The Colombian was 67th on the 162.9km stage to La Molina, 1 minute 50 seconds down on the time of Joaquim 'Purito' Rodriguez (Katusha), who won his first race of 2014.
Betancur suffered a general infectious syndrome which led to fever requiring antibiotic treatment and the 24-year-old will now enjoy a small period of rest in order to recover.
There will be no Giro d'Italia for Betancur this year as he has stated that his goal for 2014 is to win the Tour de France's best young rider jersey. Betancur was the best young rider at last year's Giro.
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