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Chapman reported feeling ill on Monday and underwent a Covid-19 test with Lister being designated his replacement until the result is known. The match started a day later than the other two first-round Plunket Shield games, so the switch was made before the toss rather than in-match.
The ICC approved Covid-19 substitutes for Test cricket in June and various domestic competitions that have started since have followed similar guidelines.
New Zealand coach Gary Stead, who was watching the match at Eden Park's outer oval, said: "I wasn't aware until I got here this morning, that Mark Chapman had been feeling ill and had to get a Covid test. But from my perspective, it's great that he's not penalised for doing the right thing in what is obviously different times we face in the world.
"Just shows that we and cricket aren't immune to that either, so following the right protocols is definitely the right thing to do."
Lister claimed Auckland's first wicket of the season when he had Cam Hawkins caught behind, finishing with 1 for 40 from 12 overs as Otago were bowled out for 186 with Michael Rippon's century lifting them from 33 for 6.