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Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2
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 (TR...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374062/ https://www.ncbi.nlm.nih.gov/pubmed/32694143 http://dx.doi.org/10.1128/mBio.01610-20 |
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author | Su, Yvonne C. F. Anderson, Danielle E. Young, Barnaby E. Linster, Martin Zhu, Feng Jayakumar, Jayanthi Zhuang, Yan Kalimuddin, Shirin Low, Jenny G. H. Tan, Chee Wah Chia, Wan Ni Mak, Tze Minn Octavia, Sophie Chavatte, Jean-Marc Lee, Raphael T. C. Pada, Surinder Tan, Seow Yen Sun, Louisa Yan, Gabriel Z. Maurer-Stroh, Sebastian Mendenhall, Ian H. Leo, Yee-Sin Lye, David Chien Wang, Lin-Fa Smith, Gavin J. D. |
author_facet | Su, Yvonne C. F. Anderson, Danielle E. Young, Barnaby E. Linster, Martin Zhu, Feng Jayakumar, Jayanthi Zhuang, Yan Kalimuddin, Shirin Low, Jenny G. H. Tan, Chee Wah Chia, Wan Ni Mak, Tze Minn Octavia, Sophie Chavatte, Jean-Marc Lee, Raphael T. C. Pada, Surinder Tan, Seow Yen Sun, Louisa Yan, Gabriel Z. Maurer-Stroh, Sebastian Mendenhall, Ian H. Leo, Yee-Sin Lye, David Chien Wang, Lin-Fa Smith, Gavin J. D. |
author_sort | Su, Yvonne C. F. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7374062 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-73740622020-07-31 Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 Su, Yvonne C. F. Anderson, Danielle E. Young, Barnaby E. Linster, Martin Zhu, Feng Jayakumar, Jayanthi Zhuang, Yan Kalimuddin, Shirin Low, Jenny G. H. Tan, Chee Wah Chia, Wan Ni Mak, Tze Minn Octavia, Sophie Chavatte, Jean-Marc Lee, Raphael T. C. Pada, Surinder Tan, Seow Yen Sun, Louisa Yan, Gabriel Z. Maurer-Stroh, Sebastian Mendenhall, Ian H. Leo, Yee-Sin Lye, David Chien Wang, Lin-Fa Smith, Gavin J. D. mBio Research Article 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. American Society for Microbiology 2020-07-21 /pmc/articles/PMC7374062/ /pubmed/32694143 http://dx.doi.org/10.1128/mBio.01610-20 Text en Copyright © 2020 Su et al. https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Article Su, Yvonne C. F. Anderson, Danielle E. Young, Barnaby E. Linster, Martin Zhu, Feng Jayakumar, Jayanthi Zhuang, Yan Kalimuddin, Shirin Low, Jenny G. H. Tan, Chee Wah Chia, Wan Ni Mak, Tze Minn Octavia, Sophie Chavatte, Jean-Marc Lee, Raphael T. C. Pada, Surinder Tan, Seow Yen Sun, Louisa Yan, Gabriel Z. Maurer-Stroh, Sebastian Mendenhall, Ian H. Leo, Yee-Sin Lye, David Chien Wang, Lin-Fa Smith, Gavin J. D. Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title | Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title_full | Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title_fullStr | Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title_full_unstemmed | Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title_short | Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2 |
title_sort | discovery and genomic characterization of a 382-nucleotide deletion in orf7b and orf8 during the early evolution of sars-cov-2 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374062/ https://www.ncbi.nlm.nih.gov/pubmed/32694143 http://dx.doi.org/10.1128/mBio.01610-20 |
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