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Abstract

Routine genomic surveillance on samples from COVID-19 patients collected in Poland during summer 2021 revealed the emergence of a SARS-CoV-2 Delta variant with a large 872 nt deletion. This change, confirmed by Sanger and deep sequencing, causes complete loss of , , and genes. The index case carrying the deletion is unknown. The standard pipeline for sequencing may mask this deletion with a long stretch of N’s. Effects of this deletion on phenotype or immune evasion needs further study.

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/content/10.2807/1560-7917.ES.2021.26.39.2100902
2021-09-30
2021-10-23
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2021.26.39.2100902
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References

  1. Global Initiative on Sharing All Influenza Data (GISAID). Munich: GISAID. [Accessed: 15 Sep 2021]. Available from: https://www.gisaid.org
  2. World Health Organization (WHO). Laboratory testing for coronavirus disease (‎COVID-19)‎ in suspected human cases: interim guidance, 19 March 2020. Geneva: WHO; 2020. Available from: https://apps.who.int/iris/handle/10665/331501
  3. Freed N, Silander O. SARS-CoV2 genome sequencing protocol (1200bp amplicon "midnight" primer set, using Nanopore Rapid kit). protocols.io. 2021.  https://doi.org/10.17504/protocols.io.bwyppfvn 
  4. Quick J. nCoV-2019 sequencing protocol v3 (LoCost). protocols.io. 2020. Available from: https://protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye
  5. Tyson J, James P, Stoddart D, Sparks N, Wickenhagen A, Hall G, et al. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv 2020.09.04.283077.  https://doi.org/10.1101/2020.09.04.283077 
  6. Duchene S, Featherstone L, Haritopoulou-Sinanidou M, Rambaut A, Lemey P, Baele G. Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol. 2020;6(2):veaa061.  https://doi.org/10.1093/ve/veaa061  PMID: 33235813 
  7. Muth D, Corman VM, Roth H, Binger T, Dijkman R, Gottula LT, et al. 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.  https://doi.org/10.1038/s41598-018-33487-8  PMID: 30310104 
  8. Pancer K, Milewska A, Owczarek K, Dabrowska A, Kowalski M, Łabaj PP, et al. The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans. PLoS Pathog. 2020;16(12):e1008959.  https://doi.org/10.1371/journal.ppat.1008959  PMID: 33301543 
  9. Pereira F. Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene. Infect Genet Evol. 2020;85:104525.  https://doi.org/10.1016/j.meegid.2020.104525  PMID: 32890763 
  10. Gamage AM, Tan KS, Chan WOY, Liu J, Tan CW, Ong YK, et al. Infection of human nasal epithelial cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles. PLoS Pathog. 2020;16(12):e1009130.  https://doi.org/10.1371/journal.ppat.1009130  PMID: 33284849 
  11. Zhang Y, Chen Y, Li Y, Huang F, Luo B, Yuan Y, et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι. Proc Natl Acad Sci USA. 2021;118(23):e2024202118.  https://doi.org/10.1073/pnas.2024202118  PMID: 34021074 
  12. Li J-Y, Liao C-H, Wang Q, Tan Y-J, Luo R, Qiu Y, et al. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020;286:198074.  https://doi.org/10.1016/j.virusres.2020.198074  PMID: 32589897 
  13. Silvas JA, Vasquez DM, Park J-G, Chiem K, Allué-Guardia A, Garcia-Vilanova A, et al. Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 human ACE2 transgenic mice. J Virol. 2021;95(17):e0040221.  https://doi.org/10.1128/JVI.00402-21  PMID: 34133899 
  14. Young BE, Fong SW, Chan YH, Mak TM, Ang LW, Anderson DE, et al. Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet. 2020;396(10251):603-11.  https://doi.org/10.1016/S0140-6736(20)31757-8  PMID: 32822564 
  15. Panzera Y, Ramos N, Frabasile S, Calleros L, Marandino A, Tomás G, et al. A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay. Transbound Emerg Dis. 2021;10.1111.  https://doi.org/10.1111/tbed.14002  PMID: 33501730 
  16. Tse H, Wong SC-Y, Ip K-F, Cheng VC-C, To KK-W, Lung DC, et al. Genome sequences of three SARS-CoV-2 ORF7a deletion variants obtained from patients in Hong Kong. Microbiol Resour Announc. 2021;10(15):7-9.  https://doi.org/10.1128/MRA.00251-21  PMID: 33858933 
  17. Addetia A, Xie H, Roychoudhury P, Shrestha L, Loprieno M, Huang M-L, et al. Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates. J Clin Virol. 2020;129:104523.  https://doi.org/10.1016/j.jcv.2020.104523  PMID: 32623351 
  18. Joonlasak K, Batty EM, Kochakarn T, Panthan B, Kümpornsin K, Jiaranai P, et al. Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a. Virus Res. 2021;292:198233.  https://doi.org/10.1016/j.virusres.2020.198233  PMID: 33227343 
  19. Su CM, Wang L, Yoo D. Activation of NF-κB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. Sci Rep. 2021;11(1):13464.  https://doi.org/10.1038/s41598-021-92941-2  PMID: 34188167 
  20. Zhou Z, Huang C, Zhou Z, Huang Z, Su L, Kang S, Chen X, Chen Q, He S, Rong X, Xiao F, Chen J, Chen S. Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes. iScience. 2021;24(3):102187.  https://doi.org/10.1016/j.isci.2021.102187  PMID: 33615195 
  21. Yang R, Zhao Q, Rao J, Zeng F, Yuan S, Ji M, et al. SARS-CoV-2 Accessory protein ORF7b mediates Tumor Necrosis Factor-α-induced apoptosis in cells. Front Microbiol. 2021;12:654709.  https://doi.org/10.3389/fmicb.2021.654709  PMID: 34484133 
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