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Joshi A, Maurya S, Mahale A, Rath SL, Tripathi T, Padhi AK. Delineating the Structure-Dynamics-Binding Differences among BA.1, BA.4/5, and BF.7 SARS-CoV-2 Variants through Atomistic Simulations: Correlation with Structural and Epidemiological Features. ACS OMEGA 2023; 8:37852-37863. [PMID: 37867647 PMCID: PMC10586286 DOI: 10.1021/acsomega.3c02904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/07/2023] [Indexed: 10/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus possessing a spike (S) protein that facilitates the entry of the virus into human cells. The emergence of highly transmissible and fit SARS-CoV-2 variants has been driven by the positive selection of mutations within the S-protein. Notable among these variants are alpha, beta, gamma, delta, and omicron (BA.1), with the latter contributing to significant global health challenges and impacting populations worldwide. Recently, a novel subvariant of BA.1, named BF.7, has surfaced, purportedly exhibiting elevated transmissibility and infectivity rates. In order to comprehend and compare the transmissibility and disease progression characteristics of distinct SARS-CoV-2 variants, we performed an extensive comparative analysis utilizing all-atom molecular dynamics (MD) simulations (in triplicate) to investigate the structural, dynamic, and binding features of BA.1, BA.4/5, and BF.7. Our simulation findings, energetic analysis, and assessment of physicochemical properties collectively illuminate the dominance of the BA.1 variant over the others, a trend that is further substantiated by the sustained global prevalence of BA.1 relative to BA.4/5 and BF.7. Additionally, our simulation results align well with the reported cryoelectron microscopy (cryo-EM) structural data and epidemiological characteristics obtained from the Global Initiative on Sharing All Influenza Data (GISAID). This study presents a comprehensive comparative elucidation of the critical structural, dynamic, and binding attributes of these variants, providing insights into the predominance of BA.1 and its propensity to continuously generate numerous novel subvariants.
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Affiliation(s)
- Aryaman Joshi
- Department
of Chemical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh India
| | - Shweata Maurya
- Laboratory
for Computational Biology & Biomolecular Design, School of Biochemical
Engineering, Indian Institute of Technology
(BHU), Varanasi 221005, Uttar Pradesh India
| | - Atharva Mahale
- Department
of Biotechnology, National Institute of
Technology, Warangal 506004, Telangana, India
| | - Soumya Lipsa Rath
- Department
of Biotechnology, National Institute of
Technology, Warangal 506004, Telangana, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Aditya K. Padhi
- Laboratory
for Computational Biology & Biomolecular Design, School of Biochemical
Engineering, Indian Institute of Technology
(BHU), Varanasi 221005, Uttar Pradesh India
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Rodriguez-Rodriguez BA, Ciabattoni GO, Valero-Jimenez AM, Crosse KM, Schinlever AR, Galvan JJR, Duerr R, Yeung ST, McGrath ME, Loomis C, Khanna KM, Desvignes L, Frieman MF, Ortigoza MB, Dittmann M. A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.04.510658. [PMID: 36238716 PMCID: PMC9558433 DOI: 10.1101/2022.10.04.510658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Small animal models have been a challenge for the study of SARS-CoV-2 transmission, with most investigators using golden hamsters or ferrets 1,2 . Mice have the advantages of low cost, wide availability, less regulatory and husbandry challenges, and the existence of a versatile reagent and genetic toolbox. However, adult mice do not transmit SARS-CoV-2 3 . Here we establish a model based on neonatal mice that allows for transmission of clinical SARS-CoV-2 isolates. We characterize tropism, respiratory tract replication and transmission of ancestral WA-1 compared to variants alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2) and omicron (B.1.1.529). We identify inter-variant differences in timing and magnitude of infectious particle shedding from index mice, both of which shape transmission to contact mice. Furthermore, we characterize two recombinant SARS-CoV-2 lacking either the ORF6 or ORF8 host antagonists. The removal of ORF8 shifts viral replication towards the lower respiratory tract, resulting in significantly delayed and reduced transmission. Our results demonstrate the potential of our neonatal mouse model to characterize viral and host determinants of SARS-CoV-2 transmission, while revealing for the first time a role for an accessory protein this context.
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Kaku CI, Starr TN, Zhou P, Dugan HL, Khalifé P, Song G, Champney ER, Mielcarz DW, Geoghegan JC, Burton DR, Raiees A, Bloom JD, Walker LM. Evolution of antibody immunity following Omicron BA.1 breakthrough infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.21.508922. [PMID: 36172124 PMCID: PMC9516849 DOI: 10.1101/2022.09.21.508922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Understanding the evolution of antibody immunity following heterologous SAR-CoV-2 breakthrough infection will inform the development of next-generation vaccines. Here, we tracked SARS-CoV-2 receptor binding domain (RBD)-specific antibody responses up to six months following Omicron BA.1 breakthrough infection in mRNA-vaccinated individuals. Cross-reactive serum neutralizing antibody and memory B cell (MBC) responses declined by two- to four-fold through the study period. Breakthrough infection elicited minimal de novo Omicron-specific B cell responses but drove affinity maturation of pre-existing cross-reactive MBCs toward BA.1. Public clones dominated the neutralizing antibody response at both early and late time points, and their escape mutation profiles predicted newly emergent Omicron sublineages. The results demonstrate that heterologous SARS-CoV-2 variant exposure drives the evolution of B cell memory and suggest that convergent neutralizing antibody responses continue to shape viral evolution.
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Affiliation(s)
- Chengzi I. Kaku
- Adimab, LLC, Lebanon, NH 03766, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tyler N. Starr
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Daniel W. Mielcarz
- Dartmouth Cancer Center, Geisel School of Medicine, Lebanon NH 03766, USA
| | | | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Andrabi Raiees
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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