1951
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Tian D, Sun Y, Zhou J, Ye Q. The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape. Front Immunol 2021; 12:751778. [PMID: 34917076 PMCID: PMC8669155 DOI: 10.3389/fimmu.2021.751778] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/08/2021] [Indexed: 12/18/2022] Open
Abstract
During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a "variant of concern (VOC)" by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.
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Affiliation(s)
| | | | | | - Qing Ye
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
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1952
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Garg AK, Mittal S, Padmanabhan P, Desikan R, Dixit NM. Increased B Cell Selection Stringency In Germinal Centers Can Explain Improved COVID-19 Vaccine Efficacies With Low Dose Prime or Delayed Boost. Front Immunol 2021; 12:776933. [PMID: 34917089 PMCID: PMC8669483 DOI: 10.3389/fimmu.2021.776933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022] Open
Abstract
The efficacy of COVID-19 vaccines appears to depend in complex ways on the vaccine dosage and the interval between the prime and boost doses. Unexpectedly, lower dose prime and longer prime-boost intervals have yielded higher efficacies in clinical trials. To elucidate the origins of these effects, we developed a stochastic simulation model of the germinal center (GC) reaction and predicted the antibody responses elicited by different vaccination protocols. The simulations predicted that a lower dose prime could increase the selection stringency in GCs due to reduced antigen availability, resulting in the selection of GC B cells with higher affinities for the target antigen. The boost could relax this selection stringency and allow the expansion of the higher affinity GC B cells selected, improving the overall response. With a longer dosing interval, the decay in the antigen with time following the prime could further increase the selection stringency, amplifying this effect. The effect remained in our simulations even when new GCs following the boost had to be seeded by memory B cells formed following the prime. These predictions offer a plausible explanation of the observed paradoxical effects of dosage and dosing interval on vaccine efficacy. Tuning the selection stringency in the GCs using prime-boost dosages and dosing intervals as handles may help improve vaccine efficacies.
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Affiliation(s)
- Amar K. Garg
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Soumya Mittal
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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1953
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Robust Representation and Efficient Feature Selection Allows for Effective Clustering of SARS-CoV-2 Variants. ALGORITHMS 2021. [DOI: 10.3390/a14120348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail, unlike any virus before it. On the one hand, this will help biologists, policymakers, and other authorities to make timely and appropriate decisions to control the spread of the coronavirus. On the other hand, such studies will help to more effectively deal with any possible future pandemic. Since the SARS-CoV-2 virus contains different variants, each of them having different mutations, performing any analysis on such data becomes a difficult task, given the size of the data. It is well known that much of the variation in the SARS-CoV-2 genome happens disproportionately in the spike region of the genome sequence—the relatively short region which codes for the spike protein(s). In this paper, we propose a robust feature-vector representation of biological sequences that, when combined with the appropriate feature selection method, allows different downstream clustering approaches to perform well on a variety of different measures. We use such proposed approach with an array of clustering techniques to cluster spike protein sequences in order to study the behavior of different known variants that are increasing at a very high rate throughout the world. We use a k-mers based approach first to generate a fixed-length feature vector representation of the spike sequences. We then show that we can efficiently and effectively cluster the spike sequences based on the different variants with the appropriate feature selection. Using a publicly available set of SARS-CoV-2 spike sequences, we perform clustering of these sequences using both hard and soft clustering methods and show that, with our feature selection methods, we can achieve higher F1 scores for the clusters and also better clustering quality metrics compared to baselines.
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1954
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Tam NM, Pham DH, Hiep DM, Tran PT, Quang DT, Ngo ST. Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations. RSC Adv 2021; 11:38495-38504. [PMID: 35493244 PMCID: PMC9044063 DOI: 10.1039/d1ra06534c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 novel coronavirus (SARS-CoV-2) worldwide has caused the coronavirus disease 2019 (COVID-19) pandemic. A hundred million people were infected, resulting in several millions of death worldwide. In order to prevent viral replication, scientists have been aiming to prevent the biological activity of the SARS-CoV-2 main protease (3CL pro or Mpro). In this work, we demonstrate that using a reasonable combination of deep-learning calculations and atomistic simulations could lead to a new approach for developing SARS-CoV-2 main protease (Mpro) inhibitors. Initially, the binding affinities of the natural compounds to SARS-CoV-2 Mpro were estimated via atomistic simulations. The compound tomatine, thevetine, and tribuloside could bind to SARS-CoV-2 Mpro with nanomolar/high-nanomolar affinities. Secondly, the deep-learning (DL) calculations were performed to chemically alter the top-lead natural compounds to improve ligand-binding affinity. The obtained results were then validated by free energy calculations using atomistic simulations. The outcome of the research will probably boost COVID-19 therapy. The hybrid DeepFrag/atomistic simulation approach could lead to a new scheme for developing SARS-CoV-2 3CLpro/Mpro inhibitors.![]()
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group, Ton Duc Thang University Ho Chi Minh City Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Duc-Hung Pham
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center Cincinnati Ohio 45229 USA
| | - Dinh Minh Hiep
- Department of Agriculture and Rural Development Ho Chi Minh City 71007 Vietnam
| | | | - Duong Tuan Quang
- Department of Chemistry, Hue University, Thua Thien Hue Province Hue City Vietnam
| | - Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam.,Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
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1955
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Das J, Thakuri B, MohanKumar K, Roy S, Sljoka A, Sun GQ, Chakraborty A. Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. ACS OMEGA 2021; 6:31312-31327. [PMID: 34805715 PMCID: PMC8592041 DOI: 10.1021/acsomega.1c05155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 05/04/2023]
Abstract
The emergence of a variety of highly transmissible SARS-CoV-2 variants, the causative agent of COVID-19, with multiple spike mutations poses serious challenges in overcoming the ongoing deadly pandemic. It is, therefore, essential to understand how these variants gain enhanced ability to evade immune responses with a higher rate of spreading infection. To address this question, here we have individually assessed the effects of SARS-CoV-2 variant-specific spike (S) protein receptor-binding domain (RBD) mutations E484K, K417N, L452Q, L452R, N501Y, and T478K that characterize and differentiate several emerging variants. Despite the hundreds of apparently neutral mutations observed in the domains other than the RBD, we have shown that each RBD mutation site is differentially engaged in an interdomain allosteric network involving mutation sites from a distant domain, affecting interactions with the human receptor angiotensin-converting enzyme-2 (ACE2). This allosteric network couples the residues of the N-terminal domain (NTD) and the RBD, which are modulated by the RBD-specific mutations and are capable of propagating mutation-induced perturbations between these domains through a combination of structural changes and effector-dependent modulations of dynamics. One key feature of this network is the inclusion of compensatory mutations segregated into three characteristically different clusters, where each cluster residue site is allosterically coupled with specific RBD mutation sites. Notably, each RBD mutation acted like a positive allosteric modulator; nevertheless, K417N was shown to have the largest effects among all of the mutations on the allostery and thereby holds the highest binding affinity with ACE2. This result will be useful for designing the targeted control measure and therapeutic efforts aiming at allosteric modulators.
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Affiliation(s)
- Jayanta
Kumar Das
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21287, United States
| | - Bikash Thakuri
- Department
of Mathematics, Sikkim University, Gangtok, Sikkim 737102, India
| | - Krishnan MohanKumar
- Department
of Pediatrics, Johns Hopkins University
School of Medicine, Baltimore, Maryland 21287, United States
| | - Swarup Roy
- Department
of Computer Applications, Sikkim University, Gangtok, Sikkim 737102, India
| | - Adnan Sljoka
- RIKEN
Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku Tokyo 103-0027, Japan
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Gui-Quan Sun
- Department
of Mathematics, North University of China, Taiyuan, Shanxi 030051, China
- Complex
Systems Research Center, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Amit Chakraborty
- Department
of Mathematics, Sikkim University, Gangtok, Sikkim 737102, India
- , . Phone: +91 9784811895
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1956
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Mathez G, Cagno V. Clinical severe acute respiratory syndrome coronavirus 2 isolation and antiviral testing. Antivir Chem Chemother 2021; 29:20402066211061063. [PMID: 34806440 PMCID: PMC8606911 DOI: 10.1177/20402066211061063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 is an RNA virus currently causing a pandemic. Due to errors during replication, mutations can occur and result in cell adaptation by the virus or in the rise of new variants. This can change the attachment receptors' usage, result in different morphology of plaques, and can affect as well antiviral development. Indeed, a molecule can be active on laboratory strains but not necessarily on circulating strains or be effective only against some viral variants. Experiments with clinical samples with limited cell adaptation should be performed to confirm the efficiency of drugs of interest. In this protocol, we present a method to culture severe acute respiratory syndrome coronavirus 2 from nasopharyngeal swabs, obtain a high viral titer while limiting cell adaptation, and assess antiviral efficiency.
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Affiliation(s)
- Gregory Mathez
- Institute of Microbiology, Lausanne University Hospital, 419236University of Lausanne, Switzerland
| | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, 419236University of Lausanne, Switzerland
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1957
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Kumar A, Parashar R, Kumar S, Faiq MA, Kumari C, Kulandhasamy M, Narayan RK, Jha RK, Singh HN, Prasoon P, Pandey SN, Kant K. Emerging SARS-CoV-2 variants can potentially break set epidemiological barriers in COVID-19. J Med Virol 2021; 94:1300-1314. [PMID: 34811761 PMCID: PMC9011477 DOI: 10.1002/jmv.27467] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/19/2021] [Indexed: 12/29/2022]
Abstract
Young age, female sex, absence of comorbidities, and prior infection or vaccination are known epidemiological barriers for contracting the new infection and/or increased disease severity. Demographic trends from the recent coronavirus disease 2019 waves, which are believed to be driven by newer severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants, indicate that the aforementioned epidemiological barriers are being breached and a larger number of younger and healthy individuals are developing severe disease. The new SARS‐CoV‐2 variants have key mutations that can induce significant changes in the virus‐host interactions. Recent studies report that, some of these mutations, singly or in a group, enhance key mechanisms, such as binding of the receptor‐binding domain (RBD) of the viral spike protein with the angiotensin‐converting enzyme 2 (ACE2) receptor in the host‐cells, increase the glycosylation of spike protein at the antigenic sites, and enhance the proteolytic cleavage of the spike protein, thus leading to improved host‐cell entry and the replication of the virus. The putative changes in the virus–host interactions imparted by the mutations in the RBD sequence can potentially be the reason behind the breach of the observed epidemiological barriers. Susceptibility for contracting SARS‐CoV‐2 infection and the disease outcomes are known to be influenced by host‐cell expressions of ACE2 and other proteases. The new variants can act more efficiently, and even with the lesser availability of the viral entry‐receptor and the associated proteases, can have more efficient host‐cell entry and greater replication resulting in high viral loads and prolonged viral shedding, widespread tissue‐injury, and severe inflammation leading to increased transmissibility and lethality. Furthermore, the accumulating evidence shows that multiple new variants have reduced neutralization by both, natural and vaccine‐acquired antibodies, indicating that repeated and vaccine breakthrough infections may arise as serious health concerns in the ongoing pandemic. Emerging SARS‐CoV‐2 variants:
Harbor key mutations altering the virus‐host interactions. Show more efficient host‐cell entry and greater replication resulting in higher viral loads, prolonged viral shedding, and greater tissue injury. Show reduced neutralization by natural and vaccine acquired antibodies. Causing symptomatic illness in increasing number of young, women, and healthy individuals.
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Affiliation(s)
- Ashutosh Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Rakesh Parashar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,India Health Lead, Oxford Policy Management Limited, Oxford, UK
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,New York University (NYU) Langone Health Center, NYU Robert I Grossman School of Medicine, New York, New York, USA
| | - Chiman Kumari
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Biochemistry, Maulana Azad Medical College (MAMC), New Delhi, India
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Rakesh K Jha
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Himanshu N Singh
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Systems Biology, Columbia University Irving Medical Center, New York, USA
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sada N Pandey
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Zoology, Banaras Hindu University (BHU), Varanasi, India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India.,Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bathinda, India
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1958
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Byun WG, Lee J, Kim S, Park SB. Harnessing stress granule formation by small molecules to inhibit the cellular replication of SARS-CoV-2. Chem Commun (Camb) 2021; 57:12476-12479. [PMID: 34734602 DOI: 10.1039/d1cc05508a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We identified small-molecule enhancers of cellular stress granules by observing molecular crowding of proteins and RNAs in a time-dependent manner. Hit molecules sensitized the IRF3-mediated antiviral mechanism in the presence of poly(I:C) and inhibited the replication of SARS-CoV-2 by inducing stress granule formation. Thus, modulating multimolecular crowding can be a promising strategy against SARS-CoV-2.
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Affiliation(s)
- Wan Gi Byun
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
| | - Jihye Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam 13488, Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
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1959
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Acharya A, Pandey K, Thurman M, Klug E, Trivedi J, Sharma K, Lorson CL, Singh K, Byrareddy SN. Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. J Virol 2021; 95:e0143721. [PMID: 34550770 PMCID: PMC8610590 DOI: 10.1128/jvi.01437-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/18/2021] [Indexed: 11/20/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 19 (COVID-19) pandemic. Despite unprecedented research and developmental efforts, SARS-CoV-2-specific antivirals are still unavailable for the treatment of COVID-19. In most instances, SARS-CoV-2 infection initiates with the binding of Spike glycoprotein to the host cell ACE2 receptor. Utilizing the crystal structure of the ACE2/Spike receptor-binding domain (S-RBD) complex (PDB file 6M0J) in a computer-aided drug design approach, we identified and validated five potential inhibitors of S-RBD and ACE-2 interaction. Two of the five compounds, MU-UNMC-1 and MU-UNMC-2, blocked the entry of pseudovirus particles expressing SARS-CoV-2 Spike glycoprotein. In live SARS-CoV-2 infection assays, both compounds showed antiviral activity with IC50 values in the micromolar range (MU-UNMC-1: IC50 = 0.67 μM and MU-UNMC-2: IC50 = 1.72 μM) in human bronchial epithelial cells. Furthermore, MU-UNMC-1 and MU-UNMC-2 effectively blocked the replication of rapidly transmitting variants of concern: South African variant B.1.351 (IC50 = 9.27 and 3.00 μM) and Scotland variant B.1.222 (IC50 = 2.64 and 1.39 μM), respectively. Following these assays, we conducted "induced-fit (flexible) docking" to understand the binding mode of MU-UNMC-1/MU-UNMC-2 at the S-RBD/ACE2 interface. Our data showed that mutation N501Y (present in B.1.351 variant) alters the binding mode of MU-UNMC-2 such that it is partially exposed to the solvent and has reduced polar contacts. Finally, MU-UNMC-2 displayed high synergy with remdesivir, the only approved drug for treating hospitalized COVID-19 patients. IMPORTANCE The ongoing coronavirus infectious disease 2019 (COVID-19) pandemic is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 207 million people have been infected globally, and 4.3 million have died due to this viral outbreak. While a few vaccines have been deployed, a SARS-CoV-2-specific antiviral for the treatment of COVID-19 is yet to be approved. As the interaction of SARS-CoV-2 Spike protein with ACE2 is critical for cellular entry, using a combination of a computer-aided drug design (CADD) approach and cell-based in vitro assays, we report the identification of five potential SARS-CoV-2 entry inhibitors. Out of the five, two compounds (MU-UNMC-1 and MU-UNMC-2) have antiviral activity against ancestral SARS-CoV-2 and emerging variants from South Africa and Scotland. Furthermore, MU-UNMC-2 acts synergistically with remdesivir (RDV), suggesting that RDV and MU-UNMC-2 can be developed as a combination therapy to treat COVID-19 patients.
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Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Michellie Thurman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Elizabeth Klug
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jay Trivedi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kalicharan Sharma
- Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Kamal Singh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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1960
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Kandimalla R, Chakraborty P, Vallamkondu J, Chaudhary A, Samanta S, Reddy PH, De Feo V, Dewanjee S. Counting on COVID-19 Vaccine: Insights into the Current Strategies, Progress and Future Challenges. Biomedicines 2021; 9:1740. [PMID: 34829969 PMCID: PMC8615473 DOI: 10.3390/biomedicines9111740] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
The emergence of a novel coronavirus viz., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019 and its subsequent substantial spread produced the coronavirus disease 2019 (COVID-19) pandemic worldwide. Given its unprecedented infectivity and pathogenicity, the COVID-19 pandemic had a devastating impact on human health, and its clinical management has been a great challenge, which has led to the development and speedy trials of several vaccine candidates against SARS-CoV-2 at an exceptional pace. As a result, several COVID-19 vaccines were made commercially available in the first half of 2021. Although several COVID-19 vaccines showed promising results, crucial insights into their epidemiology, protective mechanisms, and the propensities of reinfection are not largely reviewed. In the present report, we provided insights into the prospects of vaccination against COVID-19 and assessed diverse vaccination strategies including DNA, mRNA, protein subunits, vector-based, live attenuated, and inactivated whole/viral particle-based vaccines. Next, we reviewed major aspects of various available vaccines approved by the World Health Organization and by the local administrations to use against COVID-19. Moreover, we comprehensively assessed the success of these approved vaccines and also their untoward effects, including the possibility of reinfection. We also provided an update on the vaccines that are under development and could be promising candidates in the future. Conclusively, we provided insights into the COVID-19 vaccine epidemiology, their potency, and propensity for SARS-CoV-2 reinfection, while a careful review of their current status, strategies, success, and future challenges was also presented.
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Affiliation(s)
- Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, Telangana, India
| | - Pratik Chakraborty
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
| | | | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal 132001, Haryana, India;
| | - Sonalinandini Samanta
- Department of Dermatology (Skin & Venereology), ESIC Medical College & Hospital, Patna 801103, Bihar, India;
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
- Department of Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India;
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1961
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Emerging mutations in the SARS-CoV-2 variants and their role in antibody escape to small molecule-based therapeutic resistance. Curr Opin Pharmacol 2021; 62:64-73. [PMID: 34920267 PMCID: PMC8606259 DOI: 10.1016/j.coph.2021.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/07/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022]
Abstract
Several clinical trials started during the COVID-19 pandemic to discover effective therapeutics led to identify a few candidates from the major clinical trials. However, in the past several months, quite a few SARS-CoV-2 variants have emerged with significant mutations. Major mutations in the S-glycoprotein and other parts of the genome have led to the antibody's escape to small molecule-based therapeutic resistance. The mutations in S-glycoprotein trigger the antibody escape/resistance, and mutations in RdRp might cause remdesivir resistance. The article illustrates emerging mutations that have resulted in antibody escape to therapeutics resistance. In this direction, the article illustrates presently developed neutralizing antibodies (with their preclinical, clinical stages) and antibody escapes and associated mutations. Finally, owing to the RdRp mutations, the antiviral small molecules resistance is illustrated.
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1962
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Ghosh AK, Kaiser M, Molla MMA, Nafisa T, Yeasmin M, Ratul RH, Sharif MM, Akram A, Hosen N, Mamunur R, Amin MR, Islam A, Hoque ME, Landt O, Lytton SD. Molecular and Serological Characterization of the SARS-CoV-2 Delta Variant in Bangladesh in 2021. Viruses 2021; 13:v13112310. [PMID: 34835116 PMCID: PMC8623815 DOI: 10.3390/v13112310] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
Novel SARS-CoV-2 variants are emerging at an alarming rate. The delta variant and other variants of concern (VoC) carry spike (S)-protein mutations, which have the potential to evade protective immunity, to trigger break-through infections after COVID-19 vaccination, and to propagate future waves of COVID-19 pandemic. To identify SARS CoV-2 variants in Bangladesh, patients who are RT-PCR-positive for COVID-19 infections in Dhaka were screened by a RT-PCR melting curve analysis for spike protein mutations. To assess the anti-SARS CoV-2 antibody responses, the levels of the anti-S -proteins IgA and IgG and the anti-N-protein IgG were measured by ELISA. Of a total of 36 RT-PCR positive samples (75%), 27 were identified as delta variants, with one carrying an additional Q677H mutation and two with single nucleotide substitutions at position 23029 (compared to Wuhan-Hu-1 reference NC 045512) in the genome sequence. Three (8.3%) were identified as beta variants, two (5.5%) were identified as alpha variants, three (8.3%) were identified as having a B.1.1.318 lineage, and one sample was identified as an eta variant (B.1.525) carrying an additional V687L mutation. The trend of higher viral load (lower Cp values) among delta variants than in the alpha and beta variants was of borderline statistical significance (p = 0.045). Prospective studies with larger Bangladeshi cohorts are warranted to confirm the emergence of S-protein mutations and their association with antibody response in natural infection and potential breakthrough in vaccinated subjects.
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Affiliation(s)
- Asish Kumar Ghosh
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh; (A.K.G.); (R.H.R.); (M.M.S.); (M.R.A.)
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign GmbH, Eresburgstraße 22-23 D, 12103 Berlin, Germany;
| | - Md. Maruf Ahmed Molla
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Tasnim Nafisa
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Mahmuda Yeasmin
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Rifat Hossain Ratul
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh; (A.K.G.); (R.H.R.); (M.M.S.); (M.R.A.)
| | - Md. Mohiuddin Sharif
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh; (A.K.G.); (R.H.R.); (M.M.S.); (M.R.A.)
| | - Arifa Akram
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Nur Hosen
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Rashid Mamunur
- Bangladesh Institute Tropical Infectious Disease (BITID), Fouzderhat, Chittagong 4317, Bangladesh;
| | - Md. Robed Amin
- Department of Virology, Dhaka Medical College Hospital, Dhaka 1000, Bangladesh; (A.K.G.); (R.H.R.); (M.M.S.); (M.R.A.)
| | - Alimul Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Md. Ehsanul Hoque
- National Institute of Laboratory Medicine and Referral Center, Sher E-Bangla Nagar, Dhaka 1207, Bangladesh; (M.M.A.M.); (T.N.); (M.Y.); (A.A.); (N.H.); (M.E.H.)
| | - Olfert Landt
- TIB Molbiol GmbH, Eresburgstraße 22-23, 12103 Berlin, Germany;
| | - Simon D. Lytton
- SeraDiaLogistics, 81545 Munich, Germany
- Correspondence: ; Tel.: +49-172-49-11169
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1963
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Kayesh MEH, Kohara M, Tsukiyama-Kohara K. An Overview of Recent Insights into the Response of TLR to SARS-CoV-2 Infection and the Potential of TLR Agonists as SARS-CoV-2 Vaccine Adjuvants. Viruses 2021; 13:2302. [PMID: 34835108 PMCID: PMC8622245 DOI: 10.3390/v13112302] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to coronavirus disease (COVID-19), a global health pandemic causing millions of deaths worldwide. However, the immunopathogenesis of COVID-19, particularly the interaction between SARS-CoV-2 and host innate immunity, remains unclear. The innate immune system acts as the first line of host defense, which is critical for the initial detection of invading pathogens and the activation and shaping of adaptive immunity. Toll-like receptors (TLRs) are key sensors of innate immunity that recognize pathogen-associated molecular patterns and activate downstream signaling for pro-inflammatory cytokine and chemokine production. However, TLRs may also act as a double-edged sword, and dysregulated TLR responses may enhance immune-mediated pathology, instead of providing protection. Therefore, a proper understanding of the interaction between TLRs and SARS-CoV-2 is of great importance for devising therapeutic and preventive strategies. The use of TLR agonists as vaccine adjuvants for human disease is a promising approach that could be applied in the investigation of COVID-19 vaccines. In this review, we discuss the recent progress in our understanding of host innate immune responses in SARS-CoV-2 infection, with particular focus on TLR response. In addition, we discuss the use of TLR agonists as vaccine adjuvants in enhancing the efficacy of COVID-19 vaccine.
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Affiliation(s)
- Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan;
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal 8210, Bangladesh
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan;
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan;
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1964
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Mahindra A, Tejeda G, Rossi M, Janha O, Herbert I, Morris C, Morgan DC, Beattie W, Montezano AC, Hudson B, Tobin AB, Bhella D, Touyz RM, Jamieson AG, Baillie GS, Blair CM. Peptides derived from the SARS-CoV-2 receptor binding motif bind to ACE2 but do not block ACE2-mediated host cell entry or pro-inflammatory cytokine induction. PLoS One 2021; 16:e0260283. [PMID: 34793553 PMCID: PMC8601423 DOI: 10.1371/journal.pone.0260283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/05/2021] [Indexed: 11/19/2022] Open
Abstract
SARS-CoV-2 viral attachment and entry into host cells is mediated by a direct interaction between viral spike glycoproteins and membrane bound angiotensin-converting enzyme 2 (ACE2). The receptor binding motif (RBM), located within the S1 subunit of the spike protein, incorporates the majority of known ACE2 contact residues responsible for high affinity binding and associated virulence. Observation of existing crystal structures of the SARS-CoV-2 receptor binding domain (SRBD)-ACE2 interface, combined with peptide array screening, allowed us to define a series of linear native RBM-derived peptides that were selected as potential antiviral decoy sequences with the aim of directly binding ACE2 and attenuating viral cell entry. RBM1 (16mer): S443KVGGNYNYLYRLFRK458, RBM2A (25mer): E484GFNCYFPLQSYGFQPTNGVGYQPY508, RBM2B (20mer): F456NCYFPLQSYGFQPTNGVGY505 and RBM2A-Sc (25mer): NYGLQGSPFGYQETPYPFCNFVQYG. Data from fluorescence polarisation experiments suggested direct binding between RBM peptides and ACE2, with binding affinities ranging from the high nM to low μM range (Kd = 0.207-1.206 μM). However, the RBM peptides demonstrated only modest effects in preventing SRBD internalisation and showed no antiviral activity in a spike protein trimer neutralisation assay. The RBM peptides also failed to suppress S1-protein mediated inflammation in an endogenously expressing ACE2 human cell line. We conclude that linear native RBM-derived peptides are unable to outcompete viral spike protein for binding to ACE2 and therefore represent a suboptimal approach to inhibiting SARS-CoV-2 viral cell entry. These findings reinforce the notion that larger biologics (such as soluble ACE2, 'miniproteins', nanobodies and antibodies) are likely better suited as SARS-CoV-2 cell-entry inhibitors than short-sequence linear peptides.
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Affiliation(s)
- Amit Mahindra
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Gonzalo Tejeda
- Institute of Molecular Cell & Systems Biology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mario Rossi
- Institute of Molecular Cell & Systems Biology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Omar Janha
- Institute of Molecular Cell & Systems Biology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Imogen Herbert
- MRC Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Caroline Morris
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | | | - Wendy Beattie
- Institute of Cardiovascular and Medical Sciences, Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Augusto C. Montezano
- Institute of Cardiovascular and Medical Sciences, Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Hudson
- Institute of Molecular Cell & Systems Biology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew B. Tobin
- Institute of Molecular Cell & Systems Biology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Bhella
- MRC Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Rhian M. Touyz
- Institute of Cardiovascular and Medical Sciences, Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - George S. Baillie
- Institute of Cardiovascular and Medical Sciences, Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Connor M. Blair
- Institute of Cardiovascular and Medical Sciences, Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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1965
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Hossain MS, Pathan AQMSU, Islam MN, Tonmoy MIQ, Rakib MI, Munim MA, Saha O, Fariha A, Reza HA, Roy M, Bahadur NM, Rahaman MM. Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. INFORMATICS IN MEDICINE UNLOCKED 2021; 27:100798. [PMID: 34812411 PMCID: PMC8598266 DOI: 10.1016/j.imu.2021.100798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/06/2021] [Accepted: 11/15/2021] [Indexed: 01/31/2023] Open
Abstract
Genomic data analysis is a fundamental system for monitoring pathogen evolution and the outbreak of infectious diseases. Based on bioinformatics and deep learning, this study was designed to identify the genomic variability of SARS-CoV-2 worldwide and predict the impending mutation rate. Analysis of 259044 SARS-CoV-2 isolates identified 3334545 mutations with an average of 14.01 mutations per isolate. Globally, single nucleotide polymorphism (SNP) is the most prevalent mutational event. The prevalence of C > T (52.67%) was noticed as a major alteration across the world followed by the G > T (14.59%) and A > G (11.13%). Strains from India showed the highest number of mutations (48) followed by Scotland, USA, Netherlands, Norway, and France having up to 36 mutations. D416G, F106F, P314L, UTR:C241T, L93L, A222V, A199A, V30L, and A220V mutations were found as the most frequent mutations. D1118H, S194L, R262H, M809L, P314L, A8D, S220G, A890D, G1433C, T1456I, R233C, F263S, L111K, A54T, A74V, L183A, A316T, V212F, L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S missense mutations were found to largely decrease the structural stability of the corresponding proteins. Conversely, D3L, L5F, and S97I were found to largely increase the structural stability of the corresponding proteins. Multi-nucleotide mutations GGG > AAC, CC > TT, TG > CA, and AT > TA have come up in our analysis which are in the top 20 mutational cohort. Future mutation rate analysis predicts a 17%, 7%, and 3% increment of C > T, A > G, and A > T, respectively in the future. Conversely, 7%, 7%, and 6% decrement is estimated for T > C, G > A, and G > T mutations, respectively. T > G\A, C > G\A, and A > T\C are not anticipated in the future. Since SARS-CoV-2 is mutating continuously, our findings will facilitate the tracking of mutations and help to map the progression of the COVID-19 intensity worldwide.
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Affiliation(s)
- Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - A Q M Sala Uddin Pathan
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Nur Islam
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Maitreyee Roy
- School of Optometry and Vision Science, Faculty of Medicine and Health, University of New South Wales, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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1966
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Monoclonal Antibodies against Nucleocapsid Protein of SARS-CoV-2 Variants for Detection of COVID-19. Int J Mol Sci 2021; 22:ijms222212412. [PMID: 34830291 PMCID: PMC8623253 DOI: 10.3390/ijms222212412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/13/2021] [Accepted: 11/14/2021] [Indexed: 02/04/2023] Open
Abstract
Mitigation strategies of the coronavirus disease 2019 (COVID-19) pandemic have been greatly hindered by the continuous emergence of SARS-CoV-2 variants. New sensitive, rapid diagnostic tests for the wide-spectrum detection of viral variants are needed. We generated a panel of 41 monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein (NP) by using mice hybridoma techniques. Of these mAbs, nine exhibited high binding activities and were applied in latex-based lateral flow immunoassays (LFIAs). The LFIAs utilizing NP-mAb-7 and -40 had the best sensitivity and lowest limit of detection: 8 pg for purified NP and 625 TCID50/mL for the authentic virus (hCoV-19/Taiwan/4/2020). The specificity tests showed that the NP-mAb-40/7 LFIA strips did not cross-react with five human coronavirus strains or 20 other common respiratory pathogens. Importantly, we found that 10 NP mutants, including alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617.2) variants, could be detected by NP-mAb-40/7 LFIA strips. A clinical study (n = 60) of the NP-mAb-40/7 LFIA strips demonstrated a specificity of 100% and sensitivity of 90% in infected individuals with cycle threshold (Ct) values < 29.5. These anti-NP mAbs have strong potential for use in the clinical detection of SARS-CoV-2 infection, whether the virus is wild-type or a variant of concern.
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1967
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Khan MI, Baig MH, Mondal T, Alorabi M, Sharma T, Dong JJ, Cho JY. Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. Viruses 2021; 13:2295. [PMID: 34835101 PMCID: PMC8625741 DOI: 10.3390/v13112295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these "variants of concern" has increased immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (kappa and delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants.
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Affiliation(s)
- Mohd Imran Khan
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Tanmoy Mondal
- Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, 41345 Gothenburg, Sweden;
| | - Mohammed Alorabi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Tanuj Sharma
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea; (M.H.B.); (T.S.)
| | - Jae Yong Cho
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Gangnam-gu, Seoul 120-752, Korea;
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1968
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Roy U. Comparative structural analyses of selected spike protein-RBD mutations in SARS-CoV-2 lineages. Immunol Res 2021; 70:143-151. [PMID: 34782989 PMCID: PMC8592829 DOI: 10.1007/s12026-021-09250-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/01/2021] [Indexed: 10/31/2022]
Abstract
The severity of COVID-19 has been observed throughout the world as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) globally claimed more than 2 million lives and left a devastating impact worldwide. Recently several virulent mutant strains of this virus, such as the B.1.1.7, B.1.351, and P1 lineages, have emerged with initial predominance in UK, South Africa, and Brazil. Another extremely pathogenic B.1.617 lineage and its sub-lineages, first detected in India, are now affecting some countries at notably stronger spread-rates. The present paper computationally examines the time-based structures of B.1.1.7, B.1.351, and P1 lineages with selected spike protein mutations. The mutations in the more recently found B.1.617 lineage and its sub-lineages are explored, and the implications for multiple point mutations of the spike protein's receptor-binding domain (RBD) are described. The selected S1 mutations within the highly contagious B.1.617.2 sub-lineage, also known as the delta variant, are examined as well.
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Affiliation(s)
- Urmi Roy
- Department of Chemistry & Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699-5820, USA.
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1969
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Trimpert J, Herwig S, Stein J, Vladimirova D, Adler JM, Abdelgawad A, Firsching TC, Thoma T, Sehouli J, Osterrieder K, Gruber AD, Sawitzki B, Sander LE, Cichon G. Deciphering the Role of Humoral and Cellular Immune Responses in Different COVID-19 Vaccines-A Comparison of Vaccine Candidate Genes in Roborovski Dwarf Hamsters. Viruses 2021; 13:2290. [PMID: 34835096 PMCID: PMC8625836 DOI: 10.3390/v13112290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 01/09/2023] Open
Abstract
With the exception of inactivated vaccines, all SARS-CoV-2 vaccines currently used for clinical application focus on the spike envelope glycoprotein as a virus-specific antigen. Compared to other SARS-CoV-2 genes, mutations in the spike protein gene are more rapidly selected and spread within the population, which carries the risk of impairing the efficacy of spike-based vaccines. It is unclear to what extent the loss of neutralizing antibody epitopes can be compensated by cellular immune responses, and whether the use of other SARS-CoV-2 antigens might cause a more diverse immune response and better long-term protection, particularly in light of the continued evolution towards new SARS-CoV-2 variants. To address this question, we explored immunogenicity and protective effects of adenoviral vectors encoding either the full-length spike protein (S), the nucleocapsid protein (N), the receptor binding domain (RBD) or a hybrid construct of RBD and the membrane protein (M) in a highly susceptible COVID-19 hamster model. All adenoviral vaccines provided life-saving protection against SARS-CoV-2-infection. The most efficient protection was achieved after exposure to full-length spike. However, the nucleocapsid protein, which triggered a robust T-cell response but did not facilitate the formation of neutralizing antibodies, controlled early virus replication efficiently and prevented severe pneumonia. Although the full-length spike protein is an excellent target for vaccines, it does not appear to be the only option for future vaccine design.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Antigens, Viral/immunology
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- COVID-19/immunology
- COVID-19/pathology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/immunology
- Cricetinae
- Female
- Immunity, Cellular
- Immunity, Humoral
- Immunogenicity, Vaccine
- Inflammation
- Lung/pathology
- Lung/virology
- Male
- Mice, Inbred C57BL
- Phosphoproteins/genetics
- Phosphoproteins/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/immunology
- Mice
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Affiliation(s)
- Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.T.); (D.V.); (J.M.A.); (A.A.)
| | - Susanne Herwig
- Department of Gynecology, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany; (S.H.); (J.S.)
| | - Julia Stein
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; (J.S.); (T.T.); (B.S.)
| | - Daria Vladimirova
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.T.); (D.V.); (J.M.A.); (A.A.)
| | - Julia M. Adler
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.T.); (D.V.); (J.M.A.); (A.A.)
| | - Azza Abdelgawad
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (J.T.); (D.V.); (J.M.A.); (A.A.)
| | - Theresa C. Firsching
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (T.C.F.); (A.D.G.)
| | - Tizia Thoma
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; (J.S.); (T.T.); (B.S.)
| | - Jalid Sehouli
- Department of Gynecology, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany; (S.H.); (J.S.)
| | - Klaus Osterrieder
- Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong;
| | - Achim D. Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; (T.C.F.); (A.D.G.)
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; (J.S.); (T.T.); (B.S.)
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany;
| | - Günter Cichon
- Department of Gynecology, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany; (S.H.); (J.S.)
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1970
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Hulme KD, Noye EC, Short KR, Labzin LI. Dysregulated Inflammation During Obesity: Driving Disease Severity in Influenza Virus and SARS-CoV-2 Infections. Front Immunol 2021; 12:770066. [PMID: 34777390 PMCID: PMC8581451 DOI: 10.3389/fimmu.2021.770066] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/30/2021] [Indexed: 12/15/2022] Open
Abstract
Acute inflammation is a critical host defense response during viral infection. When dysregulated, inflammation drives immunopathology and tissue damage. Excessive, damaging inflammation is a hallmark of both pandemic influenza A virus (IAV) infections and Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) infections. Chronic, low-grade inflammation is also a feature of obesity. In recent years, obesity has been recognized as a growing pandemic with significant mortality and associated costs. Obesity is also an independent risk factor for increased disease severity and death during both IAV and SARS-CoV-2 infection. This review focuses on the effect of obesity on the inflammatory response in the context of viral respiratory infections and how this leads to increased viral pathology. Here, we will review the fundamentals of inflammation, how it is initiated in IAV and SARS-CoV-2 infection and its link to disease severity. We will examine how obesity drives chronic inflammation and trained immunity and how these impact the immune response to IAV and SARS-CoV-2. Finally, we review both medical and non-medical interventions for obesity, how they impact on the inflammatory response and how they could be used to prevent disease severity in obese patients. As projections of global obesity numbers show no sign of slowing down, future pandemic preparedness will require us to consider the metabolic health of the population. Furthermore, if weight-loss alone is insufficient to reduce the risk of increased respiratory virus-related mortality, closer attention must be paid to a patient’s history of health, and new therapeutic options identified.
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Affiliation(s)
- Katina D Hulme
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ellesandra C Noye
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Larisa I Labzin
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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1971
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. METHODS IN MICROBIOLOGY 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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1972
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Shagufta, Ahmad I. An Update on Pharmacological Relevance and Chemical Synthesis of Natural Products and Derivatives with Anti SARS-CoV-2 Activity. ChemistrySelect 2021; 6:11502-11527. [PMID: 34909460 PMCID: PMC8661826 DOI: 10.1002/slct.202103301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023]
Abstract
Natural products recognized traditionally as a vital source of active constituents in pharmacotherapy. The COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible, pathogenic, and considered an ongoing global health emergency. The emergence of COVID-19 globally and the lack of adequate treatment brought attention towards herbal medicines, and scientists across the globe instigated the search for novel drugs from medicinal plants and natural products to tackle this deadly virus. The natural products rich in scaffold diversity and structural complexity are an excellent source for antiviral drug discovery. Recently the investigation of several natural products and their synthetic derivatives resulted in the identification of promising anti SARS-CoV-2 agents. This review article will highlight the pharmacological relevance and chemical synthesis of the recently discovered natural product and their synthetic analogs as SARS-CoV-2 inhibitors. The summarized information will pave the path for the natural product-based drug discovery of safe and potent antiviral agents, particularly against SARS-CoV-2.
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Affiliation(s)
- Shagufta
- Department of Mathematics and Natural SciencesSchool of Arts and SciencesAmerican University of Ras Al KhaimahRas Al Khaimah Road, P. O. Box10021Ras Al Khaimah, UAE
| | - Irshad Ahmad
- Department of Mathematics and Natural SciencesSchool of Arts and SciencesAmerican University of Ras Al KhaimahRas Al Khaimah Road, P. O. Box10021Ras Al Khaimah, UAE
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1973
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Liu Y, Dai L, Feng X, Gao R, Zhang N, Wang B, Han J, Zou Q, Guo X, Zhu H, Liu J, Qin C, Zhang Y, Bao L, Li M. Fast and long-lasting immune response to S-trimer COVID-19 vaccine adjuvanted by PIKA. MOLECULAR BIOMEDICINE 2021; 2:29. [PMID: 34766005 PMCID: PMC8475395 DOI: 10.1186/s43556-021-00054-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
In the face of the emerging variants of SARS-CoV-2, there is an urgent need to develop a vaccine that can induce fast, effective, long-lasting and broad protective immunity against SARS-CoV-2. Here, we developed a trimeric SARS-CoV-2 S protein vaccine candidate adjuvanted by PIKA, which can induce robust cellular and humoral immune responses. The results showed a high level of neutralizing antibodies induced by the vaccine was maintained for at least 400 days. In the study of non-human primates, PIKA adjuvanted S-trimer induced high SARS-CoV-2 neutralization titers and protected from virus replication in the lung following SARS-CoV-2 challenge. In addition, the long-term neutralizing antibody response induced by S-trimer vaccine adjuvanted by PIKA could neutralize multiple SARS-CoV-2 variants and there is no obvious different among the SARS- CoV-2 variants of interest or concern, including B.1.351, B.1.1.7, P.1, B.1.617.1 and B.1.617.2 variants. These data support the utility of S-trimer protein adjuvanted by PIKA as a potential vaccine candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Yuan Liu
- YishengBio Co., Ltd, Beijing, China
| | - Lianpan Dai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Feng
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ran Gao
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | | | - Bin Wang
- YishengBio Co., Ltd, Beijing, China
| | - Jianbao Han
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qingcui Zou
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiling Guo
- National Health Commission of the People's Republic of China, Key Laboratory of Enteric Pathogenic Microbiology (Jiangsu Provincial Center for Disease Control and Prevention), Nanjing, China
| | - Hua Zhu
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Jiangning Liu
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Chuan Qin
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Yi Zhang
- YishengBio Co., Ltd, Beijing, China
| | - Linlin Bao
- National Animal Models for Human Diseases Resources Center, NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Minghua Li
- Kunming National High-Level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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1974
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Fatihi S, Rathore S, Pathak AK, Gahlot D, Mukerji M, Jatana N, Thukral L. A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Curr Res Struct Biol 2021; 3:290-300. [PMID: 34806033 PMCID: PMC8590475 DOI: 10.1016/j.crstbi.2021.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
The recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viral-host interactions. By temporally tracking 527,988 SARS-CoV-2 genomes, we identified invariant and hypervariable regions within the spike protein. We evaluated combination of mutations from SARS-CoV-2 lineages and found that maximum number of lineage-defining mutations were present in the N-terminal domain (NTD). Based on mutant 3D-structural models of known Variants of Concern (VOCs), we found that structural properties such as accessibility, secondary structural type, and intra-protein interactions at local mutation sites are greatly altered. Further, we observed significant differences between intra-protein networks of wild-type and Delta mutant, with the latter showing dense intra-protein contacts. Extensive molecular dynamics simulations of D614G mutant spike structure with hACE2 further revealed dynamic features with 47.7% of mutations mapping on flexible regions of spike protein. Thus, we propose that significant changes within spike protein structure have occurred that may impact SARS-CoV-2 pathogenesis, and repositioning of vaccine candidates is required to contain the spread of COVID-19 pathogen.
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Affiliation(s)
- Saman Fatihi
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Surabhi Rathore
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Ankit K. Pathak
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
| | - Deepanshi Gahlot
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
| | - Nidhi Jatana
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110 025, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC), Kamla Nehru Nagar, Ghaziabad, 201002, Uttar Pradesh, India
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1975
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Puligedda RD, Al-Saleem FH, Wirblich C, Kattala CD, Jović M, Geiszler L, Devabhaktuni H, Feuerstein GZ, Schnell MJ, Sack M, Livornese LL, Dessain SK. A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Diagnostics (Basel) 2021; 11:2092. [PMID: 34829439 PMCID: PMC8625484 DOI: 10.3390/diagnostics11112092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants.
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Affiliation(s)
- Rama Devudu Puligedda
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Fetweh H. Al-Saleem
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Cristoph Wirblich
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
| | - Chandana Devi Kattala
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | - Marko Jović
- Nicoya Lifesciences, Kitchener, ON N2G 2K4, Canada;
| | - Laura Geiszler
- Department of Internal Medicine, Lankenau Medical Center, Wynnewood, PA 19096, USA; (L.G.); (L.L.L.J.)
| | - Himani Devabhaktuni
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
| | | | - Matthias J. Schnell
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
| | | | - Lawrence L. Livornese
- Department of Internal Medicine, Lankenau Medical Center, Wynnewood, PA 19096, USA; (L.G.); (L.L.L.J.)
| | - Scott K. Dessain
- Center for Human Antibody Technology, Lankenau Institute for Medical Research, Wynnewood, PA 19096, USA; (R.D.P.); (F.H.A.-S.); (C.D.K.); (H.D.)
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (C.W.); (M.J.S.)
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1976
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Al-Karmalawy AA, Soltane R, Abo Elmaaty A, Tantawy MA, Antar SA, Yahya G, Chrouda A, Pashameah RA, Mustafa M, Abu Mraheil M, Mostafa A. Coronavirus Disease (COVID-19) Control between Drug Repurposing and Vaccination: A Comprehensive Overview. Vaccines (Basel) 2021; 9:1317. [PMID: 34835248 PMCID: PMC8622998 DOI: 10.3390/vaccines9111317] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 02/06/2023] Open
Abstract
Respiratory viruses represent a major public health concern, as they are highly mutated, resulting in new strains emerging with high pathogenicity. Currently, the world is suffering from the newly evolving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus is the cause of coronavirus disease 2019 (COVID-19), a mild-to-severe respiratory tract infection with frequent ability to give rise to fatal pneumonia in humans. The overwhelming outbreak of SARS-CoV-2 continues to unfold all over the world, urging scientists to put an end to this global pandemic through biological and pharmaceutical interventions. Currently, there is no specific treatment option that is capable of COVID-19 pandemic eradication, so several repurposed drugs and newly conditionally approved vaccines are in use and heavily applied to control the COVID-19 pandemic. The emergence of new variants of the virus that partially or totally escape from the immune response elicited by the approved vaccines requires continuous monitoring of the emerging variants to update the content of the developed vaccines or modify them totally to match the new variants. Herein, we discuss the potential therapeutic and prophylactic interventions including repurposed drugs and the newly developed/approved vaccines, highlighting the impact of virus evolution on the immune evasion of the virus from currently licensed vaccines for COVID-19.
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Affiliation(s)
- Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Department of Biology, Faculty of Sciences, Tunis El Manar University, Tunis 1068, Tunisia
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Mohamed A Tantawy
- Hormones Department, Medical Research and Clinical Studies Research Institute, National Research Centre, Dokki 12622, Egypt
- Stem Cells Laboratory, Center of Excellence for Advanced Sciences, National Research Centre, Dokki 12622, Egypt
| | - Samar A Antar
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Amani Chrouda
- Department of Chemistry, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11932, Saudi Arabia
- Laboratory of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University, Monastir 5000, Tunisia
- Institute of Analytical Sciences, UMR CNRS-UCBL-ENS 5280, 5 Rue la Doua, CEDEX, 69100 Villeurbanne, France
| | - Rami Adel Pashameah
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Muhamad Mustafa
- Department of Medicinal Chemistry, Deraya University, Minia 61111, Egypt
| | - Mobarak Abu Mraheil
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
| | - Ahmed Mostafa
- German Center for Infection Research (DZIF), Institute of Medical Microbiology, Justus-Liebig University, 35392 Giessen, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki 12622, Egypt
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1977
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Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Virus Res 2021; 308:198629. [PMID: 34780883 PMCID: PMC8585963 DOI: 10.1016/j.virusres.2021.198629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 12/11/2022]
Abstract
The E484K mutation at the SARS-CoV-2 Spike protein emerged independently in different variants around the world and has been widely associated with immune escape from neutralizing antibodies generated during previous infection or vaccination. In this work, the B.1 + L249S+E484K lineage was isolated along with A.1, B.1.420, and B.1.111 SARS-CoV-2 lineages without the E484K mutation and the neutralizing titer of convalescent sera was compared using microneutralization assays. While no significant differences in the neutralizing antibody titers were found between A.1 and B.lineages without the E484K mutation, the neutralizing titers against B.1 + L249S+E484K were 1.5, 1.9, 2.1, and 1.3-fold lower than against A.1, B.1.420, B.1.111-I, and B.1.111-II, respectively. However, molecular epidemiological data indicate that there is no increase in the transmissibility rate associated with this new lineage. This study supports the capability of new variants with the E484K mutation to be resistant to neutralization by humoral immunity, and therefore the need to intensify surveillance programs to determine if these lineages represent a risk for public health.
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1978
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Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T, Selent J. SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic Acids Res 2021; 50:D858-D866. [PMID: 34761257 PMCID: PMC8689960 DOI: 10.1093/nar/gkab977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
SCoV2-MD (www.scov2-md.org) is a new
online resource that systematically organizes atomistic simulations of the
SARS-CoV-2 proteome. The database includes simulations produced by leading
groups using molecular dynamics (MD) methods to investigate the
structure-dynamics-function relationships of viral proteins. SCoV2-MD
cross-references the molecular data with the pandemic evolution by tracking all
available variants sequenced during the pandemic and deposited in the GISAID
resource. SCoV2-MD enables the interactive analysis of the deposited
trajectories through a web interface, which enables users to search by viral
protein, isolate, phylogenetic attributes, or specific point mutation. Each
mutation can then be analyzed interactively combining static (e.g. a variety of
amino acid substitution penalties) and dynamic (time-dependent data derived from
the dynamics of the local geometry) scores. Dynamic scores can be computed on
the basis of nine non-covalent interaction types, including steric properties,
solvent accessibility, hydrogen bonding, and other types of chemical
interactions. Where available, experimental data such as antibody escape and
change in binding affinities from deep mutational scanning experiments are also
made available. All metrics can be combined to build predefined or custom scores
to interrogate the impact of evolving variants on protein structure and
function. SCoV2-MD is a new online resource that systematically organizes atomistic
simulations of the SARS-CoV-2 proteome. The database includes simulations
produced by leading groups using molecular dynamics (MD) methods to investigate
the structure-dynamics-function relationships of viral proteins. SCoV2-MD
cross-references the molecular data with the pandemic evolution by tracking all
available variants sequenced during the pandemic and deposited in the GISAID
resource. SCoV2-MD enables the interactive analysis of the deposited
trajectories through a web interface, which enables users to search by viral
protein, isolate, phylogenetic attributes, or specific point mutation. Each
mutation can then be analyzed interactively combining static (e.g. a variety of
amino acid substitution penalties) and dynamic (time-dependent data derived from
the dynamics of the local geometry) scores.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
| | - Alejandro Peralta-García
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Ramon Guixà-González
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.,Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Toni Giorgino
- Biophysics Institute (CNR-IBF), National Research Council of Italy, Milan 20133, Italy.,Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
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1979
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Kant R, Kareinen L, Smura T, Freitag TL, Jha SK, Alitalo K, Meri S, Sironen T, Saksela K, Strandin T, Kipar A, Vapalahti O. Common Laboratory Mice Are Susceptible to Infection with the SARS-CoV-2 Beta Variant. Viruses 2021; 13:2263. [PMID: 34835069 PMCID: PMC8619350 DOI: 10.3390/v13112263] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 01/25/2023] Open
Abstract
Small animal models are of crucial importance for assessing COVID-19 countermeasures. Common laboratory mice would be well-suited for this purpose but are not susceptible to infection with wild-type SARS-CoV-2. However, the development of mouse-adapted virus strains has revealed key mutations in the SARS-CoV-2 spike protein that increase infectivity, and interestingly, many of these mutations are also present in naturally occurring SARS-CoV-2 variants of concern. This suggests that these variants might have the ability to infect common laboratory mice. Herein we show that the SARS-CoV-2 beta variant attains infectibility to BALB/c mice and causes pulmonary changes within 2-3 days post infection, consistent with results seen in other murine models of COVID-19, at a reasonable virus dose (2 × 105 PFU). The findings suggest that common laboratory mice can serve as the animal model of choice for testing the effectiveness of antiviral drugs and vaccines against SARS-CoV-2.
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Affiliation(s)
- Ravi Kant
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Lauri Kareinen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Teemu Smura
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tobias L. Freitag
- Research Programs Unit, Immunobiology, University of Helsinki, 00290 Helsinki, Finland;
| | - Sawan Kumar Jha
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Kari Alitalo
- Translational Cancer Medicine Program, Faculty of Medicine and Helsinki Institute of Life Science, University of Helsinki, 00290 Helsinki, Finland; (S.K.J.); (K.A.)
| | - Seppo Meri
- Department of Bacteriology and Immunology and Translational Immunology Research Program, University of Helsinki, 00290 Helsinki, Finland;
| | - Tarja Sironen
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
| | - Kalle Saksela
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Tomas Strandin
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
| | - Anja Kipar
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L3 3RF, UK
| | - Olli Vapalahti
- Zoonosis Unit, Department of Virology, Medicum, University of Helsinki, 00290 Helsinki, Finland; (L.K.); (T.S.); (T.S.); (K.S.); (O.V.)
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland;
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, 00290 Helsinki, Finland
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1980
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Cueno ME, Imai K. Structural Insights on the SARS-CoV-2 Variants of Concern Spike Glycoprotein: A Computational Study With Possible Clinical Implications. Front Genet 2021; 12:773726. [PMID: 34745235 PMCID: PMC8568765 DOI: 10.3389/fgene.2021.773726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has been attributed to SARS-CoV-2 (SARS2) and, consequently, SARS2 has evolved into multiple SARS2 variants driving subsequent waves of infections. In particular, variants of concern (VOC) were identified to have both increased transmissibility and virulence ascribable to mutational changes occurring within the spike protein resulting to modifications in the protein structural orientation which in-turn may affect viral pathogenesis. However, this was never fully elucidated. Here, we generated spike models of endemic HCoVs (HCoV 229E, HCoV OC43, HCoV NL63, HCoV HKU1, SARS CoV, MERS CoV), original SARS2, and VOC (alpha, beta, gamma, delta). Model quality check, structural superimposition, and structural comparison based on RMSD values, TM scores, and contact mapping were all performed. We found that: 1) structural comparison between the original SARS2 and VOC whole spike protein model have minor structural differences (TM > 0.98); 2) the whole VOC spike models putatively have higher structural similarity (TM > 0.70) to spike models from endemic HCoVs coming from the same phylogenetic cluster; 3) original SARS2 S1-CTD and S1-NTD models are structurally comparable to VOC S1-CTD (TM = 1.0) and S1-NTD (TM > 0.96); and 4) endemic HCoV S1-CTD and S1-NTD models are structurally comparable to VOC S1-CTD (TM > 0.70) and S1-NTD (TM > 0.70) models belonging to the same phylogenetic cluster. Overall, we propose that structural similarities (possibly ascribable to similar conformational epitopes) may help determine immune cross-reactivity, whereas, structural differences (possibly associated with varying conformational epitopes) may lead to viral infection (either reinfection or breakthrough infection).
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Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan
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1981
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In Silico Identification and Clinical Validation of a Novel Long Non-Coding RNA/mRNA/miRNA Molecular Network for Potential Biomarkers for Discriminating SARS CoV-2 Infection Severity. Cells 2021; 10:cells10113098. [PMID: 34831321 PMCID: PMC8625524 DOI: 10.3390/cells10113098] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/23/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background: The coronavirus (COVID-19) pandemic is still a major global health problem, despite the development of several vaccines and diagnostic assays. Moreover, the broad symptoms, from none to severe pneumonia, and the various responses to vaccines and the assays, make infection control challenging. Therefore, there is an urgent need to develop non-invasive biomarkers to quickly determine the infection severity. Circulating RNAs have been proven to be potential biomarkers for a variety of diseases, including infectious ones. This study aimed to develop a genetic network related to cytokines, with clinical validation for early infection severity prediction. (2) Methods: Extensive analyses of in silico data have established a novel IL11RA molecular network (IL11RNA mRNA, LncRNAs RP11-773H22.4 and hsa-miR-4257). We used different databases to confirm its validity. The differential expression within the retrieved network was clinically validated using quantitative RT-PCR, along with routine assessment diagnostic markers (CRP, LDH, D-dimmer, procalcitonin, Ferritin), in100 infected subjects (mild and severe cases) and 100 healthy volunteers. (3) Results: IL11RNA mRNA and LncRNA RP11-773H22.4, and the IL11RA protein, were significantly upregulated, and there was concomitant downregulation of hsa-miR-4257, in infected patients, compared to the healthy controls, in concordance with the infection severity. (4) Conclusion: The in-silico data and clinical validation led to the identification of a potential RNA/protein signature network for novel predictive biomarkers, which is in agreement with ferritin and procalcitonin for determination of COVID-19 severity.
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1982
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Limaye S, Kasibhatla SM, Ramtirthkar M, Kinikar M, Kale MM, Kulkarni-Kale U. Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak. Viruses 2021; 13:2238. [PMID: 34835044 PMCID: PMC8619538 DOI: 10.3390/v13112238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as 'Others' in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus-host interactions, differential glycosylation, immune evasion, and escape from neutralization.
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Affiliation(s)
- Sanket Limaye
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
| | - Sunitha M. Kasibhatla
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune 411008, India
| | - Mukund Ramtirthkar
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (M.R.); (M.M.K.)
| | - Meenal Kinikar
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
| | - Mohan M. Kale
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (M.R.); (M.M.K.)
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (S.M.K.); (M.K.)
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1983
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Ramzi ZS. Hospital readmissions and post-discharge all-cause mortality in COVID-19 recovered patients; A systematic review and meta-analysis. Am J Emerg Med 2021; 51:267-279. [PMID: 34781153 PMCID: PMC8570797 DOI: 10.1016/j.ajem.2021.10.059] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The present study aimed to perform a systematic review and meta-analysis on the prevalence of one-year hospital readmissions and post-discharge all-cause mortality in recovered COVID-19 patients. Moreover, the country-level prevalence of the outcomes was investigated. METHODS An extensive search was performed in Medline (PubMed), Embase, Scopus, and Web of Science databases until the end of August 3rd, 2021. A manual search was also performed in Google and Google Scholar search engines. Cohort and cross-sectional studies were included. Two independent reviewers screened the papers, collected data, and assessed the risk of bias and level of evidence. Any disagreement was resolved through discussion. RESULTS 91 articles were included. 48 studies examined hospital readmissions; nine studies assessed post-discharge all-cause mortality, and 34 studies examined both outcomes. Analyses showed that the prevalence of hospital readmissions during the first 30 days, 90 days, and one-year post-discharge were 8.97% (95% CI: 7.44, 10.50), 9.79% (95% CI: 8.37, 11.24), and 10.34% (95% CI: 8.92, 11.77), respectively. The prevalence of post-discharge all-cause mortality during the 30 days, 90 days and one-year post-discharge was 7.87% (95% CI: 2.78, 12.96), 7.63% (95% CI: 4.73, 10.53) and 7.51% (95% CI, 5.30, 9.72), respectively. 30-day hospital readmissions and post-discharge mortality were 8.97% and 7.87%, respectively. The highest prevalence of hospital readmissions was observed in Germany (15.5%), Greece (15.5%), UK (13.5%), Netherlands (11.7%), China (10.8%), USA (10.0%) and Sweden (9.9%). In addition, the highest prevalence of post-discharge all-cause mortality belonged to Italy (12.7%), the UK (11.8%), and Iran (9.2%). Sensitivity analysis showed that the prevalence of one-year hospital readmissions and post-discharge all-cause mortality in high-quality studies were 10.38% and 4.00%, respectively. CONCLUSION 10.34% of recovered COVID-19 patients required hospital readmissions after discharge. Most cases of hospital readmissions and mortality appear to occur within 30 days after discharge. The one-year post-discharge all-cause mortality rate of COVID-19 patients is 7.87%, and the majority of patients' readmission and mortality happens within the first 30 days post-discharge. Therefore, a 30-day follow-up program and patient tracking system for discharged COVID-19 patients seems necessary.
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Affiliation(s)
- Zhian Salah Ramzi
- Department of Family and Community Medicine, College of Medicine, University of Sulaimani, Sulaimani, Iraq.
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1984
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Lou F, Li M, Pang Z, Jiang L, Guan L, Tian L, Hu J, Fan J, Fan H. Understanding the Secret of SARS-CoV-2 Variants of Concern/Interest and Immune Escape. Front Immunol 2021; 12:744242. [PMID: 34804024 PMCID: PMC8602852 DOI: 10.3389/fimmu.2021.744242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
The global pandemic of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), places a heavy burden on global public health. Four SARS-CoV-2 variants of concern including B.1.1.7, B.1.351, B.1.617.2, and P.1, and two variants of interest including C.37 and B.1.621 have been reported to have potential immune escape, and one or more mutations endow them with worrisome epidemiologic, immunologic, or pathogenic characteristics. This review introduces the latest research progress on SARS-CoV-2 variants of interest and concern, key mutation sites, and their effects on virus infectivity, mortality, and immune escape. Moreover, we compared the effects of various clinical SARS-CoV-2 vaccines and convalescent sera on epidemic variants, and evaluated the neutralizing capability of several antibodies on epidemic variants. In the end, SARS-CoV-2 evolution strategies in different transmission stages, the impact of different vaccination strategies on SARS-CoV-2 immune escape, antibody therapy strategies and COVID-19 epidemic control prospects are discussed. This review will provide a systematic and comprehensive understanding of the secret of SARS-CoV-2 variants of interest/concern and immune escape.
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Affiliation(s)
- Fuxing Lou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Jiang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Guan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jiaming Hu
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Junfen Fan
- Institute of Cerebrovascular Disease Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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1985
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Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island. Viruses 2021; 13:v13112222. [PMID: 34835031 PMCID: PMC8623489 DOI: 10.3390/v13112222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
It has been 20 months since we first heard of SARS-CoV-2, the novel coronavirus detected in the Hubei province, China, in December 2019, responsible for the ongoing COVID-19 pandemic. Since then, a myriad of studies aimed at understanding and controlling SARS-CoV-2 have been published at a pace that has outshined the original effort to combat HIV during the beginning of the AIDS epidemic. This massive response started by developing strategies to not only diagnose individual SARS-CoV-2 infections but to monitor the transmission, evolution, and global spread of this new virus. We currently have hundreds of commercial diagnostic tests; however, that was not the case in early 2020, when just a handful of protocols were available, and few whole-genome SARS-CoV-2 sequences had been described. It was mid-January 2020 when several District Health Boards across New Zealand started planning the implementation of diagnostic testing for this emerging virus. Here, we describe our experience implementing a molecular test to detect SARS-CoV-2 infection, adapting the RT-qPCR assay to be used in a random-access platform (Hologic Panther Fusion® System) in a clinical laboratory, and characterizing the first whole-genome SARS-CoV-2 sequences obtained in the South Island, right at the beginning of the SARS-CoV-2 outbreak in New Zealand. We expect that this work will help us and others prepare for the unequivocal risk of similar viral outbreaks in the future.
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1986
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Tang Q, Owens RJ, Naismith JH. Structural Biology of Nanobodies against the Spike Protein of SARS-CoV-2. Viruses 2021; 13:v13112214. [PMID: 34835020 PMCID: PMC8625641 DOI: 10.3390/v13112214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 12/28/2022] Open
Abstract
Nanobodies are 130 amino acid single-domain antibodies (VHH) derived from the unique heavy-chain-only subclass of Camelid immunogloblins. Their small molecular size, facile expression, high affinity and stability have combined to make them unique targeting reagents with numerous applications in the biomedical sciences. The first nanobody agent has now entered the clinic as a treatment against a blood disorder. The spread of the SARS-CoV-2 virus has seen the global scientific endeavour work to accelerate the development of technologies to try to defeat a pandemic that has now killed over four million people. In a remarkably short period of time, multiple studies have reported nanobodies directed against the viral Spike protein. Several agents have been tested in culture and demonstrate potent neutralisation of the virus or pseudovirus. A few agents have completed animal trials with very encouraging results showing their potential for treating infection. Here, we discuss the structural features that guide the nanobody recognition of the receptor binding domain of the Spike protein of SARS-CoV-2.
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Affiliation(s)
- Qilong Tang
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
| | - James H. Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot OX11 0FA, UK;
- The Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Headington, Oxford OX3 7BN, UK
- Correspondence: (R.J.O.); (J.H.N.)
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1987
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First whole-genome analysis of the novel coronavirus (SARS-CoV-2) obtained from COVID-19 patients from five districts in Western Serbia. Epidemiol Infect 2021. [PMCID: PMC8654520 DOI: 10.1017/s095026882100220x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
This study was endeavoured to contribute in furthering our understanding of the molecular epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by sequencing and analysing the first full-length genome sequences obtained from 48 coronavirus disease-2019 (COVID-19) patients in five districts in Western Serbia in the period April 2020–July 2020. SARS-CoV-2 sequences in Western Serbia distinguished from the Wuhan sequence in 128 SNPs in total. The phylogenetic structure of local SARS-CoV-2 isolates suggested the existence of at least four distinct groups of SARS-CoV-2 strains in Western Serbia. The first group is the most similar to the strain from Italy. These isolates included two 20A sequences and 15−30 20B sequences that displayed a newly occurring set of four conjoined mutations. The second group is the most similar to the strain from France, carrying two mutations and belonged to 20A clade. The third group is the most similar to the strain from Switzerland carrying four co-occurring mutations and belonging to 20B clade. The fourth group is the most similar to another strain from France, displaying one mutation that gave rise to a single local isolate that belonged to 20A clade.
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1988
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, Happi CT, Johnson J, Sabeti PC, Myhrvold C. Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.01.21265764. [PMID: 34751276 PMCID: PMC8575147 DOI: 10.1101/2021.11.01.21265764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Program in Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A’Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Yibin B. Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Chloe K. Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Catherine A. Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Michelle E. Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Nicole L. Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Priya P. Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G. John
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena E. Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Justin S. Lee
- Biotechnology Cores Facility Branch,Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lisa E. Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Christian T. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
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1989
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Brizzi A, Whittaker C, Servo LMS, Hawryluk I, Prete CA, de Souza WM, Aguiar RS, Araujo LJT, Bastos LS, Blenkinsop A, Buss LF, Candido D, Castro MC, Costa SF, Croda J, de Souza Santos AA, Dye C, Flaxman S, Fonseca PLC, Geddes VEV, Gutierrez B, Lemey P, Levin AS, Mellan T, Bonfim DM, Miscouridou X, Mishra S, Monod M, Moreira FRR, Nelson B, Pereira RHM, Ranzani O, Schnekenberg RP, Semenova E, Sonnabend R, Souza RP, Xi X, Sabino EC, Faria NR, Bhatt S, Ratmann O. Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.01.21265731. [PMID: 34751273 PMCID: PMC8575144 DOI: 10.1101/2021.11.01.21265731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma's spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma's detection, and were largely transient after Gamma's detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil's COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil's COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries. NOTE The following manuscript has appeared as 'Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals' at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875 . ONE SENTENCE SUMMARY COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.
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Affiliation(s)
- Andrea Brizzi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | | | - Iwona Hawryluk
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Carlos A Prete
- Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Renato S Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
| | - Leonardo J T Araujo
- Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil
| | - Leonardo S Bastos
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Lewis F Buss
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Darlan Candido
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Silvia F Costa
- Departamento de Moléstias Infecciosas e Parasitárias e Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brasil
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, United States
| | | | - Christopher Dye
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven - University of Leuven, Leuven, Belgium
| | - Anna S Levin
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Thomas Mellan
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Diego M Bonfim
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xenia Miscouridou
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen, Denmark, Copenhagen
| | - Mélodie Monod
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Filipe R R Moreira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruce Nelson
- Environmental Dynamics, INPA, National Institute for Amazon Research, Bairro Petropolis, Brazil
| | | | - Otavio Ranzani
- Barcelona Institute for Global Health, ISGlobal, Barcelona, Spain
| | - Ricardo P Schnekenberg
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizaveta Semenova
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Raphael Sonnabend
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
| | - Renan P Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Xiaoyue Xi
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Ester C Sabino
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Samir Bhatt
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, United Kingdom
- Section of Epidemiology, School of Public Health, University of Copenhagen
| | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, United Kingdom
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1990
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Duchene S, Featherstone L, Freiesleben de Blasio B, Holmes EC, Bohlin J, Pettersson JHO. The impact of public health interventions in the Nordic countries during the first year of SARS-CoV-2 transmission and evolution. Euro Surveill 2021; 26:2001996. [PMID: 34738512 PMCID: PMC8569925 DOI: 10.2807/1560-7917.es.2021.26.44.2001996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/04/2021] [Indexed: 01/03/2023] Open
Abstract
BackgroundMany countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus.AimWe aimed to assess the duration of chains of virus transmission within individual countries and the extent to which countries exported viruses to their geographical neighbours.MethodsWe analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, in countries of northern Europe. We examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the COVID-19 pandemic.ResultsThe Nordic countries differed markedly in the invasiveness of control strategies, which we found reflected in transmission chain dynamics. For example, Sweden, which compared with the other Nordic countries relied more on recommendation-based rather than legislation-based mitigation interventions, had transmission chains that were more numerous and tended to have more cases. This trend increased over the first 8 months of 2020. Together with Denmark, Sweden was a net exporter of SARS-CoV-2. Norway and Finland implemented legislation-based interventions; their transmission chain dynamics were in stark contrast to their neighbouring country Sweden.ConclusionSweden constituted an epidemiological and evolutionary refugium that enabled the virus to maintain active transmission and spread to other geographical locations. Our analysis reveals the utility of genomic surveillance where monitoring of active transmission chains is a key metric.
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Affiliation(s)
- Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Leo Featherstone
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Birgitte Freiesleben de Blasio
- Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, Australia
| | - Jon Bohlin
- Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, Australia
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
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1991
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Dupont L, Snell LB, Graham C, Seow J, Merrick B, Lechmere T, Maguire TJA, Hallett SR, Pickering S, Charalampous T, Alcolea-Medina A, Huettner I, Jimenez-Guardeño JM, Acors S, Almeida N, Cox D, Dickenson RE, Galao RP, Kouphou N, Lista MJ, Ortega-Prieto AM, Wilson H, Winstone H, Fairhead C, Su JZ, Nebbia G, Batra R, Neil S, Shankar-Hari M, Edgeworth JD, Malim MH, Doores KJ. Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern. Nat Microbiol 2021; 6:1433-1442. [PMID: 34654917 PMCID: PMC8556155 DOI: 10.1038/s41564-021-00974-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/03/2021] [Indexed: 12/17/2022]
Abstract
COVID-19 vaccine design and vaccination rollout need to take into account a detailed understanding of antibody durability and cross-neutralizing potential against SARS-CoV-2 and emerging variants of concern (VOCs). Analyses of convalescent sera provide unique insights into antibody longevity and cross-neutralizing activity induced by variant spike proteins, which are putative vaccine candidates. Using sera from 38 individuals infected in wave 1, we show that cross-neutralizing activity can be detected up to 305 days pos onset of symptoms, although sera were less potent against B.1.1.7 (Alpha) and B1.351 (Beta). Over time, despite a reduction in overall neutralization activity, differences in sera neutralization potency against SARS-CoV-2 and the Alpha and Beta variants decreased, which suggests that continued antibody maturation improves tolerance to spike mutations. We also compared the cross-neutralizing activity of wave 1 sera with sera from individuals infected with the Alpha, the Beta or the B.1.617.2 (Delta) variants up to 79 days post onset of symptoms. While these sera neutralize the infecting VOC and parental virus to similar levels, cross-neutralization of different SARS-CoV-2 VOC lineages is reduced. These findings will inform the optimization of vaccines to protect against SARS-CoV-2 variants.
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Affiliation(s)
- Liane Dupont
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Luke B Snell
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Thomas Lechmere
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sadie R Hallett
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Suzanne Pickering
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Themoula Charalampous
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Nathalia Almeida
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Daniel Cox
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Rui Pedro Galao
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marie Jose Lista
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Harry Wilson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Helena Winstone
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Cassandra Fairhead
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jia Zhe Su
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Stuart Neil
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Manu Shankar-Hari
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jonathan D Edgeworth
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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1992
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Kumar A, Narayan RK, Prasoon P, Kumari C, Kaur G, Kumar S, Kulandhasamy M, Sesham K, Pareek V, Faiq MA, Pandey SN, Singh HN, Kant K, Shekhawat PS, Raza K, Kumar S. COVID-19 Mechanisms in the Human Body-What We Know So Far. Front Immunol 2021; 12:693938. [PMID: 34790191 PMCID: PMC8592035 DOI: 10.3389/fimmu.2021.693938] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
More than one and a half years have elapsed since the commencement of the coronavirus disease 2019 (COVID-19) pandemic, and the world is struggling to contain it. Being caused by a previously unknown virus, in the initial period, there had been an extreme paucity of knowledge about the disease mechanisms, which hampered preventive and therapeutic measures against COVID-19. In an endeavor to understand the pathogenic mechanisms, extensive experimental studies have been conducted across the globe involving cell culture-based experiments, human tissue organoids, and animal models, targeted to various aspects of the disease, viz., viral properties, tissue tropism and organ-specific pathogenesis, involvement of physiological systems, and the human immune response against the infection. The vastly accumulated scientific knowledge on all aspects of COVID-19 has currently changed the scenario from great despair to hope. Even though spectacular progress has been made in all of these aspects, multiple knowledge gaps are remaining that need to be addressed in future studies. Moreover, multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged across the globe since the onset of the first COVID-19 wave, with seemingly greater transmissibility/virulence and immune escape capabilities than the wild-type strain. In this review, we narrate the progress made since the commencement of the pandemic regarding the knowledge on COVID-19 mechanisms in the human body, including virus-host interactions, pulmonary and other systemic manifestations, immunological dysregulations, complications, host-specific vulnerability, and long-term health consequences in the survivors. Additionally, we provide a brief review of the current evidence explaining molecular mechanisms imparting greater transmissibility and virulence and immune escape capabilities to the emerging SARS-CoV-2 variants.
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Affiliation(s)
- Ashutosh Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Ravi K. Narayan
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, Andaman and Nicobar Islands Institute of Medical Sciences, Port Blair, India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Pittsburgh Center for Pain Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Chiman Kumari
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Gurjot Kaur
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Santosh Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anesthesiology and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Biochemistry, Maulana Azad Medical College (MAMC), New Delhi, India
| | - Kishore Sesham
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Mangalagiri, Vijayawada, India
| | - Vikas Pareek
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Center for Cognitive and Brain Sciences, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Muneeb A. Faiq
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- New York University (NYU) Langone Health Center, NYU Robert I. Grossman School of Medicine, New York, NY, United States
| | - Sada N. Pandey
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Zoology, Banaras Hindu University (BHU), Varanasi, India
| | - Himanshu N. Singh
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, United States
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bathinda, India
| | - Prakash S. Shekhawat
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Clinical Hematology, National Institute of Medical Sciences, Jaipur, India
| | - Khursheed Raza
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Deoghar, India
| | - Sujeet Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Center for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
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1993
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Chaudhary N, Weissman D, Whitehead KA. mRNA vaccines for infectious diseases: principles, delivery and clinical translation. Nat Rev Drug Discov 2021; 20:817-838. [PMID: 34433919 PMCID: PMC8386155 DOI: 10.1038/s41573-021-00283-5] [Citation(s) in RCA: 551] [Impact Index Per Article: 183.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Over the past several decades, messenger RNA (mRNA) vaccines have progressed from a scepticism-inducing idea to clinical reality. In 2020, the COVID-19 pandemic catalysed the most rapid vaccine development in history, with mRNA vaccines at the forefront of those efforts. Although it is now clear that mRNA vaccines can rapidly and safely protect patients from infectious disease, additional research is required to optimize mRNA design, intracellular delivery and applications beyond SARS-CoV-2 prophylaxis. In this Review, we describe the technologies that underlie mRNA vaccines, with an emphasis on lipid nanoparticles and other non-viral delivery vehicles. We also overview the pipeline of mRNA vaccines against various infectious disease pathogens and discuss key questions for the future application of this breakthrough vaccine platform.
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Affiliation(s)
- Namit Chaudhary
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn A Whitehead
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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1994
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Carreño JM, Alshammary H, Singh G, Raskin A, Amanat F, Amoako A, Gonzalez-Reiche AS, van de Guchte A, Study Group P, Srivastava K, Sordillo EM, Sather DN, van Bakel H, Krammer F, Simon V. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. EBioMedicine 2021; 73:103626. [PMID: 34688034 PMCID: PMC8527879 DOI: 10.1016/j.ebiom.2021.103626] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/06/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Highly efficacious vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed. However, the emergence of viral variants that are more infectious than the earlier SARS-CoV-2 strains is concerning. Several of these viral variants have the potential to partially escape neutralizing antibody responses, warranting continued immune-monitoring. METHODS We used a panel of 30 post-mRNA vaccination sera to determine neutralization and RBD and spike binding activity against a number of emerging viral variants. The virus neutralization was determined using authentic SARS-CoV-2 clinical isolates in an assay format that mimics physiological conditions. FINDINGS We tested seven currently circulating viral variants of concern/interest, including the three Iota sublineages, Alpha (E484K), Beta, Delta and Lambda in neutralization assays. We found only small decreases in neutralization against Iota and Delta. The reduction was stronger against a sub-variant of Lambda, followed by Beta and Alpha (E484K). Lambda is currently circulating in parts of Latin America and was detected in Germany, the US and Israel. Of note, reduction in a receptor binding domain and spike binding assay that also included Gamma, Kappa and A.23.1 was negligible. INTERPRETATION Taken together, these findings suggest that mRNA SARS-CoV-2 vaccines may remain effective against these viral variants of concern/interest and that spike binding antibody tests likely retain specificity in the face of evolving SARS-CoV-2 diversity. FUNDING This work is part of the PARIS/SPARTA studies funded by the NIAID Collaborative Influenza Vaccine Innovation Centers (CIVIC) contract 75N93019C00051. In addition, this work was also partially funded by the Centers of Excellence for Influenza Research and Surveillance (CEIRS, contract # HHSN272201400008C), the JPB Foundation, the Open Philanthropy Project (research grant 2020-215611 (5384), by anonymous donors and by the Serological Sciences Network (SeroNet) in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024, Task Order No. 75N91020F00003.
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Affiliation(s)
- Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ariel Raskin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angela Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paris Study Group
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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1995
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Kleanthous H, Silverman JM, Makar KW, Yoon IK, Jackson N, Vaughn DW. Scientific rationale for developing potent RBD-based vaccines targeting COVID-19. NPJ Vaccines 2021; 6:128. [PMID: 34711846 PMCID: PMC8553742 DOI: 10.1038/s41541-021-00393-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/01/2021] [Indexed: 12/31/2022] Open
Abstract
Vaccination of the global population against COVID-19 is a great scientific, logistical, and moral challenge. Despite the rapid development and authorization of several full-length Spike (S) protein vaccines, the global demand outweighs the current supply and there is a need for safe, potent, high-volume, affordable vaccines that can fill this gap, especially in low- and middle-income countries. Whether SARS-CoV-2 S-protein receptor-binding domain (RBD)-based vaccines could fill this gap has been debated, especially with regards to its suitability to protect against emerging viral variants of concern. Given a predominance for elicitation of neutralizing antibodies (nAbs) that target RBD following natural infection or vaccination, a key biomarker of protection, there is merit for selection of RBD as a sole vaccine immunogen. With its high-yielding production and manufacturing potential, RBD-based vaccines offer an abundance of temperature-stable doses at an affordable cost. In addition, as the RBD preferentially focuses the immune response to potent and recently recognized cross-protective determinants, this domain may be central to the development of future pan-sarbecovirus vaccines. In this study, we review the data supporting the non-inferiority of RBD as a vaccine immunogen compared to full-length S-protein vaccines with respect to humoral and cellular immune responses against both the prototype pandemic SARS-CoV-2 isolate and emerging variants of concern.
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Affiliation(s)
| | | | | | - In-Kyu Yoon
- Coalition for Epidemic Preparedness Innovations, Greater London, UK
| | - Nicholas Jackson
- Coalition for Epidemic Preparedness Innovations, Greater London, UK.
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1996
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Shekhar R, Garg I, Pal S, Kottewar S, Sheikh AB. COVID-19 Vaccine Booster: To Boost or Not to Boost. Infect Dis Rep 2021; 13:924-929. [PMID: 34842753 PMCID: PMC8628913 DOI: 10.3390/idr13040084] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 01/14/2023] Open
Abstract
Developing safe and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at a breakneck speed has been an exceptional human achievement. It remains our best hope of containing the coronavirus disease 2019 (COVID-19) pandemic. However, newer, more aggressive SARS-CoV-2 viral strains, as well as the possibility of fading immunity following vaccination, have prompted health officials to investigate the necessity for additional immunization. This has put further pressure on disregarded human life in lower-income countries that already have minimal access to COVID-19 vaccines. The Centers for Disease Control and Prevention (CDC) have recommended a third COVID-19 vaccine dose in immunocompromised individuals in a recent announcement. Governments and health care officials need to develop usage guidelines for COVID-19 vaccine booster doses while considering the dangers of potential waning immunity and new viral strains and prioritizing vulnerable populations everywhere, including those living in lower-income countries.
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Affiliation(s)
- Rahul Shekhar
- Health Sciences Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (S.P.); (A.B.S.)
- Correspondence:
| | - Ishan Garg
- Department of Internal Medicine, Maimonides Medical Center, Brooklyn, NY 11219, USA;
| | - Suman Pal
- Health Sciences Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (S.P.); (A.B.S.)
| | - Saket Kottewar
- Department of Medicine, Division of Hospital Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Abu Baker Sheikh
- Health Sciences Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; (S.P.); (A.B.S.)
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1997
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A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. J Virol 2021; 95:e0112621. [PMID: 34495697 PMCID: PMC8549516 DOI: 10.1128/jvi.01126-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and has been responsible for the still ongoing coronavirus disease 2019 (COVID-19) pandemic. Prophylactic vaccines have been authorized by the U.S. Food and Drug Administration (FDA) for the prevention of COVID-19. Identification of SARS-CoV-2-neutralizing antibodies (NAbs) is important to assess vaccine protection efficacy, including their ability to protect against emerging SARS-CoV-2 variants of concern (VoC). Here, we report the generation and use of a recombinant (r)SARS-CoV-2 USA/WA1/2020 (WA-1) strain expressing Venus and an rSARS-CoV-2 strain expressing mCherry and containing mutations K417N, E484K, and N501Y found in the receptor binding domain (RBD) of the spike (S) glycoprotein of the South African (SA) B.1.351 (beta [β]) VoC in bifluorescent-based assays to rapidly and accurately identify human monoclonal antibodies (hMAbs) able to neutralize both viral infections in vitro and in vivo. Importantly, our bifluorescent-based system accurately recapitulated findings observed using individual viruses. Moreover, fluorescent-expressing rSARS-CoV-2 strain and the parental wild-type (WT) rSARS-CoV-2 WA-1 strain had similar viral fitness in vitro, as well as similar virulence and pathogenicity in vivo in the K18 human angiotensin-converting enzyme 2 (hACE2) transgenic mouse model of SARS-CoV-2 infection. We demonstrate that these new fluorescent-expressing rSARS-CoV-2 can be used in vitro and in vivo to easily identify hMAbs that simultaneously neutralize different SARS-CoV-2 strains, including VoC, for the rapid assessment of vaccine efficacy or the identification of prophylactic and/or therapeutic broadly NAbs for the treatment of SARS-CoV-2 infection. IMPORTANCE SARS-CoV-2 is responsible of the COVID-19 pandemic that has warped daily routines and socioeconomics. There is still an urgent need for prophylactics and therapeutics to treat SARS-CoV-2 infections. In this study, we demonstrate the feasibility of using bifluorescent-based assays for the rapid identification of hMAbs with neutralizing activity against SARS-CoV-2, including VoC in vitro and in vivo. Importantly, results obtained with these bifluorescent-based assays recapitulate those observed with individual viruses, demonstrating their feasibility to rapidly advance our understanding of vaccine efficacy and to identify broadly protective human NAbs for the therapeutic treatment of SARS-CoV-2.
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1998
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Haslwanter D, Dieterle ME, Wec AZ, O’Brien CM, Sakharkar M, Florez C, Tong K, Rappazzo CG, Lasso G, Vergnolle O, Wirchnianski AS, Bortz RH, Laudermilch E, Fels JM, Mengotto A, Malonis RJ, Georgiev GI, Quiroz JA, Wrapp D, Wang N, Dye KE, Barnhill J, Dye JM, McLellan JS, Daily JP, Lai JR, Herbert AS, Walker LM, Chandran K, Jangra RK. A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. mBio 2021; 12:e0247321. [PMID: 34607456 PMCID: PMC8546647 DOI: 10.1128/mbio.02473-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
Most known SARS-CoV-2 neutralizing antibodies (nAbs), including those approved by the FDA for emergency use, inhibit viral infection by targeting the receptor-binding domain (RBD) of the spike (S) protein. Variants of concern (VOC) carrying mutations in the RBD or other regions of S reduce the effectiveness of many nAbs and vaccines by evading neutralization. Therefore, therapies that are less susceptible to resistance are urgently needed. Here, we characterized the memory B-cell repertoire of COVID-19 convalescent donors and analyzed their RBD and non-RBD nAbs. We found that many of the non-RBD-targeting nAbs were specific to the N-terminal domain (NTD). Using neutralization assays with authentic SARS-CoV-2 and a recombinant vesicular stomatitis virus carrying SARS-CoV-2 S protein (rVSV-SARS2), we defined a panel of potent RBD and NTD nAbs. Next, we used a combination of neutralization-escape rVSV-SARS2 mutants and a yeast display library of RBD mutants to map their epitopes. The most potent RBD nAb competed with hACE2 binding and targeted an epitope that includes residue F490. The most potent NTD nAb epitope included Y145, K150, and W152. As seen with some of the natural VOC, the neutralization potencies of COVID-19 convalescent-phase sera were reduced by 4- to 16-fold against rVSV-SARS2 bearing Y145D, K150E, or W152R spike mutations. Moreover, we found that combining RBD and NTD nAbs did not enhance their neutralization potential. Notably, the same combination of RBD and NTD nAbs limited the development of neutralization-escape mutants in vitro, suggesting such a strategy may have higher efficacy and utility for mitigating the emergence of VOC. IMPORTANCE The U.S. FDA has issued emergency use authorizations (EUAs) for multiple investigational monoclonal antibody (MAb) therapies for the treatment of mild to moderate COVID-19. These MAb therapeutics are solely targeting the receptor-binding domain of the SARS-CoV-2 spike protein. However, the N-terminal domain of the spike protein also carries crucial neutralizing epitopes. Here, we show that key mutations in the N-terminal domain can reduce the neutralizing capacity of convalescent-phase COVID-19 sera. We report that a combination of two neutralizing antibodies targeting the receptor-binding and N-terminal domains may be beneficial to combat the emergence of virus variants.
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Affiliation(s)
- Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - M. Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Cecilia M. O’Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
- The Geneva Foundation, Tacoma, Washington, USA
| | | | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, New York, USA
| | - Karen Tong
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Gorka Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Olivia Vergnolle
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - Ariel S. Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - Robert H. Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Amanda Mengotto
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York, USA
| | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - George I. Georgiev
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - Jose A. Quiroz
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Kathryn E. Dye
- Department of Science, Mount St. Mary’s University, Emmitsburg, Maryland, USA
| | - Jason Barnhill
- Department of Chemistry and Life Science, United States Military Academy at West Point, West Point, New York, USA
- Department of Radiology and Radiological Services, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Johanna P. Daily
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, New York, New York, USA
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
- The Geneva Foundation, Tacoma, Washington, USA
| | - Laura M. Walker
- Adimab LLC, Lebanon, New Hampshire, USA
- Adagio Therapeutics Inc., Waltham, Massachusetts, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
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1999
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Nasker SS, Nanda A, Ramadass B, Nayak S. Epidemiological Analysis of SARS-CoV-2 Transmission Dynamics in the State of Odisha, India: A Yearlong Exploratory Data Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11203. [PMID: 34769722 PMCID: PMC8582922 DOI: 10.3390/ijerph182111203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022]
Abstract
COVID-19 remains a matter of global public health concern. Previous research suggested the association between local environmental factors and viral transmission. We present a multivariate observational analysis of SARS-CoV-2 transmission in the state of Odisha, India, hinting at a seasonal activity. We aim to investigate the demographic characteristics of COVID-19 in the Indian state of Odisha for two specific timelines in 2020 and 2021. For a comparative outlook, we chose similar datasets from the state of New York, USA. Further, we present a critical analysis pertaining to the effects of environmental factors and the emergence of variants on SARS-CoV-2 transmission and persistence. We assessed the datasets for confirmed cases, death, age, and gender for 29 February 2020 to 31 May 2020, and 1 March 2021 to 31 May 2021. We determined the case fatalities, crude death rates, sex ratio, and incidence rates for both states along with monthly average temperature analysis. A yearlong epi-curve analysis was conducted to depict the coronavirus infection spread pattern in the respective states. The Indian state of Odisha reported a massive 436,455 confirmed cases and 875 deaths during the 2021 timeline as compared to a mere 2223 cases and 7 deaths during the 2020 timeline. We further discuss the demographic and temperature association of SARS-CoV-2 transmission during early 2020 and additionally comment on the variant-associated massive rise in cases during 2021. Along with the rapid rise of variants, the high population density and population behavior seem to be leading causes for the 2021 pandemic, whereas factors such as age group, gender, and average local temperature were prominent during the 2020 spread. A seasonal occurrence of SARS-CoV-2 transmission is also observed from the yearlong epidemiological plot. The recent second wave of COVID-19 is a lesson that emphasizes the significance of continuous epidemiological surveillance to predict the relative risk of viral transmission for a specific region.
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Affiliation(s)
- Sourya Subhra Nasker
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India; (S.S.N.); (A.N.)
| | - Ananya Nanda
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India; (S.S.N.); (A.N.)
| | | | - Sasmita Nayak
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India; (S.S.N.); (A.N.)
- Kalinga Institute of Medical Sciences, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
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2000
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Arora P, Rocha C, Kempf A, Nehlmeier I, Graichen L, Winkler MS, Lier M, Schulz S, Jäck HM, Cossmann A, Stankov MV, Behrens GMN, Pöhlmann S, Hoffmann M. The spike protein of SARS-CoV-2 variant A.30 is heavily mutated and evades vaccine-induced antibodies with high efficiency. Cell Mol Immunol 2021; 18:2673-2675. [PMID: 34697413 PMCID: PMC8543421 DOI: 10.1038/s41423-021-00779-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Prerna Arora
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Cheila Rocha
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Martin S Winkler
- Department of Anesthesiology, University of Göttingen Medical Center, Georg-August University of Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Martin Lier
- Department of Anesthesiology, University of Göttingen Medical Center, Georg-August University of Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Glückstraße 6, 91054, Erlangen, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Metodi V Stankov
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany. .,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany. .,Faculty of Biology and Psychology, Georg-August-University Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany.
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