Identification of nsp1 gene as the target of SARS-CoV-2

J. Med. Virol. · Nov 2020

Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole-genome sequencing.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic. Accurate detection of SARS-CoV-2 using molecular assays is critical for patient management and the control of the COVID-19 pandemic. However, there is an increasing number of SARS-CoV-2 viruses with mutations at the primer or probe binding sites, and these mutations may affect the sensitivity of currently available real-time reverse transcription-polymerase chain reaction (RT-PCR) assays targeting the nucleocapsid (N), envelope (E), and open reading frame 1a or 1b genes. ⋯ Validation with 101 clinical specimens showed that our nsp1 RT-PCR assay has a sensitivity of 93.1% (95% confidence interval [CI]: 86.2%-97.2%), which was similar to those of N and E gene RT-PCR assays. The diagnostic specificity was 100% (95% CI: 92.9%-100%). The addition of nsp1 for multitarget 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.

expand abstract… or not…
- 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, and Kelvin Kai-Wang To.
- State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China.
- J. Med. Virol. 2020 Nov 1; 92 (11): 2725-2734.
AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic. Accurate detection of SARS-CoV-2 using molecular assays is critical for patient management and the control of the COVID-19 pandemic. However, there is an increasing number of SARS-CoV-2 viruses with mutations at the primer or probe binding sites, and these mutations may affect the sensitivity of currently available real-time reverse transcription-polymerase chain reaction (RT-PCR) assays targeting the nucleocapsid (N), envelope (E), and open reading frame 1a or 1b genes. Using sequence-independent single-primer amplification and nanopore whole-genome sequencing, we have found that the nonstructural protein 1 (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 of different clinical severity. Based on this finding, we have developed a novel nsp1 real-time RT-PCR assay. The primers and probes are highly specific for SARS-CoV-2. Validation with 101 clinical specimens showed that our nsp1 RT-PCR assay has a sensitivity of 93.1% (95% confidence interval [CI]: 86.2%-97.2%), which was similar to those of N and E gene RT-PCR assays. The diagnostic specificity was 100% (95% CI: 92.9%-100%). The addition of nsp1 for multitarget 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.© 2020 Wiley Periodicals LLC.

Pubmed Full text Copy Citation Plaintext

Add institutional full text...
Notes
Knowledge, pearl, summary or comment to share?

User can't be blank.

Content can't be blank.

Content is too short (minimum is 15 characters).

300 characters remaining

help

You can also include formatting, links, images and footnotes in your notes

Simple formatting can be added to notes, such as *italics*, _underline_ or **bold**.

Superscript can be denoted by <sup>text</sup> and subscript <sub>text</sub>.

Numbered or bulleted lists can be created using either numbered lines 1. 2. 3., hyphens - or asterisks *.

Links can be included with: [my link to pubmed](http://pubmed.com)

Images can be included with: ![alt text](https://bestmedicaljournal.com/study_graph.jpg "Image Title Text")

For footnotes use [^1](This is a footnote.) inline.

Or use an inline reference [^1] to refer to a longer footnote elseweher in the document [^1]: This is a long footnote..
hide…

Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole-genome sequencing.

Notes

300 characters remaining

help

You can also include formatting, links, images and footnotes in your notes

What will the 'Medical Journal of You' look like?

Start your free 21 day trial now.