Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

Vanaerschot, M.; Mann, S. A.; Webber, J. T.; Kamm, J.; Bell, S. M.; Bell, J.; Hong, S. N.; Nguyen, M. P.; Chan, L. Y.; Bhatt, K. D.; Tan, M.; Detweiler, A. M.; Espinosa, A.; Wu, W.; Batson, J.; Dynerman, D.; CLIAHUB Consortium,; Wadford, D. A.; Puschnik, A.; Neff, N.; Ahyong, V.; Miller, S.; Ayscue, P.; Tato, C. M.; Paul, S.; Kistler, A.; DeRisi, J. L.; Crawford, E. D.

doi:10.1101/2020.08.25.265074

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bioRxiv · 10.1101/2020.08.25.265074

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

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Abstract

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

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Vanaerschot, M., Mann, S. A., Webber, J. T., Kamm, J., Bell, S. M., Bell, J., Hong, S. N., Nguyen, M. P., Chan, L. Y., Bhatt, K. D., Tan, M., Detweiler, A. M., Espinosa, A., Wu, W., Batson, J., Dynerman, D., CLIAHUB Consortium,, Wadford, D. A., Puschnik, A., Neff, N., Ahyong, V., Miller, S., Ayscue, P., Tato, C. M., Paul, S., Kistler, A., DeRisi, J. L., Crawford, E. D.. 2020-08-26. Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay. https://doi.org/10.1101/2020.08.25.265074

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