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The 42-year-old, who passed the mark of Cape Horn on Christmas Day after 48 days at sea, is behind only race leader Armel Le Cleac'h.
The Welshman is aiming to become the first Briton to win the race.
Thomson had led for the majority of the race but was overtaken by Le Cleac'h when he suffered a damaged foil.
The leaders are now well up their South Atlantic ascent and, after rounding Cape Horn, the skippers begin their journey north back across the Atlantic towards the finish port at Les Sables-d'Olonne.
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Thomson regained the lead in the round-the-world race north of the Kerguelen Islands in the Indian Ocean on 30 November, but has since lost ground.
He  broke two race records prior to being overtaken, as he reached the Cape of Good Hope in record time.
The Vendee Globe takes place every four years. Since the first race in 1989, only 71 of 138 starters have completed the voyage, which is known for being one of the most gruelling sporting challenges in the world.
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Alex Thomson is attempting to overturn a deficit of about 140 miles in the Vendee Globe Trophy, with the leaders now past the halfway point of the race.