Journal article
Discovery and genomic characterization of a 382-nucleotide deletion in ORF7B and orf8 during the early evolution of SARS-CoV-2
YCF Su, DE Anderson, BE Young, M Linster, F Zhu, J Jayakumar, Y Zhuang, S Kalimuddin, JGH Low, CW Tan, WN Chia, TM Mak, S Octavia, JM Chavatte, RTC Lee, S Pada, SY Tan, L Sun, GZ Yan, S Maurer-Stroh Show all
Mbio | AMER SOC MICROBIOLOGY | Published : 2020
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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Awarded by National Institutes of Health
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.