Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2

Yvonne CF Su; Danielle E Anderson; Barnaby E Young; Martin Linster; Feng Zhu; Jayanthi Jayakumar; Yan Zhuang; Shirin Kalimuddin; Jenny GH Low; Chee Wah Tan; Wan Ni Chia; Tze Minn Mak; Sophie Octavia; Jean-Marc Chavatte; Raphael TC Lee; Surinder Pada; Seow Yen Tan; Louisa Sun; Gabriel Z Yan; Sebastian Maurer-Stroh; Ian H Mendenhall; Yee-Sin Leo; David Chien Lye; Lin-Fa Wang; Gavin JD Smith

Journal article

Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2

Yvonne CF Su, Danielle E Anderson, Barnaby E Young, Martin Linster, Feng Zhu, Jayanthi Jayakumar, Yan Zhuang, Shirin Kalimuddin, Jenny GH Low, Chee Wah Tan, Wan Ni Chia, Tze Minn Mak, Sophie Octavia, Jean-Marc Chavatte, Raphael TC Lee, Surinder Pada, Seow Yen Tan, Louisa Sun, Gabriel Z Yan, Sebastian Maurer-Stroh Show all

mBio | AMER SOC MICROBIOLOGY | Published : 2020

DOI: 10.1128/mBio.01610-20

Abstract

To date, limited genetic changes in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome have been described. Here, we report a 382-nucleotide (nt) deletion in SARS-CoV-2 that truncates open reading frame 7b (ORF7b) and ORF8, removing the ORF8 transcription regulatory sequence (TRS) and eliminating ORF8 transcription. The earliest 382-nt deletion variant was detected in Singapore on 29 January 2020, with the deletion viruses circulating in the country and accounting for 23.6% (45/191) of SARS-CoV-2 samples screened in this study. SARS-CoV-2 with the same deletion has since been detected in Taiwan, and other ORF7b/8 deletions of various lengths, ranging from 62 nt to 345 nt..

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University of Melbourne Researchers

Danielle Anderson Author Microbiology and Immunology

Grants

Awarded by National Medical Research Council

Awarded by National Research Foundation Singapore

Awarded by National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services

Funding Acknowledgements

This study was supported by the Duke-NUS Signature Research Programme funded by the Ministry of Health, Singapore; by the National Medical Research Council under its COVID-19 Research Fund (NMRC project no. COVID19RF-001 and COVID19RF-004); and by National Research Foundation Singapore grant NRF2016NRFNSFC002-013 (Combating the Next SARS-or MERS-Like Emerging Infectious Disease Outbreak by Improving Active Surveillance). R.T.C.L. and S.M.-S. were supported by A*STAR. Y.C.F.S. and G.J.D.S. are supported by contract HHSN272201400006C from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services.