An 81-Nucleotide Deletion in SARS-CoV-2 ORF7a Identified from Sentinel Surveillance in Arizona (January to March 2020)

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2020 May 3

PMID 32357959

Citations 89

Authors

LaRinda A Holland

Emily A Kaelin

Rabia Maqsood

Bereket Estifanos

Lily I Wu

Arvind Varsani

Rolf U Halden

Brenda G Hogue

Matthew Scotch

Efrem S Lim

Affiliations

Soon will be listed here.

Citing Articles

SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions.

Timilsina U, Ivey E, Duffy S, Plianchaisuk A, The Genotype To Phenotype Japan G P-Japan Consortium , Ito J Int J Mol Sci. 2024; 25(4).

PMID: 38397027 PMC: 10889720. DOI: 10.3390/ijms25042351.

Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022.

Scotch M, Lauer K, Wieben E, Cherukuri Y, Cunningham J, Klee E mSphere. 2023; 8(6):e0023223.

PMID: 37882516 PMC: 10871168. DOI: 10.1128/msphere.00232-23.

The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection.

Bykova A, Saura A, Glazko G, Roche-Lima A, Yurchenko V, Rogozin I BMC Genomics. 2023; 24(1):387.

PMID: 37430204 PMC: 10332002. DOI: 10.1186/s12864-023-09482-3.

Evolution of the newest diagnostic methods for COVID-19: a Chinese perspective.

Liu M, Lyu J, Zheng X, Liang Z, Lei B, Chen H J Zhejiang Univ Sci B. 2023; 24(6):463-484.

PMID: 37309039 PMC: 10264177. DOI: 10.1631/jzus.B2200625.

Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture.

Simas M, Costa S, Gomes P, Cruz N, Correa I, de Souza M Viruses. 2023; 15(3).

PMID: 36992509 PMC: 10051148. DOI: 10.3390/v15030801.

References

Suchard M, Lemey P, Baele G, Ayres D, Drummond A, Rambaut A . Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018; 4(1):vey016. PMC: 6007674. DOI: 10.1093/ve/vey016. View

Tan Y, Fielding B, Goh P, Shen S, Tan T, Lim S . Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway. J Virol. 2004; 78(24):14043-7. PMC: 533950. DOI: 10.1128/JVI.78.24.14043-14047.2004. View

Yang Z . Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 1994; 39(3):306-14. DOI: 10.1007/BF00160154. View

Su Y, Anderson D, Young B, Linster M, Zhu F, Jayakumar J . Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2. mBio. 2020; 11(4). PMC: 7374062. DOI: 10.1128/mBio.01610-20. View

Taylor J, Coleman C, Postel S, Sisk J, Bernbaum J, Venkataraman T . Severe Acute Respiratory Syndrome Coronavirus ORF7a Inhibits Bone Marrow Stromal Antigen 2 Virion Tethering through a Novel Mechanism of Glycosylation Interference. J Virol. 2015; 89(23):11820-33. PMC: 4645327. DOI: 10.1128/JVI.02274-15. View

Schaecher S, Touchette E, Schriewer J, Buller R, Pekosz A . Severe acute respiratory syndrome coronavirus gene 7 products contribute to virus-induced apoptosis. J Virol. 2007; 81(20):11054-68. PMC: 2045523. DOI: 10.1128/JVI.01266-07. View

Muth D, Corman V, Roth H, Binger T, Dijkman R, Gottula L . Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission. Sci Rep. 2018; 8(1):15177. PMC: 6181990. DOI: 10.1038/s41598-018-33487-8. View

Patel A, Jernigan D . Initial Public Health Response and Interim Clinical Guidance for the 2019 Novel Coronavirus Outbreak - United States, December 31, 2019-February 4, 2020. MMWR Morb Mortal Wkly Rep. 2020; 69(5):140-146. PMC: 7004396. DOI: 10.15585/mmwr.mm6905e1. View

Hasegawa M, Kishino H, Yano T . Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985; 22(2):160-74. DOI: 10.1007/BF02101694. View

10.

Rambaut A, Drummond A, Xie D, Baele G, Suchard M . Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018; 67(5):901-904. PMC: 6101584. DOI: 10.1093/sysbio/syy032. View

11.

Corman V, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu D . Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020; 25(3). PMC: 6988269. DOI: 10.2807/1560-7917.ES.2020.25.3.2000045. View

12.

Nelson C, Pekosz A, Lee C, Diamond M, Fremont D . Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein. Structure. 2005; 13(1):75-85. PMC: 7125549. DOI: 10.1016/j.str.2004.10.010. View

13.

Pybus O, Rambaut A . GENIE: estimating demographic history from molecular phylogenies. Bioinformatics. 2002; 18(10):1404-5. DOI: 10.1093/bioinformatics/18.10.1404. View

14.

Yuan X, Wu J, Shan Y, Yao Z, Dong B, Chen B . SARS coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway. Virology. 2005; 346(1):74-85. PMC: 7111786. DOI: 10.1016/j.virol.2005.10.015. View

15.

Lauer S, Grantz K, Bi Q, Jones F, Zheng Q, Meredith H . The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med. 2020; 172(9):577-582. PMC: 7081172. DOI: 10.7326/M20-0504. View

16.

Rambaut A, Holmes E, OToole A, Hill V, McCrone J, Ruis C . A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020; 5(11):1403-1407. PMC: 7610519. DOI: 10.1038/s41564-020-0770-5. View

17.

Polgreen P, Bohnett L, Yang M, Pentella M, Cavanaugh J . A spatial analysis of the spread of mumps: the importance of college students and their spring-break-associated travel. Epidemiol Infect. 2009; 138(3):434-41. PMC: 2956339. DOI: 10.1017/S0950268809990719. View