We would need more information about the retroviral vaccine and pregnancy stage of the mother, but it seems that only her and her pups will survive and they will be the original ancestors of all future dogs to come. Considering this situation, the mother and her pups face a grim future, since the next reasonable step would be to exploit them by keeping them constantly pregnant via artificial insemination in order to increase the gene pool and avoid a genetic bottleneck that would only postpone the extinction of dogs for a few more generations. Thus, trying to save a specific dog breed would not be a good solution, since we would need as much genetic diversity as possible.
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