[Journal of Medical Virology] Identification of nsp1 gene as the target of SARS‐CoV‐2 real‐time RT‐PCR using nanopore whole genome sequencing

Wan‐Mui Chan, Jonathan Daniel Ip, Allen Wing‐Ho Chu, Cyril Chik‐Yan Yip, Lap‐Sum Lo, Kwok‐Hung Chan, Anthony Chin‐Ki Ng, Rosana Wing‐Shan Poon, Wing‐Kin To, Owen Tak‐Yin Tsang, Wai‐Shing Leung, Mike Yat‐Wah Kwan, Gilbert T. Chua, Tom Wai‐Hin Chung, Ivan Fan‐Ngai Hung, Kin‐Hang Kok, Vincent Chi‐Chung Cheng, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen, Kelvin Kai‐Wang To

05 June, 2020

Highlights:

• There is an increasing number of SARS‐CoV‐2 viruses with mutations at the primer or probe binding sites
• These mutations may affect the sensitivity of currently available real‐time reverse transcription–polymerase chain reaction (RT‐PCR) assays targeting the N, E, and ORF1a/b genes
• The nsp1 gene, located at the 5’ end of the SARS‐CoV‐2 genome, was highly expressed in the nasopharyngeal or saliva specimens of 9 COVID‐19 patients
• Developed a novel nsp1 real‐time RT‐PCR assay which involve primers and probes that are highly specific for SARS‐CoV‐2
• The addition of nsp1 for multi‐target detection of SARS‐CoV‐2 can avoid false negative results due to mutations at the primers/probes binding sites of currently available RT‐PCR assays

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