the El Salvador daily La Prensa Grafica, told the BBC that the other worst affected areas were La Libertad, La Paz and Cuscatlan.
60 people are still missing, and about 7,000 more are in shelters.