Loss of Detection of SgN Precedes Viral Abridged Replication in COVID-19-Affected Patients-A Target for SARS-CoV-2 Propagation

The development of prophylactic agents against the SARS-CoV-2 virus is a public health priority in the search for new surrogate markers of active virus replication. Early detection markers are needed to follow disease progression and foresee patient negativization. Subgenomic RNA transcripts (with a focus on sgN) were evaluated in oro/nasopharyngeal swabs from COVID-19-affected patients with an analysis of 315 positive samples using qPCR technology. Cut-off Cq values for sgN (Cq < 33.15) and sgE (Cq < 34.06) showed correlations to high viral loads. The specific loss of sgN in home-isolated and hospitalized COVID-19-positive patients indicated negativization of patient condition, 3-7 days from the first swab, respectively. A new detection kit for sgN, gene E, gene ORF1ab, and gene RNAse P was developed recently. In addition, in vitro studies have shown that 2'--methyl antisense RNA (related to the sgN sequence) can impair SARS-CoV-2 N protein synthesis, viral replication, and syncytia formation in human cells (i.e., HEK-293T cells overexpressing ACE2) upon infection with VOC Alpha (B.1.1.7)-SARS-CoV-2 variant, defining the use that this procedure might have for future therapeutic actions against SARS-CoV-2.

Citing Articles

Modulation of innate immunity related genes resulting in prophylactic antimicrobial and antiviral properties.

Ferrucci V, Miceli M, Pagliuca C, Bianco O, Castaldo L, Izzo L J Transl Med. 2024; 22(1):574.

PMID: 38886736 PMC: 11184722. DOI: 10.1186/s12967-024-05378-2.

Targeting ATP2B1 impairs PI3K/Akt/FOXO signaling and reduces SARS-COV-2 infection and replication.

De Antonellis P, Ferrucci V, Miceli M, Bibbo F, Asadzadeh F, Gorini F EMBO Rep. 2024; 25(7):2974-3007.

PMID: 38816514 PMC: 11239940. DOI: 10.1038/s44319-024-00164-z.

Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition.

Iacobucci I, Monaco V, Cane L, Bibbo F, Cioffi V, Cozzolino F Front Mol Biosci. 2022; 9:975570.

PMID: 36225252 PMC: 9550266. DOI: 10.3389/fmolb.2022.975570.

A Novel Human Neutralizing mAb Recognizes Delta, Gamma and Omicron Variants of SARS-CoV-2 and Can Be Used in Combination with Sotrovimab.

Passariello M, Ferrucci V, Sasso E, Manna L, Rapuano Lembo R, Pascarella S Int J Mol Sci. 2022; 23(10).

PMID: 35628365 PMC: 9146290. DOI: 10.3390/ijms23105556.

SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets.

Boccia A, Tufano R, Ferrucci V, Sepe L, Bianchi M, Pascarella S Int J Mol Sci. 2022; 23(8).

PMID: 35456974 PMC: 9029933. DOI: 10.3390/ijms23084155.

References

Sola I, Almazan F, Zuniga S, Enjuanes L . Continuous and Discontinuous RNA Synthesis in Coronaviruses. Annu Rev Virol. 2016; 2(1):265-88. PMC: 6025776. DOI: 10.1146/annurev-virology-100114-055218. View

Bussani R, Schneider E, Zentilin L, Collesi C, Ali H, Braga L . Persistence of viral RNA, pneumocyte syncytia and thrombosis are hallmarks of advanced COVID-19 pathology. EBioMedicine. 2020; 61:103104. PMC: 7677597. DOI: 10.1016/j.ebiom.2020.103104. View

Cantuti-Castelvetri L, Ojha R, Pedro L, Djannatian M, Franz J, Kuivanen S . Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science. 2020; 370(6518):856-860. PMC: 7857391. DOI: 10.1126/science.abd2985. View

Lin L, Li Q, Wang Y, Shi Y . Syncytia formation during SARS-CoV-2 lung infection: a disastrous unity to eliminate lymphocytes. Cell Death Differ. 2021; 28(6):2019-2021. PMC: 8114657. DOI: 10.1038/s41418-021-00795-y. View

Rajah M, Hubert M, Bishop E, Saunders N, Robinot R, Grzelak L . SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. EMBO J. 2021; 40(24):e108944. PMC: 8646911. DOI: 10.15252/embj.2021108944. View

Kim D, Lee J, Yang J, Kim J, Kim V, Chang H . The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020; 181(4):914-921.e10. PMC: 7179501. DOI: 10.1016/j.cell.2020.04.011. View

De Antonellis P, Liguori L, Falanga A, Carotenuto M, Ferrucci V, Andolfo I . MicroRNA 199b-5p delivery through stable nucleic acid lipid particles (SNALPs) in tumorigenic cell lines. Naunyn Schmiedebergs Arch Pharmacol. 2013; 386(4):287-302. DOI: 10.1007/s00210-013-0837-4. View

Vkovski P, Kratzel A, Steiner S, Stalder H, Thiel V . Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol. 2020; 19(3):155-170. PMC: 7592455. DOI: 10.1038/s41579-020-00468-6. View

Ferrucci V, Kong D, Asadzadeh F, Marrone L, Boccia A, Siciliano R . Long-chain polyphosphates impair SARS-CoV-2 infection and replication. Sci Signal. 2021; 14(690). PMC: 8432949. DOI: 10.1126/scisignal.abe5040. View

10.

Long S . SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses. 2021; 13(10). PMC: 8539008. DOI: 10.3390/v13101923. View

11.

Li T, Zhang Y, Fu L, Yu C, Li X, Li Y . siRNA targeting the leader sequence of SARS-CoV inhibits virus replication. Gene Ther. 2005; 12(9):751-61. PMC: 7091583. DOI: 10.1038/sj.gt.3302479. View

12.

Kgatle M, Lawal I, Mashabela G, Boshomane T, Koatale P, Mahasha P . COVID-19 Is a Multi-Organ Aggressor: Epigenetic and Clinical Marks. Front Immunol. 2021; 12:752380. PMC: 8531724. DOI: 10.3389/fimmu.2021.752380. View

13.

Zollo M, Ferrucci V, Izzo B, Quarantelli F, Di Domenico C, Comegna M . SARS-CoV-2 Subgenomic N () Transcripts in Oro-Nasopharyngeal Swabs Correlate with the Highest Viral Load, as Evaluated by Five Different Molecular Methods. Diagnostics (Basel). 2021; 11(2). PMC: 7923082. DOI: 10.3390/diagnostics11020288. View

14.

Buchrieser J, Dufloo J, Hubert M, Monel B, Planas D, Rajah M . Syncytia formation by SARS-CoV-2-infected cells. EMBO J. 2021; 40(3):e107405. PMC: 7849166. DOI: 10.15252/embj.2020107405. View

15.

Wolfel R, Corman V, Guggemos W, Seilmaier M, Zange S, Muller M . Virological assessment of hospitalized patients with COVID-2019. Nature. 2020; 581(7809):465-469. DOI: 10.1038/s41586-020-2196-x. View

16.

Dai L, Gao G . Viral targets for vaccines against COVID-19. Nat Rev Immunol. 2020; 21(2):73-82. PMC: 7747004. DOI: 10.1038/s41577-020-00480-0. View

17.

Braga L, Ali H, Secco I, Chiavacci E, Neves G, Goldhill D . Drugs that inhibit TMEM16 proteins block SARS-CoV-2 spike-induced syncytia. Nature. 2021; 594(7861):88-93. PMC: 7611055. DOI: 10.1038/s41586-021-03491-6. View

18.

Alexandersen S, Chamings A, Bhatta T . SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat Commun. 2020; 11(1):6059. PMC: 7695715. DOI: 10.1038/s41467-020-19883-7. View

19.

Zhang Z, Zheng Y, Niu Z, Zhang B, Wang C, Yao X . SARS-CoV-2 spike protein dictates syncytium-mediated lymphocyte elimination. Cell Death Differ. 2021; 28(9):2765-2777. PMC: 8056997. DOI: 10.1038/s41418-021-00782-3. View

20.

Wang D, Jiang A, Feng J, Li G, Guo D, Sajid M . The SARS-CoV-2 subgenome landscape and its novel regulatory features. Mol Cell. 2021; 81(10):2135-2147.e5. PMC: 7927579. DOI: 10.1016/j.molcel.2021.02.036. View