Co-evolution of SARS-CoV-2 Variants and Host Immune Response Trajectories Underlie COVID-19 Pandemic to Epidemic Transition

Overview

Journal iScience

Publisher Cell Press

Date 2023 Nov 29

PMID 38025778

Authors

Ranjeet Maurya

Aparna Swaminathan

Uzma Shamim

Smriti Arora

Pallavi Mishra

Aakarshan Raina

Varsha Ravi

Bansidhar Tarai

Sandeep Budhiraja

Rajesh Pandey

Affiliations

Soon will be listed here.

Abstract

COVID-19 pandemic saw emergence of multiple SAR-CoV-2 variants. Exacerbated risk of severe outcome and hospital admissions led us to comprehend differential host-immune kinetics associated with SARS-CoV-2 variants. Longitudinal investigation was conducted through different time periods of Pre-VOC and VOCs (Delta & Omicron) mapping host transcriptome features. Robust antiviral type-1 interferon response marked Omicron infection, which was largely missing during Pre-VOC and Delta waves. SARS-CoV-2-host protein-protein interactions and docking complexes highlighted N protein to interact with HNRNPA1 in Pre-VOC, demonstrating its functional role for enhanced viral replication. Omicron revealed enhanced binding efficiency of LARP1 to N protein, probably potentiating antiviral effects of LARP1. Differential expression of zinc finger protein genes, especially in Omicron, mechanistically support induction of strong IFN (Interferon) response, thereby strengthening early viral clearance. Study highlights eventual adaptation of host to immune activation patterns that interrupt virus evolution with enhanced immune-evasion mutations and counteraction mechanisms, delimiting the next phase of COVID-19 pandemic.

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References

Chu J, Li Y, He M, Zhang H, Yang L, Yang M . Zinc finger and SCAN domain containing 1, ZSCAN1, is a novel stemness-related tumor suppressor and transcriptional repressor in breast cancer targeting TAZ. Front Oncol. 2023; 13:1041688. PMC: 10009259. DOI: 10.3389/fonc.2023.1041688. View

Ravikumar N, Randhawa M, Nallasamy K, Angurana S, Kumar M, Mohi G . Impact of Recent SARS-CoV-2 Infection on the Course and Severity of Dengue in Children: A Prospective Observational Study from North India. Am J Trop Med Hyg. 2021; 105(3):751-755. PMC: 8592356. DOI: 10.4269/ajtmh.21-0586. View

Ghimire D, Rai M, Gaur R . Novel host restriction factors implicated in HIV-1 replication. J Gen Virol. 2018; 99(4):435-446. DOI: 10.1099/jgv.0.001026. View

Butt A, Dargham S, Chemaitelly H, Al Khal A, Tang P, Hasan M . Severity of Illness in Persons Infected With the SARS-CoV-2 Delta Variant vs Beta Variant in Qatar. JAMA Intern Med. 2021; 182(2):197-205. PMC: 8696690. DOI: 10.1001/jamainternmed.2021.7949. View

Li J, Guo M, Tian X, Wang X, Yang X, Wu P . Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis. Med. 2020; 2(1):99-112.e7. PMC: 7373048. DOI: 10.1016/j.medj.2020.07.002. View

van Zundert G, Rodrigues J, Trellet M, Schmitz C, Kastritis P, Karaca E . The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol. 2015; 428(4):720-725. DOI: 10.1016/j.jmb.2015.09.014. View

Zhou Y, Liu Y, Gupta S, Paramo M, Hou Y, Mao C . A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nat Biotechnol. 2022; 41(1):128-139. PMC: 9851973. DOI: 10.1038/s41587-022-01474-0. View

Chemudupati M, Kenney A, Bonifati S, Zani A, McMichael T, Wu L . From APOBEC to ZAP: Diverse mechanisms used by cellular restriction factors to inhibit virus infections. Biochim Biophys Acta Mol Cell Res. 2018; 1866(3):382-394. PMC: 6334645. DOI: 10.1016/j.bbamcr.2018.09.012. View

Blom K, Marking U, Havervall S, Greilert Norin N, Gordon M, Garcia M . Immune responses after omicron infection in triple-vaccinated health-care workers with and without previous SARS-CoV-2 infection. Lancet Infect Dis. 2022; 22(7):943-945. PMC: 9183210. DOI: 10.1016/S1473-3099(22)00362-0. View

10.

Li H . Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18):3094-3100. PMC: 6137996. DOI: 10.1093/bioinformatics/bty191. View

11.

Mao R, Nie H, Cai D, Zhang J, Liu H, Yan R . Inhibition of hepatitis B virus replication by the host zinc finger antiviral protein. PLoS Pathog. 2013; 9(7):e1003494. PMC: 3708887. DOI: 10.1371/journal.ppat.1003494. View

12.

Li X, Wu K, Zeng S, Zhao F, Fan J, Li Z . Viral Infection Modulates Mitochondrial Function. Int J Mol Sci. 2021; 22(8). PMC: 8073244. DOI: 10.3390/ijms22084260. View

13.

Li D, Liu Y, Lu Y, Gao S, Zhang L . Palmitoylation of SARS-CoV-2 S protein is critical for S-mediated syncytia formation and virus entry. J Med Virol. 2021; 94(1):342-348. PMC: 8661603. DOI: 10.1002/jmv.27339. View

14.

Bick M, Carroll J, Gao G, Goff S, Rice C, MacDonald M . Expression of the zinc-finger antiviral protein inhibits alphavirus replication. J Virol. 2003; 77(21):11555-62. PMC: 229374. DOI: 10.1128/jvi.77.21.11555-11562.2003. View

15.

Xu N, Pan J, Sun L, Zhou C, Huang S, Chen M . Interferon α-2b spray shortened viral shedding time of SARS-CoV-2 Omicron variant: An open prospective cohort study. Front Immunol. 2022; 13:967716. PMC: 9390999. DOI: 10.3389/fimmu.2022.967716. View

16.

Kuruppuarachchi K, Jang Y, Seo S . Comparison of the Pathogenicity of SARS-CoV-2 Delta and Omicron Variants by Analyzing the Expression Patterns of Immune Response Genes in K18-hACE2 Transgenic Mice. Front Biosci (Landmark Ed). 2022; 27(11):316. DOI: 10.31083/j.fbl2711316. View

17.

Alfi O, Hamdan M, Wald O, Yakirevitch A, Wandel O, Oiknine-Djian E . SARS-CoV-2 Omicron Induces Enhanced Mucosal Interferon Response Compared to other Variants of Concern, Associated with Restricted Replication in Human Lung Tissues. Viruses. 2022; 14(7). PMC: 9318963. DOI: 10.3390/v14071583. View

18.

Laine L, Skon M, Vaisanen E, Julkunen I, Osterlund P . SARS-CoV-2 variants Alpha, Beta, Delta and Omicron show a slower host cell interferon response compared to an early pandemic variant. Front Immunol. 2022; 13:1016108. PMC: 9561549. DOI: 10.3389/fimmu.2022.1016108. View

19.

Nath H, Mallick A, Roy S, Kayal T, Ranjan S, Sengupta S . COVID-19 serum can be cross-reactive and neutralizing against the dengue virus, as observed by the dengue virus neutralization test. Int J Infect Dis. 2022; 122:576-584. PMC: 9262656. DOI: 10.1016/j.ijid.2022.07.013. View

20.

Yu G, Wang L, Han Y, He Q . clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284-7. PMC: 3339379. DOI: 10.1089/omi.2011.0118. View