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Novel indel mutation in the N gene of SARS-CoV-2 clinical samples that were diagnosed positive in a commercial RT-PCR assay

Authors
 Sanghoo Lee  ;  DongJu Won  ;  Chang-Ki Kim  ;  Jinwoo Ahn  ;  Youngkee Lee  ;  Hyeongkyun Na  ;  Yun-Tae Kim  ;  Mi-Kyeong Lee  ;  Jong Rak Choi  ;  Hwan-Sub Lim  ;  Kyoung-Ryul Lee 
Citation
 VIRUS RESEARCH, Vol.297 : 198398, 2021-05 
Journal Title
VIRUS RESEARCH
ISSN
 0168-1702 
Issue Date
2021-05
MeSH
COVID-19 / diagnosis ; COVID-19 / virology* ; COVID-19 Nucleic Acid Testing ; Coronavirus Nucleocapsid Proteins / genetics* ; False Negative Reactions ; Genes, Viral ; Humans ; INDEL Mutation* ; Mass Screening ; Pandemics ; RNA, Viral / analysis ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2 / genetics* ; SARS-CoV-2 / isolation & purification
Keywords
Different geographical origins ; Indel mutation ; Nucleocapsid gene ; SARS-CoV-2 ; Viral genome sequencing
Abstract
Commercially available reverse transcription-polymerase chain reaction (RT-PCR) kits are being used as an important tool to diagnose SARS-CoV-2 infection in clinical laboratories worldwide. However, some kits lack sufficient clinical evaluation due to the need for emergency use caused by the current COVID-19 pandemic. Here we found that a novel insertion/deletion mutation in the nucleocapsid (N) gene of SARS-CoV-2 samples is a cause of negative results for the N gene in a widely used assay that received emergency use authorization (EUA) from US FDA and Conformite Europeenne-in vitro diagnostics (CE-IVD) from EU. Although SARS-CoV-2 is diagnosed positive by other target probes in the assay, our findings provide an evidence of the genetic variability and rapid evolution of SARS-CoV-2 as well as a reference in designing commercial RT-PCR assays.
DOI
10.1016/j.virusres.2021.198398
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Won, Dongju(원동주) ORCID logo https://orcid.org/0000-0002-0084-0216
Choi, Jong Rak(최종락) ORCID logo https://orcid.org/0000-0002-0608-2989
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/190941
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