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Sudan stayed in the hunt for a top-two finish in Group C thanks to a 2-0 away win over Sao Tome e Principe, the lowest ranked team in the group phase as it lies 51st in Africa and 187th in the world.
Mohamed Abdel Rahman broke the deadlock on 27 minutes in the island nation off the Gabonese coast and Seifeldin Malik netted early in the second half.
Ghana, South Africa and Sudan are all former champions and have nine points each ahead of a clash between Bafana Bafana (The Boys) and the Black Stars in Soweto Friday.
The Burkinabe secured a place for the sixth time in its last seven attempts by forcing a 0-0 Group B draw away to Uganda near Kampala.
Uganda must avoid defeat in Malawi Monday to join Burkina Faso at the 24-team tournament, which has been delayed one year by the coronavirus pandemic.
Malawi kept hopes of a first Cup of Nations appearance since 2010 alive by edging South Sudan 1-0 through a Richard Mbulu goal in Sudan as the national stadium in Juba is being renovated.
Guinea booked a place from Group A by defeating already-qualified Mali 1-0 in Conakry via a goal from substitute Seydouba Soumah with 15 minutes remaining.
Burkina Faso and Guinea join defending champion Algeria, Mali, Senegal, Tunisia and automatic qualifier as host Cameroon in securing places, leaving 17 places up for grabs.
Ethiopia rose from third to first in Group K with an unexpectedly convincing triumph over Madagascar, which was the surprise side of the 2019 Cup of Nations in Egypt, reaching the quarter-finals as debutants.
The Ethiopians are ranked 42nd in Africa -- 21 places below the Malagasys -- but it was hard to believe that fact as they dominated the first half in Bahir Dar to turn over with a three-goal advantage.
Amanuel Gebremichael was first to score for a country that has featured at the Cup of Nations only once since 1976, followed by Getaneh Kebede and Abubeker Nassir.
Egypt-based Shimelis Bekele, the only starter who plays his club football outside Ethiopia, completed the rout four minutes from time.