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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused a global public health emergency in humans from 2020 to 2023 and was associated with over 7 million human deaths. Besides humans, SARS-CoV-2 has been detected in a wide range of animals, including companion, farm, zoo, and wild animals. At least 61 animal species from 29 animal families of 12 animal orders have tested SARS-CoV-2 positive. Documented evidence reported that not only human-to-animal transmission but also animal-to-human transmission events occurred. During the course of the pandemic progression in humans, SARS-CoV-2 strains in animals evolved in parallel with those in humans. Continued monitoring of SARS-CoV-2 in animals is needed to safeguard both human and animal health. In this study, we report investigation of two outbreaks of SARS-CoV-2 Omicron variant infection in tigers and gorillas in two zoological institutions. In the first zoo, six tigers tested positive by SARS-CoV-2 real-time RT-PCR and shed viral nucleic acid in feces for up to two weeks. Three of the tigers showed intermittent shedding patterns, while the other tigers shed only for 7–10 days. No other species, including cheetah, otter, lion, anteater, gibbon, and tamarin, tested positive. During the outbreak at the second zoo, a total of six gorillas were tested positive for SARS-CoV-2, while other primates housed in the same building (colobus and orangutan) tested negative. Follow-up testing revealed that two gorillas tested positive for SARS-CoV-2 over a one-month period (30 and 33 days, respectively), while the other four gorillas had positive SARS-CoV-2 PCR results for 14 to 25 days. Four gorillas had intermittent shedding patterns. Notably, compared to tigers, gorillas had a prolonged duration of fecal viral shedding. Sequencing was performed on the positive samples, and analysis indicated that strains detected in tigers and gorillas belonged to SARS-CoV-2 Omicron BQ.1.10 and XBB.1.16, respectively. Overall, this study offers valuable insights into the duration of viral RNA shedding for SARS-CoV-2 Omicron in zoo animals, facilitating accurate diagnostic evaluation and management of infected tigers and gorillas.