SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming

Cell

2022 Dec 02

Wu, CT;Lidsky, PV;Xiao, Y;Cheng, R;Lee, IT;Nakayama, T;Jiang, S;He, W;Demeter, J;Knight, MG;Turn, RE;Rojas-Hernandez, LS;Ye, C;Chiem, K;Shon, J;Martinez-Sobrido, L;Bertozzi, CR;Nolan, GP;Nayak, JV;Milla, C;Andino, R;Jackson, PK;
PMID: 36580912 | DOI: 10.1016/j.cell.2022.11.030

How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger formation of apically extended and highly branched microvilli that organize viral egress from the microvilli back into the mucus layer, supporting a model of virus dispersion throughout airway tissue via mucociliary transport. Phosphoproteomics and kinase inhibition reveal that microvillar remodeling is regulated by p21-activated kinases (PAK). Importantly, Omicron variants bind with higher affinity to motile cilia and show accelerated viral entry. Our work suggests that motile cilia, microvilli, and mucociliary-dependent mucus flow are critical for efficient virus replication in nasal epithelia.

Exposure Route Influences Disease Severity in the COVID-19 Cynomolgus Macaque Model

Viruses

2022 May 10

Bixler, SL;Stefan, CP;Jay, AN;Rossi, FD;Ricks, KM;Shoemaker, CJ;Moreau, AM;Zeng, X;Hooper, JW;Dyer, DN;Frick, OM;Koehler, JW;Kearney, BJ;DiPinto, N;Liu, J;Tostenson, SD;Clements, TL;Smith, JM;Johnson, JA;Berrier, KL;Esham, HL;Delp, KL;Coyne, SR;Bloomfield, HA;Kuehnert, PA;Akers, K;Gibson, KM;Minogue, TD;Nalca, A;Pitt, MLM;
PMID: 35632755 | DOI: 10.3390/v14051013

The emergence of SARS-CoV-2 and the subsequent pandemic has highlighted the need for animal models that faithfully replicate the salient features of COVID-19 disease in humans. These models are necessary for the rapid selection, testing, and evaluation of potential medical countermeasures. Here, we performed a direct comparison of two distinct routes of SARS-CoV-2 exposure-combined intratracheal/intranasal and small particle aerosol-in two nonhuman primate species, rhesus and cynomolgus macaques. While all four experimental groups displayed very few outward clinical signs, evidence of mild to moderate respiratory disease was present on radiographs and at necropsy. Cynomolgus macaques exposed via the aerosol route also developed the most consistent fever responses and had the most severe respiratory disease and pathology. This study demonstrates that while all four models produced suitable representations of mild COVID-like illness, aerosol exposure of cynomolgus macaques to SARS-CoV-2 produced the most severe disease, which may provide additional clinical endpoints for evaluating therapeutics and vaccines.

SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence

Nature cell biology

2023 Mar 09

Gioia, U;Tavella, S;Martínez-Orellana, P;Cicio, G;Colliva, A;Ceccon, M;Cabrini, M;Henriques, AC;Fumagalli, V;Paldino, A;Presot, E;Rajasekharan, S;Iacomino, N;Pisati, F;Matti, V;Sepe, S;Conte, MI;Barozzi, S;Lavagnino, Z;Carletti, T;Volpe, MC;Cavalcante, P;Iannacone, M;Rampazzo, C;Bussani, R;Tripodo, C;Zacchigna, S;Marcello, A;d'Adda di Fagagna, F;
PMID: 36894671 | DOI: 10.1038/s41556-023-01096-x

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response. Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair. Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs' biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence.

An Engineered IgG-VHH Bispecific Antibody against SARS-CoV-2 and Its Variants

Small methods

2022 Oct 27

Chi, H;Wang, L;Liu, C;Cheng, X;Zheng, H;Lv, L;Tan, Y;Zhang, N;Zhao, S;Wu, M;Luo, D;Qiu, H;Feng, R;Fu, W;Zhang, J;Xiong, X;Zhang, Y;Zu, S;Chen, Q;Ye, Q;Yan, X;Hu, Y;Zhang, Z;Yan, R;Yin, J;Lei, P;Wang, W;Lang, G;Shao, J;Deng, Y;Wang, X;Qin, C;
PMID: 36300882 | DOI: 10.1002/smtd.202200932

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibodies are shown to be effective therapeutics for providing coronavirus disease 2019 (COVID-19) protection. However, recurrent variants arise and facilitate significant escape from current antibody therapeutics. Bispecific antibodies (bsAbs) represent a unique platform to increase antibody breadth and to reduce neutralization escape. Herein, a novel immunoglobulin G-variable domains of heavy-chain-only antibody (IgG-VHH) format bsAb derived from a potent human antibody R15-F7 and a humanized nanobody P14-F8-35 are rationally engineered. The resulting bsAb SYZJ001 efficiently neutralizes wild-type SARS-CoV-2 as well as the alpha, beta, gamma, and delta variants, with superior efficacy to its parental antibodies. Cryo-electron microscopy structural analysis reveals that R15-F7 and P14-F8-35 bind to nonoverlapping epitopes within the RBD and sterically hindered ACE2 receptor binding. Most importantly, SYZJ001 shows potent prophylactic and therapeutic efficacy against SARS-CoV-2 in three established mouse models. Collectively, the current results demonstrate that the novel bsAb format is feasible and effective, suggesting great potential as an inspiring antiviral strategy.

Rational development of a combined mRNA vaccine against COVID-19 and influenza

NPJ vaccines

2022 Jul 26

Ye, Q;Wu, M;Zhou, C;Lu, X;Huang, B;Zhang, N;Zhao, H;Chi, H;Zhang, X;Ling, D;Zhang, RR;Li, Z;Luo, D;Huang, YJ;Qiu, HY;Song, H;Tan, W;Xu, K;Ying, B;Qin, CF;
PMID: 35882870 | DOI: 10.1038/s41541-022-00478-w

As the world continues to experience the COVID-19 pandemic, seasonal influenza remain a cause of severe morbidity and mortality globally. Worse yet, coinfection with SARS-CoV-2 and influenza A virus (IAV) leads to more severe clinical outcomes. The development of a combined vaccine against both COVID-19 and influenza is thus of high priority. Based on our established lipid nanoparticle (LNP)-encapsulated mRNA vaccine platform, we developed and characterized a novel mRNA vaccine encoding the HA antigen of influenza A (H1N1) virus, termed ARIAV. Then, ARIAV was combined with our COVID-19 mRNA vaccine ARCoV, which encodes the receptor-binding domain (RBD) of the SARS-CoV-2 S protein, to formulate the final combined vaccine, AR-CoV/IAV. Further characterization demonstrated that immunization with two doses of AR-CoV/IAV elicited robust protective antibodies as well as antigen-specific cellular immune responses against SARS-CoV-2 and IAV. More importantly, AR-CoV/IAV immunization protected mice from coinfection with IAV and the SARS-CoV-2 Alpha and Delta variants. Our results highlight the potential of the LNP-mRNA vaccine platform in preventing COVID-19 and influenza, as well as other respiratory diseases.

In situ detection of vaccine mRNA in the cytoplasm of hepatocytes during COVID19 vaccine-related hepatitis

Journal of hepatology

2022 Sep 15

Martin-Navarro, L;de Andrea, C;Sangro, B;Argemi, J;
PMID: 36116717 | DOI: 10.1016/j.jhep.2022.08.039

Spike Protein-independent Attenuation of SARS-CoV-2 Omicron Variant in Laboratory Mice

Cell Reports

2022 Aug 01

Liu, S;Selvaraj, P;Sangare, K;Luan, B;Wang, T;
| DOI: 10.1016/j.celrep.2022.111359

Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration; Silver Spring, Maryland, USA, 20993

HISTOLOGICAL FINDINGS IN TRANSBRONCHIAL CRYOBIOPSIES OBTAINED FROM PATIENTS AFTER COVID-19

Chest

2021 Sep 25

Culebras, M;Loor, K;Sansano, I;Persiva, Ó;Clofent, D;Polverino, E;Felipe, A;Osorio, J;Muñoz, X;Álvarez, A;Se-COVID-19 team, ;
PMID: 34582842 | DOI: 10.1016/j.chest.2021.09.016

Immunological and pathological outcomes of SARS-CoV-2 challenge following formalin-inactivated vaccine in ferrets and rhesus macaques

Science advances

2021 Sep 10

Bewley, KR;Gooch, K;Thomas, KM;Longet, S;Wiblin, N;Hunter, L;Chan, K;Brown, P;Russell, RA;Ho, C;Slack, G;Humphries, HE;Alden, L;Allen, L;Aram, M;Baker, N;Brunt, E;Cobb, R;Fotheringham, S;Harris, D;Kennard, C;Leung, S;Ryan, K;Tolley, H;Wand, N;White, A;Sibley, L;Sarfas, C;Pearson, G;Rayner, E;Xue, X;Lambe, T;Charlton, S;Gilbert, S;Sattentau, QJ;Gleeson, F;Hall, Y;Funnell, S;Sharpe, S;Salguero, FJ;Gorringe, A;Carroll, M;
PMID: 34516768 | DOI: 10.1126/sciadv.abg7996

[Figure: see text].

Persistence of SARS-CoV-2 RNA in lung tissue after mild COVID-19

The Lancet. Respiratory medicine

2021 Jun 09

Ceulemans, LJ;Khan, M;Yoo, SJ;Zapiec, B;Van Gerven, L;Van Slambrouck, J;Vanstapel, A;Van Raemdonck, D;Vos, R;Wauters, E;Wauters, J;Carmeliet, P;Mombaerts, P;
PMID: 34118186 | DOI: 10.1016/S2213-2600(21)00240-X

ACE2 expression is regulated by AhR in SARS-CoV-2-infected macaques

Cellular & molecular immunology

2021 Apr 01

Lv, J;Yu, P;Wang, Z;Deng, W;Bao, L;Liu, J;Li, F;Zhu, Q;Zhou, N;Lv, Q;Wang, G;Wang, S;Zhou, Y;Song, J;Tong, WM;Liu, Y;Qin, C;Huang, B;
PMID: 33795851 | DOI: 10.1038/s41423-021-00672-1

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	Description
sense Example: Hs-LAG3-sense	Standard probes for RNA detection are in antisense. Sense probe is reverse complent to the corresponding antisense probe.
Intron# Example: Mm-Htt-intron2	Probe targets the indicated intron in the target gene, commonly used for pre-mRNA detection
Pool/Pan Example: Hs-CD3-pool (Hs-CD3D, Hs-CD3E, Hs-CD3G)	A mixture of multiple probe sets targeting multiple genes or transcripts
No-XSp Example: Hs-PDGFB-No-XMm	Does not cross detect with the species (Sp)
XSp Example: Rn-Pde9a-XMm	designed to cross detect with the species (Sp)
O# Example: Mm-Islr-O1	Alternative design targeting different regions of the same transcript or isoforms
CDS Example: Hs-SLC31A-CDS	Probe targets the protein-coding sequence only
EnEm	Probe targets exons n and m
En-Em	Probe targets region from exon n to exon m
Retired Nomenclature
tvn Example: Hs-LEPR-tv1	Designed to target transcript variant n
ORF Example: Hs-ACVRL1-ORF	Probe targets open reading frame
UTR Example: Hs-HTT-UTR-C3	Probe targets the untranslated region (non-protein-coding region) only
5UTR Example: Hs-GNRHR-5UTR	Probe targets the 5' untranslated region only
3UTR Example: Rn-Npy1r-3UTR	Probe targets the 3' untranslated region only
Pan Example: Pool	A mixture of multiple probe sets targeting multiple genes or transcripts

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