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Barca lost this fixture 5-4 last season as they missed out on an unbeaten season in La Liga, but their win was emphatic this time.
Coach Ernesto Valverde opted for three at the back and after something of a slow start, Messi went on a remarkable run across the box before cutting back for Luis Suarez to volley home the opener after 35 minutes.
Eight minutes later, the Argentine ran on to a Sergio Busquets pass and raced away to score with his right foot, before adding a third shortly after half-time and then completing his hat-trick on the hour as he finished off a fantastic team move.
The five-time Ballon d’Or winner then assisted Gerard Pique for Barca’s fifth with two minutes left to complete a comprehensive victory as the Catalans moved three points clear of Sevilla and Atletico at the top of the table after 16 rounds of matches.