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

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About: Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 Goto Sponge NotDistinct Permalink

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2
Creator	Kalimuddin, Shirin Schultz-Cherry, Stacey Wang, Lin-Fa Zhu, Feng Leo, Yee-Sin Maurer-Stroh, Sebastian Jayakumar, Jayanthi Pada, Surinder Yan, Gabriel Linster, Martin Low, Jenny Leo, Y-S Anderson, Danielle Jude, St Lee, Raphael Lye, David Mendenhall, Ian Smith, Gavin Su, Yvonne Young, Barnaby Chee, Wah Chia, Wan Tan, Wang, L-F Mak, Tze Linster, M Sun, Louisa Tan, Seow Chavatte, Jean-Marc Octavia, Sophie Zhuang, Yan Be, Young Chavatte, Octavia Cw, Tan Dc, Lye De, Anderson Gz, Yan Ih, Mendenhall Rtc, Lee Sy, Tan Tm, Mak Wn, Chia Ycf, Su
Source	Medline; PMC
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, have been observed in other geographic locations, including Australia, Bangladesh, and Spain. Mutations or deletions in ORF8 of SARS-CoV have been associated with reduced replicative fitness and virus attenuation. In contrast, the SARS-CoV-2 382-nt deletion viruses showed significantly higher replicative fitness in vitro than the wild type, while no difference was observed in patient viral load, indicating that the deletion variant viruses retained their replicative fitness. A robust antibody response to ORF8 has been observed in SARS-CoV-2 infection, suggesting that the emergence of ORF8 deletions may be due to immune-driven selection and that further deletion variants may emerge during the sustained transmission of SARS-CoV-2 in humans.
has issue date	2020-07-21(xsd:dateTime)
bibo:doi	10.1128/mbio.01610-20
bibo:pmid	32694143
has license	cc-by
sha1sum (hex)	b30a5b42f4cd2da1f50a53ee254799c7a938543d
schema:url	https://doi.org/10.1128/mbio.01610-20
resource representing a document's title	Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2
has PubMed Central identifier	PMC7374062
has PubMed identifier	32694143
schema:publication	mBio
resource representing a document's body	covid:b30a5b42f4cd2da1f50a53ee254799c7a938543d#body_text
is schema:about of	named entity 'genetic' named entity 'screened' named entity 'nucleotide' named entity 'reduced' named entity 'removing' named entity 'WILD TYPE' named entity 'CIRCULATING' named entity 'REPORT' named entity 'genome' named entity 'SARS-CoV-2' named entity 'fitness' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'samples' named entity 'replicative' named entity 'selection' named entity 'Mutations' named entity 'locations' named entity 'truncates' named entity 'transmission' named entity 'open reading frame' named entity 'severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)' named entity 'TRS' named entity 'contrast' named entity 'virus' named entity 'viruses' named entity 'SARS-CoV-2' named entity 'Singapore' named entity 'deletions' named entity 'viruses' named entity 'transcription' named entity 'infection' named entity 'wild type' named entity 'regulatory sequence' named entity 'transcription' named entity 'Spain' named entity 'SARS-CoV-2' named entity 'SARS epidemic' named entity 'immune response'

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