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Pyke AT, Nair N, van den Hurk AF, Burtonclay P, Nguyen S, Barcelon J, Kistler C, Schlebusch S, McMahon J, Moore F. Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene. Viruses 2021; 13:v13061087. [PMID: 34200386 PMCID: PMC8227137 DOI: 10.3390/v13061087] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is a readily transmissible and potentially deadly pathogen which is currently re-defining human susceptibility to pandemic viruses in the modern world. The recent emergence of several genetically distinct descendants known as variants of concern (VOCs) is further challenging public health disease management, due to increased rates of virus transmission and potential constraints on vaccine effectiveness. We report the isolation of SARS-CoV-2 VOCs imported into Australia belonging to the B.1.351 lineage, first described in the Republic of South Africa (RSA), and the B.1.1.7 lineage originally reported in the United Kingdom, and directly compare the replication kinetics of these two VOCs in Vero E6 cells. In this analysis, we also investigated a B.1.1.7 VOC (QLD1516/2021) carrying a 7-nucleotide deletion in the open reading frame 7a (ORF7a) gene, likely truncating and rendering the ORF7a protein of this virus defective. We demonstrate that the replication of the B.1.351 VOC (QLD1520/2020) in Vero E6 cells can be detected earlier than the B.1.1.7 VOCs (QLD1516/2021 and QLD1517/2021), before peaking at 48 h post infection (p.i.), with significantly higher levels of virus progeny. Whilst replication of the ORF7a defective isolate QLD1516/2021 was delayed longer than the other viruses, slightly more viral progeny was produced by the mutant compared to the unmutated isolate QLD1517/2021 at 72 h p.i. Collectively, these findings contribute to our understanding of SARS-CoV-2 replication and evolutionary dynamics, which have important implications in the development of future vaccination, antiviral therapies, and epidemiological control strategies for COVID-19.
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Affiliation(s)
- Alyssa T. Pyke
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
- Correspondence:
| | - Neelima Nair
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Andrew F. van den Hurk
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Peter Burtonclay
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Son Nguyen
- Public Health Microbiology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia;
| | - Jean Barcelon
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Carol Kistler
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Sanmarié Schlebusch
- Public and Environmental Health, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia;
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia
- School of Medicine, Faculty of Medicine, University of Queensland, Herston, QLD 4072, Australia
| | - Jamie McMahon
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
| | - Frederick Moore
- Public Health Virology Laboratory, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, QLD 4108, Australia; (N.N.); (A.F.v.d.H.); (P.B.); (J.B.); (C.K.); (J.M.); (F.M.)
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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