The scheduled first one-dayer got called off one hour before the toss in Cape Town on Friday.
Manjra said he is "surprised" by the news of a positive case within the hosts' camp.
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"New tests will now be conducted on Saturday ahead of what is now planned as the opening encounter in the three-match series in Paarl on Sunday," reported AFP.
"There would be further tests after the planned second match in Cape Town on Monday, ahead of the scheduled final match on Wednesday."
The moment the ODI was called off less than an hour before the toss, reports emerged that the Proteas indeed broke health protocols during the T20I series that just went by. Further such breach and additional cases could mean a premature end of England's tour.
"We will re-test all our players and hotel staff on Saturday and await the results and determine a course of action," said Dr Manjra.
"This test has surprised us because we had confidence in the bio-secure environment."
"There has been some kind of breach which we’ve investigated in great detail to try and determine where this happened, by speaking to the player and looking at security camera footage."
There have been concerns raised from the touring side since both the teams were staying at the same hotel in Cape Town near the iconic Newlands ground.
"England are questioning the confidence they have in the bio-secure environment – and rightfully so. We respect that concern and have met with the England medical teams," said Manjra.
Ashley Giles, managing director of England men’s cricket, said in a statement, "The England party will remain at is base in Cape Town on Friday and Saturday and we are hopeful that the three-match series will be played before we depart next Thursday."
Suggestions have been made that the issues faced in adjusting to the bio-security protocols are perhaps understandable given this is South Africa's first series amid the pandemic.
But Dr Manjra quickly dismissed what one team spokesman said was a rumour that at least one player had left the hotel without any official clearance.
"I can categorically state that no player would be able to leave the hotel environment," he said, adding "It is impossible to leave except in an official vehicle with an official driver."
(Inputs from AFP)