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Background: Blood centers in India have published individual donor nucleic acid testing (ID-NAT) data based on an algorithm (Algorithm A) where serologically negative, NAT reactive sample was subsequently tested with discriminatory NAT (d-NAT), and on the basis of d-NAT, initial reactive samples were classified as “NAT yield” or inconclusive. We followed Algorithm B based on replicate testing and Ultrio Plus assay and compared the results with Algorithm A with Ultrio assay. Materials and Methods: Results of ID-NAT using two algorithms were analyzed. Results: A total of 88,583 (31,844 with Algorithm A and 56,739 with Algorithm B) samples were tested. Among serology nonreactive donations, NAT inconclusive results came down from 95.2% in Algorithm A to 73.1% in Algorithm B (P = 0.0001). Discriminated yield (DY) rate went up from 4.7% in Algorithm A to 21.9% in Algorithm B (P = 0.001). Conclusion: The study data suggest that replicate testing strategy and Ultrio Plus reduce the number of “inconclusive results” seen with earlier commonly used algorithm. We recommend a replicate testing strategy in ID-NAT testing since it will increase the DY and will eliminate the unnecessary discriminatory tests.