The University of Louisville Journal of Respiratory Infections

20.0786, 20.0257, 05.0556


he author(s) received no specific funding for this work


During the first two years of the coronavirus disease 2019 (COVID-19) pandemic, nasopharyngeal (NP) specimens were the gold standard for clinical diagnostic testing. As information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the pandemic continued to be shared, it was clear that the virus could be detected in other specimen types during an active infection. The University of Louisville Infectious Diseases Laboratory accepted non-traditional specimen types, most without a paired, positive NP result, for research purposes only to support local epidemiology efforts. A real-time reverse transcription-polymerase chain reaction (RT-PCR) assay originally validated for NP specimens was used for non-traditional specimen types using a variety of specimen preparation methods. Limit of detection (LOD) studies allowed for direct comparison between NP, sputum, and breast milk specimen types. The primary aim of the study was to determine whether SARS-CoV-2 RNA could be detected in different human specimen types. The results showed that the non-traditional specimens were not inherently inhibitory since SARS-CoV-2 RNA was detected in 36 (14.5%) out of 249 non-traditional specimens, and the limit of detection for SARS-CoV-2 in breast milk and sputum was the same as for NP specimens. SARS-CoV-2 was not detected in 15 breast milk specimens from mothers with positive SARS-CoV-2 NP results. In addition, a direct comparison study showed that NP specimens performed better than paired nasal specimens. In conclusion, by analyzing real-time RT-PCR test results for these non-traditional specimen types, two benefits were realized. Health care providers gained additional epidemiologic information (since information was not to be used for managing or treating patients), and the laboratory gathered important information about specimen types for which complete method validation studies could be pursued in the future.



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