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Da Silva was among a large group of golfers unable to complete their first round at East London Golf Club on Thursday because of a three-hour delay due to winds that reached 30 kilometres an hour.
Overnight clubhouse leader Jaco van Zyl of South Africa retained second place on 66 and John Parry of England held third spot after carding a 68 over the par-72, 6,066-metre course that overlooks the Indian Ocean.
Those on 69 include South Africans Oliver Bekker, Wallie Coetzee, Andrew Curlewis, Derik Ferreira, Darren Fichardt and James Kingston, Ignacio Garrido of Spain, Tommy Fleetwood of England, Michael Jonzon of Sweden, Mark Tullo of Chile and Phillip Price of Wales.
South Africa-based Da Silva birdied five of his first six holes Thursday and was six under after eight holes when bad light stopped play just before 1900 local time.
He birdied the ninth when play resumed early Friday, picked up an eagle on the 15th and back-to-back birdies completed a memorable round over a short course, whose chief defences are thick bush bordering fairways, and the wind.
South African Major winners Louis Oosthuizen (twice) and Charl Schwartzel won previous editions of the Africa Open since it was co-sanctioned by the European Tour and Sunshine Tour.
But neither entered the championship this year as they are preparing for the World Golf Championship-Accenture Match Play Championship in Dove Mountain, Arizona, next week.
Fellow South Africans Richard Sterne, winner of the Joburg Open last weekend, George Coetzee and Branden Grace are absent for the same reason, raising the prospect of a first foreign winner of the Africa Open.