Author

P.-Y. Shi

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 46 Immunology· 11 Biophysics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 56 Research Focus:host-pathogen & immune response· 50 Organism:human· 28 Organism:mouse· 20 Research Focus:drug response / drug discovery· 15 Assay:proteomics· 8 Approach:statistical model· 5 Organism:virus· 5

Frequent Co-Authors

X. Xie· 41 shared J. Zou· 22 shared H. Xia· 18 shared V. D. Menachery· 15 shared C. Kurhade· 14 shared Y. Liu· 13 shared P. Ren· 12 shared J. Liu· 11 shared

Activity by Year

2017-2024 · peak 23/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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41 shared papersMicrobiology

X. Xie

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Author profile →

58 papers

Recent·Most cited

Targeting G9a translational mechanism of SARS-CoV-2 pathogenesis for multifaceted therapeutics of COVID-19 and its sequalae

A. Muneer, L. Xie, X. Xie, F. Zhang, J. Wrobel, X. Yan, X. Yu, C. Wang, C. Gheorghe, P. Wu, J. Song, G.-L. Ming, J. Jin, H. Song, P.-Y. Shi, X. Chen

This paper identifies G9a's role in SARS-CoV-2-induced pathogenesis by regulating translation of viral and host proteins, showing that G9a inhibitors can reverse disease-related proteomic changes.

bioRxiv · Mar 4, 2024Immunology

A Murine Model of Post-acute Neurological Sequelae Following SARS-CoV-2 Variant Infection

A. Singh, A. Adam, A. Aditi, B.-H. Peng, X. Yu, J. Zou, V. V. Kulkarni, P. Kan, W. Jiang, P.-Y. Shi, P. Samir, I. Cisneros, T. Wang

This study uses a murine model to investigate persistent neurological symptoms after SARS-CoV-2 Delta variant infection, finding long-term immune activation and behavioral abnormalities.

bioRxiv · Jan 3, 2024Microbiology

Resistance mechanisms of SARS-CoV-2 3CLpro to the non-covalent inhibitor WU-04

L. Zhang, X. Xie, H. Luo, H. Yu, J. Huang, P.-Y. Shi, Q. Hu

This study identifies two double mutations in SARS-CoV-2 3CLpro that confer resistance to the non-covalent inhibitor WU-04 and reveals trade-offs between catalytic activity, thermostability, and drug resistance.

bioRxiv · Nov 1, 2023Microbiology

Less neutralization evasion of SARS-CoV-2 BA.2.86 than XBB sublineages and CH.1.1

Y. Hu, J. Zou, C. Kurhade, X. Deng, H. C. Chang, D. K. Kim, P.-Y. Shi, P. Ren, X. Xie

This study compares the neutralization evasion of SARS-CoV-2 variants BA.2.86, XBB sublineages, and CH.1.1, finding BA.2.86 less evasive than XBB sublineages but CH.1.1 most evasive.

bioRxiv · Sep 10, 2023Microbiology

A single-dose of intranasal vaccination with a live-attenuated SARS-CoV-2 vaccine candidate promotes protective mucosal and systemic immunity

A. Adam, B. Kalveram, J. Y.-C. Chen, J. Yeung, L. Rodriguez, A. Singh, P.-Y. Shi, X. Xie, T. Wang

bioRxiv · Apr 17, 2023Microbiology

S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness

L. Yurkovetskiy, S. Egri, C. Kurhade, M. A. Diaz-Salinas, J. A. Jaimes, T. Nyalile, X. Xie, M. C. Choudhary, A. Dauphin, J. Z. Li, J. B. Munro, P.-Y. Shi, K. Shen, J. Luban

This study shows that S:D614G and S:H655Y mutations enhance SARS-CoV-2 infectivity by stabilizing the Spike protein in an open RBD conformation, acting epistatically with the polybasic S1/S2 cleavage site.

bioRxiv · Mar 30, 2023 · PreprintMicrobiology

Improved Neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with Bivalent BA.4/5 Vaccine

J. Zou, C. Kurhade, S. Patel, N. Kitchin, K. Tompkins, M. Cutler, D. Cooper, Q. Yang, H. Cai, A. Muik, Y. Zhang, D.-Y. Lee, U. Sahin, A. S. Anderson, W. C. Gruber, , P.-Y. Shi

This study compares the neutralizing antibody responses induced by monovalent and bivalent BA.4/5 vaccines against multiple Omicron sublineages in individuals over 55 years old, finding the bivalent vaccine elicits stronger neutralization.

bioRxiv · Nov 17, 2022 · PreprintMicrobiology

Cross-neutralization and viral fitness of SARS-CoV-2 Omicron sublineages

H. Xia, J. Yeung, B. Kalveram, C. J. Bills, J. Y.-C. Chen, C. Kurhade, j. Zou, S. G. Widen, B. R. Mann, R. J. Kondor, T. C. Davis, B. Zhou, D. E. Wentworth, X. Xie, P.-Y. Shi

This study examines the replication and cross-neutralization of SARS-CoV-2 Omicron sublineages in mice and human airway cultures, finding distinct antigenic profiles and bivalent vaccine support.

bioRxiv · Nov 8, 2022Microbiology

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1, and XBB.1 by 4 doses of parental mRNA vaccine or a BA.5-bivalent booster

C. Kurhade, J. Zou, H. Xia, M. Liu, H. C. Chang, P. Ren, X. Xie, P.-Y. Shi

This study evaluates the neutralization effectiveness of parental mRNA vaccines and BA.5-bivalent boosters against new SARS-CoV-2 variants, showing limited neutralization against BA.2.75.2, BQ.1.1, and XBB.1.

bioRxiv · Oct 31, 2022Microbiology

Determinants and Mechanisms of the Low Fusogenicity and Endosomal Entry of Omicron Subvariants

P. Qu, J. P. Evans, C. Kurhade, C. Zeng, Y.-M. Zheng, K. Xu, P.-Y. Shi, X. Xie, S.-L. Liu

This study identifies mutations in the Omicron subvariant spike protein that reduce fusogenicity and increase endosomal entry, revealing mechanisms behind their immune evasion and pathogenesis.

bioRxiv · Oct 15, 2022 · PreprintMicrobiology

Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro

N. Hou, L. Shuai, L. Zhang, X. Xie, K. Tang, Y. Zhu, Y. Yu, W. Zhang, Q. Tan, G. Zhong, Z. Wen, C. Wang, X. He, H. Huo, H. Gao, , Q. Hu

This study develops a potent non-covalent inhibitor of SARS-CoV-2 3CLpro, showing effective antiviral activity in human cells and animal models.

bioRxiv · Aug 10, 2022 · PreprintMicrobiology

Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of mRNA vaccine

X. Xie, J. Zou, C. Kurhade, M. Liu, P. Ren, P.-Y. Shi

This study evaluates the neutralization of SARS-CoV-2 Omicron sublineages by different vaccination regimens and finds that 4-dose mRNA vaccines provide lower neutralization compared to 2-dose plus BA.1 infection.

bioRxiv · Jul 29, 2022 · PreprintMicrobiology

Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis.

B. A. Johnson, Y. Zhou, K. G. Lokugamage, M. N. Vu, N. E. Bopp, P. A. Crocquet-Valdes, B. Kalveram, C. Schindewolf, Y. Liu, D. Scharton, J. A. Plante, X. Xie, P. Aguilar, S. Weaver, P.-Y. Shi, , V. D. Menachery

This study shows that mutations in the SARS-CoV-2 nucleocapsid protein enhance viral replication and pathogenesis by increasing phosphorylation and resisting kinase inhibition.

PLOS Pathogens · Jun 21, 2022Peer-reviewedMicrobiology

Neutralization of Omicron sublineages and Deltacron SARS-CoV-2 by 3 doses of BNT162b2 vaccine or BA.1 infection

C. Kurhade, j. Zou, H. Xia, M. Liu, Q. Yang, M. Cutler, D. Cooper, A. Muik, U. Sahin, K. U. Jansen, P. Ren, X. Xie, K. A. Swanson, P.-Y. Shi

This study evaluates the neutralization of Omicron sublineages and Deltacron by BNT162b2 vaccine or BA.1 infection, finding BA.4/5 shows highest evasion.

bioRxiv · Jun 5, 2022Microbiology

Antibody escape and cryptic cross-domain stabilization in the SARS CoV-2 Omicron spike protein

K. Javanmardi, T. H. Segall-Shapiro, C.-W. Chou, D. R. Boutz, R. J. Olsen, X. Xie, H. Xia, P.-Y. Shi, C. D. Johnson, A. Annapareddy, S. Weaver, J. M. Musser, A. D. Ellington, I. J. Finkelstein, J. D. Gollihar

This study examines the molecular effects of Omicron spike mutations on ACE2 binding and antibody escape, revealing compensatory stabilizing mutations that enable high mutation counts.

bioRxiv · Apr 18, 2022Immunology

SARS-CoV-2 Delta breakthrough infections in vaccinated patients

J. Zou, X. Xie, M. Liu, P.-Y. Shi, P. Ren

This study assesses neutralizing antibody titers in vaccinated individuals who experienced SARS-CoV-2 Delta breakthrough infections, finding that all had titers below 70.

bioRxiv · Apr 12, 2022 · PreprintMicrobiology

Cross neutralization of Omicron BA.1 against BA.2 and BA.3 SARS-CoV-2

J. Zou, C. Kurhade, H. Xia, M. Liu, X. Xie, P. Ren, P.-Y. Shi

The paper assesses cross-neutralization of Omicron BA.1 sera against BA.2, BA.3, and a pre-Omicron strain, finding reduced neutralizing titers against heterologous variants.

bioRxiv · Mar 30, 2022Microbiology

Neutralization of Omicron BA.1, BA.2, and BA.3 SARS-CoV-2 by 3 doses of BNT162b2 vaccine

C. Kurhade, j. Zou, H. Xia, H. Cai, Q. Yang, M. W. Cutler, D. Cooper, A. Muik, K. Jansen, X. Xie, K. Swanson, P.-Y. Shi

This study assesses the neutralization of Omicron sublineages BA.1, BA.2, and BA.3 by BNT162b2 vaccine sera, finding reduced neutralization compared to the original SARS-CoV-2 strain.

bioRxiv · Mar 24, 2022Microbiology

A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions

Y. Liu, X. Zhang, J. Liu, H. Xia, J. Zou, A. E. Muruato, S. Periasamy, J. A. Plante, N. E. Bopp, C. Kurhade, A. Bukreyev, P. Ren, T. Wang, V. D. Menachery, K. S. Plante, , P.-Y. Shi

This paper describes a live-attenuated SARS-CoV-2 vaccine candidate with deleted ORFs that shows reduced replication and attenuation in animal models, and reports its protective efficacy against wild-type virus challenge.

bioRxiv · Feb 14, 2022Microbiology

Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants

J. Pitts, J. Li, J. Perry, V. Du Pont, N. Riola, L. Rodriguez, X. Lu, C. Kurhade, X. Xie, G. Camus, S. Manhas, R. Martin, P.-Y. Shi, T. Cihlar, D. P. Porter, , J. P. Bilello

This study assesses the antiviral activity of remdesivir and GS-441524 against multiple SARS-CoV-2 variants, finding they remain effective against Delta, Omicron, and other variants.

bioRxiv · Feb 9, 2022Microbiology

Engineering SARS-CoV-2 cocktail antibodies into a bispecific format improves neutralizing potency and breadth

Z. Ku, X. Xie, J. Lin, P. Gao, A. E. Sahili, H. Su, Y. Liu, X. Ye, X. Li, X. Fan, B. C. Goh, W. Xiong, H. Boyd, A. E. Muruato, H. Deng, , Z. An

This study engineers bispecific antibodies against SARS-CoV-2, showing that one design outperforms a cocktail in neutralizing activity and breadth against variants.

bioRxiv · Feb 1, 2022 · PreprintMicrobiology

Neutralization of Omicron SARS-CoV-2 by 2 or 3 doses of BNT162b2 vaccine

H. Xia, J. Zou, C. Kurhade, H. Cai, Q. Yang, M. Cutler, D. Cooper, A. Muik, K. U. Jansen, X. Xie, K. A. Swanson, P.-Y. Shi

This study evaluates the neutralization of Omicron SARS-CoV-2 by two or three doses of the BNT162b2 vaccine, showing increased neutralization with three doses but reduced durability over time.

bioRxiv · Jan 21, 2022 · PreprintMicrobiology

Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection

j. Zou, H. Xia, X. Xie, C. Kurhade, R. R. Machado, S. C. Weaver, P. Ren, P.-Y. Shi

This study assesses cross-neutralization against Omicron SARS-CoV-2 from prior non-Omicron infections and finds significantly lower neutralization titers compared to the original strain.

bioRxiv · Dec 20, 2021Microbiology

Combinatorial mRNA vaccination enhances protection against SARS-CoV-2 delta variant

R. L. Hajnik, J. A. Plante, Y. Liang, M.-G. Alameh, J. Tang, C. Zhong, A. Adam, D. Scharton, G. H. Rafael, Y. Liu, N. C. Hazell, J. Sun, L. Soong, P.-Y. Shi, T. Wang, , H. Hu

This study shows that combining mRNA vaccines targeting the SARS-CoV-2 spike and nucleoprotein proteins enhances protection against the delta variant in animal models.

bioRxiv · Dec 8, 2021 · PreprintMicrobiology

Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines

L. Wang, M. H. Kainulainen, N. Jiang, H. Di, G. Bonenfant, L. Mills, M. Currier, P. Shrivastava-Ranjan, B. M. Calderon, M. Sheth, B. R. Mann, J. Hossain, X. Lin, S. Lester, E. Pusch, , Davis

This study evaluates how well antibodies from mRNA vaccines neutralize SARS-CoV-2 variants, finding that Omicron shows the most escape but booster doses maintain moderate neutralizing activity.

bioRxiv · Nov 24, 2021Microbiology

A modified porous silicon microparticle promotes mucosal delivery of SARS-CoV-2 antigen and induction of potent and durable systemic and mucosal T helper 1 skewed protective immunity

A. Adam, Q. Shi, B. Wang, J. Zou, J. Mai, S. R. Osman, W. Wu, X. Xie, P. V. Aguilar, X. Bao, P.-Y. Shi, H. Shen, T. Wang

bioRxiv · Nov 22, 2021 · PreprintImmunology

BNT162b2-Elicited Neutralization of Delta Plus, Lambda, and Other Variants

J. Liu, Y. Liu, H. Xia, J. Zou, S. Weaver, K. A. Swanson, H. Cai, M. Cutler, D. Cooper, A. Muik, K. U. Jansen, U. Sahin, X. Xie, P. R. Dormitzer, P.-Y. Shi

The paper assesses the neutralization ability of BNT162b2-elicited sera against SARS-CoV-2 variants, finding that all sera neutralize variants to titers of ≥80, indicating vaccine effectiveness against emerging strains.

bioRxiv · Sep 13, 2021 · PreprintMicrobiology

Distinct neutralizing kinetics and magnitudes elicited by different SARS-CoV-2 variant spikes

Y. Liu, J. Liu, J. Zou, P. Ren, S. Weaver, X. Xie, P.-Y. Shi

This study shows that immunization with different SARS-CoV-2 variant spikes leads to varying neutralizing kinetics and magnitudes against other variants, with significant differences in titers between homologous and heterologous variants.

bioRxiv · Sep 2, 2021 · PreprintMicrobiology

Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant

Y. Liu, J. Liu, B. A. Johnson, H. Xia, Z. Ku, C. Schindewolf, S. G. Widen, Z. An, S. Weaver, V. D. Menachery, X. Xie, P.-Y. Shi

This study identifies the P681R mutation in the Delta variant's spike protein as critical for enhanced viral replication compared to the Alpha variant through increased furin cleavage of the spike protein.

bioRxiv · Aug 12, 2021Microbiology

One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2

M. F. Tioni, R. Jordan, A. Silva Pena, A. Garg, D. Wu, S. I. Phan, X. Cheng, J. Greenhouse, T. Orekov, D. Valentin, S. Kar, L. Pessaint, H. Andersen, C. C. Stobart, M. H. Bloodworth, , R. S. Tang

This study shows that a single mucosal dose of the live attenuated RSV-based vaccine MV-014-212 protects non-human primates from SARS-CoV-2 infection by reducing viral shedding and inducing neutralizing antibodies.

bioRxiv · Jul 16, 2021Immunology