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Hasan Z, Masood KI, Qaiser S, Kanji A, Mwenda F, Alenquer M, Iqbal J, Ferreira F, Wassan Y, Balouch S, Yameen M, Hussain S, Begum K, Feroz K, Muhammad S, Sadiqa A, Akhtar M, Habib A, Ahmed SMA, Mian AA, Hussain R, Amorim MJ, Bhutta ZA. Comparative study of humoral and cellular immunity against SARS-CoV-2 induced by different COVID-19 vaccine types: Insights into protection against wildtype, Delta and JN.1 omicron strains. Vaccine 2025; 59:127270. [PMID: 40408899 DOI: 10.1016/j.vaccine.2025.127270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/19/2025] [Accepted: 05/12/2025] [Indexed: 05/25/2025]
Abstract
We investigated the effectiveness of different COVID-19 vaccinations administered in Pakistan by studying the effect of inactivated virus, mRNA and vector formulations. This study in 916 participants was conducted between October 2021 and July 2022. Subjects receiving inactivated (A), mRNA (B), one-dose vector (C), and two-dose vector (D) vaccines were sampled at baseline, 6, 12, and 24 weeks. Serum IgG antibodies to wildtype Spike and its receptor binding domain (RBD) were measured. Pseudovirus particle-based neutralizing assays against wildtype, Delta, and JN.1 variants were performed. T cell IFN-γ responses to SARS-CoV-2 antigens were measured. Participants were aged 37.05 ± 14.44 years and comprised 48.6 % females. Baseline Spike seropositivity rose from 90 % to 96 % by 24 weeks; and 40 % to 90 % against RBD. Group B participants had the highest anti-RBD levels which peaked by 6 weeks. IgG RBD in group A and C increased up until 24 weeks. Anti-RBD levels were reduced in those over 50 years. At baseline neutralizing titers were present at 38.5 % against wildtype and in 34.2 % against Delta variants. Titers doubled in vaccine groups A-C by 12 weeks, with highest titers in B and lowest in group C participants. At baseline, neutralizing titers against the JN.1 variant were absent but low titers were evident in 10 % of participants after 12 weeks. T cell reactivity to SARS-CoV-2 increased from 31 % at baseline to 50 % in group A and 73 % in group B participants by 6 weeks after vaccination. Presence of immunity against wildtype and Delta variants in one-third of participants at baseline could be due to sub-clinical infections. Increase in humoral and cellular immunity was greater after mRNA as compared with inactivated vaccinations. As COVID-19 morbidity in the population remained low, our data supports effectiveness of multiple vaccine formulations in protecting against severe COVID-19 in this high transmission population.
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Affiliation(s)
- Zahra Hasan
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan.
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Shama Qaiser
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Fridah Mwenda
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Marta Alenquer
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Junaid Iqbal
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Filipe Ferreira
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Yaqub Wassan
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Sadaf Balouch
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Shahneel Hussain
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Kehkashan Begum
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Khalid Feroz
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Sajid Muhammad
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Ayesha Sadiqa
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Mishgan Akhtar
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Atif Habib
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | | | - Afsar Ali Mian
- Center for Regenerative Medicine, AKU, Karachi, Pakistan
| | - Rabia Hussain
- Department of Pathology and Laboratory Medicine(1), The Aga Khan University (AKU), Karachi, Pakistan
| | - Maria Joao Amorim
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Zulfiqar A Bhutta
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan; Centre for Global Child Health, Hospital for Sick Children, Toronto, Canada
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Sangeet S, Sinha A, Nair MB, Mahata A, Sarkar R, Roy S. EVOLVE: A Web Platform for AI-Based Protein Mutation Prediction and Evolutionary Phase Exploration. J Chem Inf Model 2025; 65:4293-4310. [PMID: 40309917 DOI: 10.1021/acs.jcim.5c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
Abstract
While predicting structure-function relationships from sequence data is fundamental in biophysical chemistry, identifying prospective single-point and collective mutation sites in proteins can help us stay ahead in understanding their potential effects on protein structure and function. Addressing the challenges of large sequence-space analysis, we present EVOLVE, a web tool enabling researchers to explore prospective mutation sites and their collective behavior. EVOLVE integrates a statistical mechanics-guided machine learning algorithms to predict probable mutational sites, with statistical mechanics calculating mutational entropy to accurately identify mutational hotspots. Validation against a number of viral protein sequences confirms its ability to predict mutations and their functional consequences. By leveraging statistical mechanics of phase transition concept, EVOLVE also quantifies mutational entropy fluctuations, offering a quantitative foundation for identifying Variants of Concern (VOC) or Variants under Monitoring (VUM) as per World Health Organization (WHO) guidelines. EVOLVE streamlines data upload and analysis with a user-friendly interface and comprehensive tutorials. Access EVOLVE free at https://evolve-iiserkol.com.
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Affiliation(s)
- Satyam Sangeet
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
- School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anushree Sinha
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
| | - Madhav B Nair
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
| | - Arpita Mahata
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
| | - Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India
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3
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Anraku Y, Kita S, Onodera T, Sato A, Tadokoro T, Ito S, Adachi Y, Kotaki R, Suzuki T, Sasaki J, Shiwa-Sudo N, Iwata-Yoshikawa N, Nagata N, Kobayashi S, Kazuki Y, Oshimura M, Nomura T, Sasaki M, Orba Y, Suzuki T, Sawa H, Hashiguchi T, Fukuhara H, Takahashi Y, Maenaka K. Structural and virological identification of neutralizing antibody footprint provides insights into therapeutic antibody design against SARS-CoV-2 variants. Commun Biol 2025; 8:483. [PMID: 40121330 PMCID: PMC11929858 DOI: 10.1038/s42003-025-07827-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 02/26/2025] [Indexed: 03/25/2025] Open
Abstract
Medical treatments using potent neutralizing SARS-CoV-2 antibodies have achieved remarkable improvements in clinical symptoms, changing the situation for the severity of COVID-19 patients. We previously reported an antibody, NT-108 with potent neutralizing activity. However, the structural and functional basis for the neutralizing activity of NT-108 has not yet been understood. Here, we demonstrated the therapeutic effects of NT-108 in a hamster model and its protective effects at low doses. Furthermore, we determined the cryo-EM structure of NT-108 in complex with SARS-CoV-2 spike. The single-chain Fv construction of NT-108 improved the cryo-EM maps because of the prevention of preferred orientations induced by Fab orientation. The footprints of NT-108 illuminated how escape mutations such as E484K evade from class 2 antibody recognition without ACE2 affinity attenuation. The functional and structural basis for the potent neutralizing activity of NT-108 provides insights into the rational design of therapeutic antibodies.
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Affiliation(s)
- Yuki Anraku
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Taishi Onodera
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akihiko Sato
- Laboratory for Drug Discovery & Disease Research, Shionogi & Co., Ltd., Osaka, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Takashi Tadokoro
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Shiori Ito
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Adachi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryutaro Kotaki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tateki Suzuki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Nozomi Shiwa-Sudo
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Souta Kobayashi
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, Tottori, Japan
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, Tottori, Japan
| | | | - Takao Nomura
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirofumi Sawa
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Global Virus Network, Baltimore, MD, USA
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
- Kyoto University Immunomonitoring Center, Kyoto University, Kyoto, Japan
| | - Hideo Fukuhara
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
- Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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Hasan Z, Masood KI, Veldhoen M, Qaiser S, Alenquer M, Akhtar M, Balouch S, Iqbal J, Wassan Y, Hussain S, Feroz K, Muhammad S, Habib A, Kanji A, Khan E, Mian AA, Hussain R, Amorim MJ, Bhutta ZA. Pre-existing IgG antibodies to HCoVs NL63 and OC43 Spike increased during the pandemic and after COVID-19 vaccination. Heliyon 2025; 11:e42171. [PMID: 39916832 PMCID: PMC11795784 DOI: 10.1016/j.heliyon.2025.e42171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 01/21/2025] [Accepted: 01/21/2025] [Indexed: 02/09/2025] Open
Abstract
Preexisting immunity may be associated with increased protection against non-related pathogens such as, SARS-CoV-2. There is little information regarding endemic human coronaviruses (HCOVs) from Pakistan, which experienced a relatively low COVID-19 morbidity and mortality. We investigated antibodies to SARS-CoV-2 and HCoVs NL63 and OC43, comparing sera from prepandemic controls (PPC) period with responses in healthy controls from the pandemic (HC 2021). Further, we investigated the effect of inactivated and mRNA COVID-19 vaccinations on antibody responses to the pandemic and endemic coronaviruses. We measured IgG antibodies to Spike of SARS-CoV-2, HCoV-NL63 and HCoV-OC43 by ELISA. Serum neutralizing capacity was determined using a SARS-CoV-2 psuedotyped virus assay. Vaccinees were sampled prior to vaccination as well after 6, 12 and 24 weeks after COVID-19 inactivated (Sinovac), or mRNA (BNT162b2) vaccine administration. PPC sera showed seropositivity of 15 % to SARS-CoV-2, whilst it was 45 % in the HC 2021 group. Five percent of sera showed virus neutralizing activity in PPC whilst it was 50 % in HC 2021. IgG antibodies to Spike of NL63 and OC43 were also present in PPC; anti-NL63 was 2.9-fold, and anti-OC43 was 10.1-fold higher than to anti-SARS-CoV-2 levels. IgG antibodies to Spike SARS-CoV-2 were positively correlated with HCoV-NL63 in HC 2021, indicating recognition of shared conserved epitopes. IgG antibody levels increased during the pandemic; 2.7-fold to HCoV-NL63 and 1.9-fold to HCoV-OC43. SinoVac and BNT162b2 vaccine induced an increase in IgG antibodies to Spike SARS-CoV-2 as well as HCoV-NL63 and HCoV-OC43. Our data show that antibodies to spike protein of endemic coronaviruses were present in the prepandemic population. Antibodies to SARS-CoV-2, NL63 and OC43 were all raised during the pandemic and further enhanced after COVID-19 vaccinations. The increase in antibodies to spike of coronaviruses would contribute to protection against SARS-CoV-2.
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Affiliation(s)
- Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Marc Veldhoen
- Instituto de Medicina Molecular | João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Shama Qaiser
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Marta Alenquer
- Catolica Biomedical Research Center, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023, Lisboa, Portugal
| | - Mishgan Akhtar
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Sadaf Balouch
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Junaid Iqbal
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Yaqub Wassan
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Shahneel Hussain
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Khalid Feroz
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Sajid Muhammad
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Atif Habib
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Erum Khan
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Afsar Ali Mian
- Center for Regenerative Medicine, AKU, Karachi, Pakistan
| | - Rabia Hussain
- Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan
| | - Maria Joao Amorim
- Catolica Biomedical Research Center, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023, Lisboa, Portugal
| | - Zulfiqar A. Bhutta
- Center of Excellence in Women and Child Health, AKU, Karachi, Pakistan
- Centre for Global Child Health, Hospital for Sick Children, Toronto, Canada
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5
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Valério M, Buga CC, Melo MN, Soares CM, Lousa D. Viral entry mechanisms: the role of molecular simulation in unlocking a key step in viral infections. FEBS Open Bio 2025; 15:269-284. [PMID: 39402013 PMCID: PMC11788750 DOI: 10.1002/2211-5463.13908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 09/13/2024] [Accepted: 09/24/2024] [Indexed: 02/04/2025] Open
Abstract
Viral infections are a major global health concern, affecting millions of people each year. Viral entry is one of the crucial stages in the infection process, but its details remain elusive. Enveloped viruses are enclosed by a lipid membrane that protects their genetic material and these viruses are linked to various human illnesses, including influenza, and COVID-19. Due to the advancements made in the field of molecular simulation, significant progress has been made in unraveling the dynamic processes involved in viral entry of enveloped viruses. Simulation studies have provided deep insight into the function of the proteins responsible for attaching to the host receptors and promoting membrane fusion (fusion proteins), deciphering interactions between these proteins and receptors, and shedding light on the functional significance of key regions, such as the fusion peptide. These studies have already significantly contributed to our understanding of this critical aspect of viral infection and assisted the development of effective strategies to combat viral diseases and improve global health. This review focuses on the vital role of fusion proteins in facilitating the entry process of enveloped viruses and highlights the contributions of molecular simulation studies to uncover the molecular details underlying their mechanisms of action.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Carolina C. Buga
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
- Instituto de Medicina MolecularFaculdade de Medicina da Universidade de LisboaLisbonPortugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Diana Lousa
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
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6
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Chakraborty C, Bhattacharya M, Pal S, Lee SS. Prompt engineering-enabled LLM or MLLM and instigative bioinformatics pave the way to identify and characterize the significant SARS-CoV-2 antibody escape mutations. Int J Biol Macromol 2025; 287:138547. [PMID: 39657873 DOI: 10.1016/j.ijbiomac.2024.138547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 12/06/2024] [Accepted: 12/06/2024] [Indexed: 12/12/2024]
Abstract
The research aims to identify and characterize the antibody escape mutations of NTD and RBD regions of SARS-CoV-2 using prompt engineering-enabled combined LLMs (large language models) and instigative bioinformatics techniques. We used two LLMs (ChatGPT and Mistral 7B) and one MLLM (Gemini model) to retrieve the significant NTD and RBD mutations. The retrieved significant mutations were characterized through the in silico servers. The retrieved 15 NTD significant mutations (six deletions and nine-point mutations) and 17 RBD point mutations were noted. We further characterized them in terms of distribution, count, ΔΔG of mutation (ΔΔG stability mCSM, ΔΔGstability DUET, ΔΔGstabilitySDM) to understand the stabilized or destabilized mutation, interaction interface, distance to PPI interface, Δvibrational entropy energy (ΔΔSVib ENCoM), and change in the flexibility. Here, we analyzed every mutation's ΔΔG, interaction, and related parameters using the trimeric Spike protein complex. In NTD mutations, our five analyzed mutations show two destabilising (G142D, R190S) and three showing stabilising properties (D215G, A222V, and R246I). Some RBD mutations are noted as entirely destabilising (K417N, K417T, L452R, F490S). N440K, N460K, and Q493R show stabilising and neutral properties. Combined LLMs and instigative bioinformatics techniques were used to identify and characterize the antibody escape mutations. With our strategy, the LLM and MLLM can help to fight future pandemic viruses by quickly identifying mutations and their significance.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore 756020, Odisha, India
| | - Soumen Pal
- School of Mechanical Engineering, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, Gangwon-Do 24252, Republic of Korea
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7
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Seow J, Jefferson GCE, Keegan MD, Yau Y, Snell LB, Doores KJ. Profiling serum immunodominance following SARS-CoV-2 primary and breakthrough infection reveals distinct variant-specific epitope usage and immune imprinting. PLoS Pathog 2024; 20:e1012724. [PMID: 39556615 DOI: 10.1371/journal.ppat.1012724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 11/03/2024] [Indexed: 11/20/2024] Open
Abstract
Over the course of the COVID-19 pandemic, variants have emerged with increased mutations and immune evasive capabilities. This has led to breakthrough infections (BTI) in vaccinated individuals, with a large proportion of the neutralizing antibody response targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike glycoprotein. Immune imprinting, where prior exposure of the immune system to an antigen can influence the response to subsequent exposures, and its role in a population with heterogenous exposure histories has important implications in future vaccine design. Here, we develop an accessible approach to map epitope immunodominance of the neutralizing antibody response in sera. By using a panel of mutant Spike proteins in a pseudotyped virus neutralization assay, we observed distinct epitope usage in convalescent donors infected during wave 1, or infected with the Delta, or BA.1 variants, highlighting the antigenic diversity of the variant Spikes. Analysis of longitudinal serum samples taken spanning 3 doses of COVID-19 vaccine and subsequent breakthrough infection, showed the influence of immune imprinting from the ancestral-based vaccine, where reactivation of existing B cells elicited by the vaccine resulted in the enrichment of the pre-existing epitope immunodominance. However, subtle shifts in epitope usage in sera were observed following BTI by Omicron sub-lineage variants. Antigenic distance of Spike, time after last exposure, and number of vaccine boosters may play a role in the persistence of imprinting from the vaccine. This study provides insight into RBD neutralizing epitope usage in individuals with varying exposure histories and has implications for design of future SARS-CoV-2 vaccines.
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Affiliation(s)
- Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - George C E Jefferson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Michael D Keegan
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Yeuk Yau
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
| | - Luke B Snell
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
- Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
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Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, et alHunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591666. [PMID: 38746185 PMCID: PMC11092452 DOI: 10.1101/2024.04.29.591666] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.
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Affiliation(s)
- Martin Hunt
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Daniel Anderson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lily Karim
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Bethany L Dearlove
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Jeff Knaggs
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Bede Constantinides
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Teresa Street
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Sheila Lumley
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK
| | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christopher Ruis
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Benjamin Kotzen
- Department of Infectious Diseases, Massachusetts General Hospital., Boston, Massachusetts, USA
| | - Nicola de Maio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Dominic S Y Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Martin Avaro
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Reuben Ayivor-Djanie
- Laboratory for Medical Biotechnology and Biomanufacturing, International Centre for Genetic Engineering and Biotechnology, Tristie, Italy
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | | | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Elizabeth M Batty
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Denise De Belder
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Estefania Benedetti
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Andreas Bergthaler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Stefan A Boers
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Rosina Afua Ampomah Carr
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA
| | | | - Facundo Cuba
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Maria Elena Dattero
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kwabena Obeng Duedu
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- College of Life Sciences, Birmingham City University, Birmingham, UK
| | - Lukas Endler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Ilka Engelmann
- Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Français du Sang, Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Ngiambudulu M Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Etienne Z Gnimpieba
- Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD 57107
| | - Soraya Groc
- Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Jones Gyamfi
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
| | - Dennis Heemskerk
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nei-Yuan Hsiao
- Divison of Medical Virology, University of Cape Town and National Health Laboratory Service
| | - Matthew Huska
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | | | - Hanna Jarva
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Bani Jolly
- Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - Ravi Kant
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland
| | | | - Satu Kurkela
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maija Lappalainen
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marie Lataretu
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Jacob Lemieux
- Department of Infectious Diseases, Massachusetts General Hospital., Boston, Massachusetts, USA
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Tapfumanei Mashe
- Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe
| | - Juthathip Mongkolsapaya
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Jose Arturo Molina Mora
- Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Bernard Mvula
- Public Health Institute of Malawi, Ministry of Health, Malawi
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Joana Paula da Paixão
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomas Poklepovich
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Peter K Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Diyanath Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Mara Russo
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - James Emmanuel San
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710
- University of KwaZulu Natal, Durban, South Africa, 4001
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village, West Mumbai, Maharashtra, 400086, India
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Tarja Sironen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Teemu Smura
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chayaporn Suphavilai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Bryan Tegomoh
- Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Cameroun
- University of California, Berkeley, Berkeley, California, USA
- Nebraska Department of Health and Human Services, Lincoln, Nebraska, USA
| | - Olli Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert J Wilkinson
- Francis Crick Institute, London, UK
- Centre for Infectious Diseases Research in Africa, University of Cape Town
- Imperial College London, UK
| | | | - Xavier Zair
- Saw Swee Hock School of Public Health, National Univeristy of Singapore
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, South Africa
| | - Timothy Ea Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Zamin Iqbal
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Milner Centre for Evolution, University of Bath, UK
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9
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Merchant M, Ashraf J, Masood KI, Yameen M, Hussain R, Nasir A, Hasan Z. SARS-CoV-2 variants induce increased inflammatory gene expression but reduced interferon responses and heme synthesis as compared with wild type strains. Sci Rep 2024; 14:25734. [PMID: 39468120 PMCID: PMC11519399 DOI: 10.1038/s41598-024-76401-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 10/14/2024] [Indexed: 10/30/2024] Open
Abstract
SARS-CoV-2 variants of concern (VOC) have been associated with increased viral transmission and disease severity. We investigated the mechanisms of pathogenesis caused by variants using a host blood transcriptome profiling approach. We analysed transcriptional signatures of COVID-19 patients comparing those infected with wildtype (wt), alpha, delta or omicron strains seeking insights into infection in Asymptomatic cases.Comparison of transcriptional profiles of Symptomatic and Asymptomatic COVID-19 cases showed increased differentially regulated gene (DEGs) of inflammatory, apoptosis and blood coagulation pathways, with decreased T cell and Interferon stimulated genes (ISG) activation. Between SARS-CoV-2 strains, an increasing number of DEGs occurred in comparisons between wt and alpha (196), delta (1425) or, omicron (2313) infections. COVID-19 cases with alpha or, delta variants demonstrated suppression transcripts of innate immune pathways. EGR1 and CXCL8 were highly upregulated in those infected with VOC; heme biosynthetic pathway genes (ALAS2, HBB, HBG1, HBD9) and ISGs were downregulated. Delta and omicron infections upregulated ribosomal pathways, reflecting increased viral RNA translation. Asymptomatic COVID-19 cases infected with delta infections showed increased cytokines and ISGs expression. Overall, increased inflammation, with reduced host heme synthesis was associated with infections caused by VOC infections, with raised type I interferon in cases with less severe disease.
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Affiliation(s)
- Mariam Merchant
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rabia Hussain
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.
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10
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Schoefbaenker M, Günther T, Lorentzen EU, Romberg ML, Hennies MT, Neddermeyer R, Müller MM, Mellmann A, Bojarzyn CR, Lenz G, Stelljes M, Hrincius ER, Vollenberg R, Ludwig S, Tepasse PR, Kühn JE. Characterisation of the antibody-mediated selective pressure driving intra-host evolution of SARS-CoV-2 in prolonged infection. PLoS Pathog 2024; 20:e1012624. [PMID: 39405332 PMCID: PMC11508484 DOI: 10.1371/journal.ppat.1012624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 10/25/2024] [Accepted: 09/28/2024] [Indexed: 10/26/2024] Open
Abstract
Neutralising antibodies against the SARS-CoV-2 spike (S) protein are major determinants of protective immunity, though insufficient antibody responses may cause the emergence of escape mutants. We studied the humoral immune response causing intra-host evolution in a B-cell depleted, haemato-oncologic patient experiencing clinically severe, prolonged SARS-CoV-2 infection with a virus of lineage B.1.177.81. Following bamlanivimab treatment at an early stage of infection, the patient developed a bamlanivimab-resistant mutation, S:S494P. After five weeks of apparent genetic stability, the emergence of additional substitutions and deletions within the N-terminal domain (NTD) and the receptor binding domain (RBD) of S was observed. Notably, the composition and frequency of escape mutations changed in a short period with an unprecedented dynamic. The triple mutant S:Delta141-4 E484K S494P became dominant until virus elimination. Routine serology revealed no evidence of an antibody response in the patient. A detailed analysis of the variant-specific immune response by pseudotyped virus neutralisation test, surrogate virus neutralisation test, and immunoglobulin-capture enzyme immunoassay showed that the onset of an IgM-dominated antibody response coincided with the appearance of escape mutations. The formation of neutralising antibodies against S:Delta141-4 E484K S494P correlated with virus elimination. One year later, the patient experienced clinically mild re-infection with Omicron BA.1.18, which was treated with sotrovimab and resulted in an increase in Omicron-reactive antibodies. In conclusion, the onset of an IgM-dominated endogenous immune response in an immunocompromised patient coincided with the appearance of additional mutations in the NTD and RBD of S in a bamlanivimab-resistant virus. Although virus elimination was ultimately achieved, this humoral immune response escaped detection by routine diagnosis and created a situation temporarily favouring the rapid emergence of various antibody escape mutants with known epidemiological relevance.
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Affiliation(s)
| | - Theresa Günther
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Eva Ulla Lorentzen
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | | | - Marc Tim Hennies
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Rieke Neddermeyer
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | | | - Alexander Mellmann
- Institute of Hygiene, University Hospital Muenster, University of Muenster, Muenster, Germany
| | | | - Georg Lenz
- Department of Medicine A, Haematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Matthias Stelljes
- Department of Medicine A, Haematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | | | - Richard Vollenberg
- Department of Medicine B for Gastroenterology, Hepatology, Endocrinology and Clinical Infectiology, University Hospital Muenster, Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Phil-Robin Tepasse
- Department of Medicine B for Gastroenterology, Hepatology, Endocrinology and Clinical Infectiology, University Hospital Muenster, Muenster, Germany
| | - Joachim Ewald Kühn
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
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11
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Rosales R, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Diaz-Tapia R, Benjamin J, Rai DK, Cardin RD, Anderson AS, Sordillo EM, van Bakel H, Simon V, García-Sastre A, White KM. Nirmatrelvir and molnupiravir maintain potent in vitro and in vivo antiviral activity against circulating SARS-CoV-2 omicron subvariants. Antiviral Res 2024; 230:105970. [PMID: 39067667 DOI: 10.1016/j.antiviral.2024.105970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/27/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
Variants of SARS-CoV-2 pose significant challenges in public health due to their increased transmissibility and ability to evade natural immunity, vaccine protection, and monoclonal antibody therapeutics. The emergence of the highly transmissible Omicron variant and subsequent subvariants, characterized by an extensive array of over 32 mutations within the spike protein, intensifies concerns regarding vaccine evasion. In response, multiple antiviral therapeutics have received FDA emergency use approval, targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and main protease (Mpro) regions, known to have relatively fewer mutations across novel variants. In this study, we evaluated the efficacy of nirmatrelvir (PF-07321332) and other clinically significant SARS-CoV-2 antivirals against a diverse panel of SARS-CoV-2 variants, encompassing the newly identified Omicron subvariants XBB1.5 and JN.1, using live-virus antiviral assays. Our findings demonstrate that while the last Omicron subvariants exhibited heightened pathogenicity in our animal model, nirmatrelvir and other clinically relevant antivirals consistently maintained their efficacy against all tested variants, including the XBB1.5 subvariant.
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Affiliation(s)
- Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Diaz-Tapia
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jared Benjamin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Devendra K Rai
- Worldwide Research and Development, Pfizer Inc., Pearl River, NY, 10965, USA
| | - Rhonda D Cardin
- Worldwide Research and Development, Pfizer Inc., Pearl River, NY, 10965, USA
| | | | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Artificial Intelligence And Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Genomics Institute, 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; Global Health Emerging Pathogens Institute, 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; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, 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; Tisch Cancer Institute, 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
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
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13
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Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, Kwenda G, Musonda K, Munsaka S, Chilengi R, Sichinga K, Simulundu E. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study. Int J Mol Sci 2024; 25:6338. [PMID: 38928045 PMCID: PMC11203853 DOI: 10.3390/ijms25126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
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Affiliation(s)
| | - Herman M. Chambaro
- Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Duncan Chanda
- University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Macha Research Trust, Choma 20100, Zambia
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14
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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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15
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Magaret CA, Li L, deCamp AC, Rolland M, Juraska M, Williamson BD, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Heng F, Sun Y, Carpp LN, Bai H, Dearlove BL, Giorgi EE, Jongeneelen M, Brandenburg B, McCallum M, Bowen JE, Veesler D, Sadoff J, Gray GE, Roels S, Vandebosch A, Stieh DJ, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert PA, de Sousa LP, Silva MST, Casapia M, Losso MH, Little SJ, Gaur A, Bekker LG, Garrett N, Truyers C, Van Dromme I, Swann E, Marovich MA, Follmann D, Neuzil KM, Corey L, Greninger AL, Roychoudhury P, Hyrien O, Gilbert PB. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Nat Commun 2024; 15:2175. [PMID: 38467646 PMCID: PMC10928100 DOI: 10.1038/s41467-024-46536-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
In the ENSEMBLE randomized, placebo-controlled phase 3 trial (NCT04505722), estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were determined from 484 vaccine and 1,067 placebo recipients who acquired COVID-19. In this set of prespecified analyses, we show that in Latin America, VE was significantly lower against Lambda vs. Reference and against Lambda vs. non-Lambda [family-wise error rate (FWER) p < 0.05]. VE differed by residue match vs. mismatch to the vaccine-insert at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20); significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 antibody-epitope escape scores and 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccinee sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against the most distant viruses.
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Affiliation(s)
- Craig A Magaret
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Li Li
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Allan C deCamp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Morgane Rolland
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Michal Juraska
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian D Williamson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Biostatistics Division, Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - James Ludwig
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cindy Molitor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Benkeser
- Departments of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Alex Luedtke
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Brian Simpkins
- Department of Computer Science, Pitzer College, Claremont, CA, USA
| | - Fei Heng
- University of North Florida, Jacksonville, FL, USA
| | - Yanqing Sun
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hongjun Bai
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Elena E Giorgi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mandy Jongeneelen
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Boerries Brandenburg
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Jerald Sadoff
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
| | - Sanne Roels
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - An Vandebosch
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Daniel J Stieh
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Mathieu Le Gars
- Johnson & Johnson Innovative Medicine, Janssen Vaccines & Prevention B.V, Leiden, The Netherlands
| | - Johan Vingerhoets
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Beatriz Grinsztejn
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leonardo Paiva de Sousa
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Mayara Secco Torres Silva
- Evandro Chagas National Institute of Infectious Diseases-Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Martin Casapia
- Facultad de Medicina Humana, Universidad Nacional de la Amazonia Peru, Iquitos, Peru
| | - Marcelo H Losso
- Hospital General de Agudos José María Ramos Mejia, Buenos Aires, Argentina
| | - Susan J Little
- Division of Infectious Diseases, University of California San Diego, La Jolla, CA, USA
| | - Aditya Gaur
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Linda-Gail Bekker
- The Desmond Tutu HIV Centre, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Carla Truyers
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Ilse Van Dromme
- Janssen R&D, a division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Edith Swann
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary A Marovich
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dean Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA.
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16
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Delgado S, Somovilla P, Ferrer-Orta C, Martínez-González B, Vázquez-Monteagudo S, Muñoz-Flores J, Soria ME, García-Crespo C, de Ávila AI, Durán-Pastor A, Gadea I, López-Galíndez C, Moran F, Lorenzo-Redondo R, Verdaguer N, Perales C, Domingo E. Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps. Proc Natl Acad Sci U S A 2024; 121:e2317851121. [PMID: 38416684 PMCID: PMC10927536 DOI: 10.1073/pnas.2317851121] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
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Affiliation(s)
- Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos, Universidad Politécnica de Madrid, Madrid28031, Spain
| | - Pilar Somovilla
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid28049, Spain
| | - Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | | | - María Eugenia Soria
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Carlos García-Crespo
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
| | - Ana Isabel de Ávila
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en retrovirus, Centro Nacional de Microbiología, Instituto de salud Carlos III, Majadahonda28222, Spain
| | - Federico Moran
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid28040, Spain
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL60611
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Esteban Domingo
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
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17
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Korosec CS, Wahl LM, Heffernan JM. Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted from symptomatic infections? Virus Evol 2024; 10:veae006. [PMID: 38425472 PMCID: PMC10904108 DOI: 10.1093/ve/veae006] [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] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
Despite a relatively low mutation rate, the large number of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has allowed for substantial genetic change, leading to a multitude of emerging variants. Using a recently determined mutation rate (per site replication), as well as within-host parameter estimates for symptomatic SARS-CoV-2 infection, we apply a stochastic transmission-bottleneck model to describe the survival probability of de novo SARS-CoV-2 mutations as a function of bottleneck size and selection coefficient. For narrow bottlenecks, we find that mutations affecting per-target-cell attachment rate (with phenotypes associated with fusogenicity and ACE2 binding) have similar transmission probabilities to mutations affecting viral load clearance (with phenotypes associated with humoral evasion). We further find that mutations affecting the eclipse rate (with phenotypes associated with reorganization of cellular metabolic processes and synthesis of viral budding precursor material) are highly favoured relative to all other traits examined. We find that mutations leading to reduced removal rates of infected cells (with phenotypes associated with innate immune evasion) have limited transmission advantage relative to mutations leading to humoral evasion. Predicted transmission probabilities, however, for mutations affecting innate immune evasion are more consistent with the range of clinically estimated household transmission probabilities for de novo mutations. This result suggests that although mutations affecting humoral evasion are more easily transmitted when they occur, mutations affecting innate immune evasion may occur more readily. We examine our predictions in the context of a number of previously characterized mutations in circulating strains of SARS-CoV-2. Our work offers both a null model for SARS-CoV-2 mutation rates and predicts which aspects of viral life history are most likely to successfully evolve, despite low mutation rates and repeated transmission bottlenecks.
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Affiliation(s)
- Chapin S Korosec
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
| | - Lindi M Wahl
- Applied Mathematics, Western University, 1151 Richmond St, London, ON N6A 5B7, Canada
| | - Jane M Heffernan
- Modelling Infection and Immunity Lab, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
- Centre for Disease Modelling, Mathematics and Statistics, York University, 4700 Keele St, Toronto, ON M3J 1P3, Canada
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Selvavinayagam ST, Karishma SJ, Hemashree K, Yong YK, Suvaithenamudhan S, Rajeshkumar M, Aswathy B, Kalaivani V, Priyanka J, Kumaresan A, Kannan M, Gopalan N, Chandramathi S, Vignesh R, Murugesan A, Anshad AR, Ganesh B, Joseph N, Babu H, Govindaraj S, Larsson M, Kandasamy SL, Palani S, Singh K, Byrareddy SN, Velu V, Shankar EM, Raju S. Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 19:100272. [PMID: 38076717 PMCID: PMC10709680 DOI: 10.1016/j.lansea.2023.100272] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/13/2023] [Accepted: 08/20/2023] [Indexed: 04/14/2024]
Abstract
BACKGROUND Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India. METHODS Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients. FINDINGS Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population. INTERPRETATION Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the 'next' predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants. FUNDING National Health Mission (India), SIDASARC, VINNMER (Sweden), ORIP/NIH (USA).
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Affiliation(s)
- Sivaprakasam T. Selvavinayagam
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Sree J. Karishma
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Kannan Hemashree
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Yean K. Yong
- Laboratory Centre, Xiamen University Malaysia, Sepang, Selangor 43 900, Malaysia
| | - Suvaiyarasan Suvaithenamudhan
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
- Department of Bioinformatics, Bishop Heber College, Tiruchirappalli, Tamil Nadu 620 017, India
| | - Manivannan Rajeshkumar
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Bijulal Aswathy
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Vasudevan Kalaivani
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Jayapal Priyanka
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Anandhazhvar Kumaresan
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Meganathan Kannan
- Blood and Vascular Biology, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Natarajan Gopalan
- Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Samudi Chandramathi
- Department of Medical Microbiology, University of Malaya, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Ramachandran Vignesh
- Faculty of Medicine, Preclinical Department, Royal College of Medicine Perak, Universiti Kuala Lumpur, Ipoh, Perak 30450, Malaysia
| | - Amudhan Murugesan
- Department of Microbiology, The Government Theni Medical College and Hospital, Theni, India
| | - Abdul R. Anshad
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Balasubramanian Ganesh
- National Institute of Epidemiology, Indian Council of Medical Research, Ayappakkam, Chennai 600 077, India
| | - Narcisse Joseph
- Department of Medical Microbiology, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Hemalatha Babu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Sakthivel Govindaraj
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Marie Larsson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Sweden
| | - Shree L. Kandasamy
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Sampath Palani
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
| | - Kamalendra Singh
- Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68131, USA
| | - Vijayakumar Velu
- Division of Microbiology and Immunology, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Emory National Primate Research Center, Emory Vaccine Center, Atlanta, GA 30329, USA
| | - Esaki M. Shankar
- Infection and Inflammation, Department of Biotechnology, Central University of Tamil Nadu, Thiruvarur 610 005, India
| | - Sivadoss Raju
- State Public Health Laboratory, Directorate of Public Health and Preventive Medicine, DMS Campus, Teynampet, Chennai, Tamil Nadu 600 006, India
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19
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Chen C, Wang X, Zhang Z. Humoral and cellular immunity against diverse SARS-CoV-2 variants. J Genet Genomics 2023; 50:934-947. [PMID: 37865193 DOI: 10.1016/j.jgg.2023.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, the virus has rapidly spread worldwide. This has led to an unprecedented global pandemic, marked by millions of COVID-19 cases and a significant number of fatalities. Over a relatively short period, several different vaccine platforms are developed and deployed for use globally to curb the pandemic. However, the genome of SARS-CoV-2 continuously undergoes mutation and/or recombination, resulting in the emergence of several variants of concern (VOC). These VOCs can elevate viral transmission and evade the neutralizing antibodies induced by vaccines, leading to reinfections. Understanding the impact of the SARS-CoV-2 genomic mutation on viral pathogenesis and immune escape is crucial for assessing the threat of new variants to public health. This review focuses on the emergence and pathogenesis of VOC, with particular emphasis on their evasion of neutralizing antibodies. Furthermore, the memory B cell, CD4+, and CD8+ T cell memory induced by different COVID-19 vaccines or infections are discussed, along with how these cells recognize VOC. This review summarizes the current knowledge on adaptive immunology regarding SARS-CoV-2 infection and vaccines. Such knowledge may also be applied to vaccine design for other pathogens.
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Affiliation(s)
- Changxu Chen
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Xin Wang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China
| | - Zeli Zhang
- Center for Infectious Disease Research, School of Life Science, Westlake University, Hangzhou, Zhejiang 310001, China.
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20
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Wu Y, Shi J, He X, Lu J, Gao X, Zhu X, Chen X, Zhang M, Fang L, Zhang J, Yuan Z, Xiao G, Zhou P, Pan X. Protection of the receptor binding domain (RBD) dimer against SARS-CoV-2 and its variants. J Virol 2023; 97:e0127923. [PMID: 37843372 PMCID: PMC10688353 DOI: 10.1128/jvi.01279-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/16/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants achieved immune escape and became less virulent and easily transmissible through rapid mutation in the spike protein, thus the efficacy of vaccines on the market or in development continues to be challenged. Updating the vaccine, exploring compromise vaccination strategies, and evaluating the efficacy of candidate vaccines for the emerging variants in a timely manner are important to combat complex and volatile SARS-CoV-2. This study reports that vaccines prepared from the dimeric receptor-binding domain (RBD) recombinant protein, which can be quickly produced using a mature and stable process platform, had both good immunogenicity and protection in vivo and could completely protect rodents from lethal challenge by SARS-CoV-2 and its variants, including the emerging Omicron XBB.1.16, highlighting the value of dimeric recombinant vaccines in the post-COVID-19 era.
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Affiliation(s)
- Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Shi
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | - Xiaoxue He
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jia Lu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiao Gao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xuerui Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xinlan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Man Zhang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | | | - Jing Zhang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | - Zhiming Yuan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | | | - Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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21
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Katsaouni N, Llavona P, Khodamoradi Y, Otto AK, Körber S, Geisen C, Seidl C, Vehreschild MJGT, Ciesek S, Ackermann J, Koch I, Schulz MH, Krause DS. Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection. PLoS One 2023; 18:e0287725. [PMID: 37971979 PMCID: PMC10653545 DOI: 10.1371/journal.pone.0287725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/09/2023] [Indexed: 11/19/2023] Open
Abstract
The SARS-CoV-2 pandemic has affected nations globally leading to illness, death, and economic downturn. Why disease severity, ranging from no symptoms to the requirement for extracorporeal membrane oxygenation, varies between patients is still incompletely understood. Consequently, we aimed at understanding the impact of genetic factors on disease severity in infection with SARS-CoV-2. Here, we provide data on demographics, ABO blood group, human leukocyte antigen (HLA) type, as well as next-generation sequencing data of genes in the natural killer cell receptor family, the renin-angiotensin-aldosterone and kallikrein-kinin systems and others in 159 patients with SARS-CoV-2 infection, stratified into seven categories of disease severity. We provide single-nucleotide polymorphism (SNP) data on the patients and a protein structural analysis as a case study on a SNP in the SIGLEC7 gene, which was significantly associated with the clinical score. Our data represent a resource for correlation analyses involving genetic factors and disease severity and may help predict outcomes in infections with future SARS-CoV-2 variants and aid vaccine adaptation.
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Affiliation(s)
- Nikoletta Katsaouni
- Computational Epigenomics & Systems Cardiology, Institute of Cardiovascular Regeneration, Goethe University and University Clinic, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Pablo Llavona
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Ann-Kathrin Otto
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Stephanie Körber
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Christof Geisen
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Christian Seidl
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University, Frankfurt, Germany
- German Centre for Infection Research, External Partner Site, Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany
| | - Jörg Ackermann
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Marcel H. Schulz
- Computational Epigenomics & Systems Cardiology, Institute of Cardiovascular Regeneration, Goethe University and University Clinic, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Daniela S. Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
- Institute of Biochemistry II and Institute of General Pharmacology and Toxicology, Goethe-University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
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22
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Zappa M, Verdecchia P, Andolina A, Angeli F. The old and the new: The EG.5 ('Eris') sub-variant of Coronavirus. Eur J Intern Med 2023; 117:123-125. [PMID: 37690919 DOI: 10.1016/j.ejim.2023.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Affiliation(s)
- Martina Zappa
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Paolo Verdecchia
- Fondazione Umbra Cuore e Ipertensione-ONLUS and Division of Cardiology, Hospital S. Maria della Misericordia, Perugia, Italy
| | - Andrea Andolina
- Istituti Clinici Scientifici Maugeri IRCCS, Divisions of General Internal Medicine and Cardiac Rehabilitation, Tradate, Italy
| | - Fabio Angeli
- Istituti Clinici Scientifici Maugeri IRCCS, Divisions of General Internal Medicine and Cardiac Rehabilitation, Tradate, Italy; Department of Medicine and Technological Innovation (DiMIT), University of Insubria, Varese, Italy.
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23
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de Mello Malta F, Amgarten D, Marra AR, Petroni RC, da Silva Nali LH, Siqueira RA, Neto MC, Oler SC, Pinho JRR. Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection. BMC Infect Dis 2023; 23:714. [PMID: 37872472 PMCID: PMC10591358 DOI: 10.1186/s12879-023-08707-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2. METHODS Total nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates. RESULTS We identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target. CONCLUSIONS This study highlights the importance of genomic data to update molecular tests and vaccines.
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Affiliation(s)
- Fernanda de Mello Malta
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Deyvid Amgarten
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Alexandre Rodrigues Marra
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Roberta Cardoso Petroni
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Luiz Henrique da Silva Nali
- Post-Graduation Program in Health Sciences, Santo Amaro University, Rua Prof. Enéas de Siqueira Neto, 340 - Jardim das Imbuias, Sao Paulo, SP, Brazil
| | - Ricardo Andreotti Siqueira
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Miguel Cendoroglo Neto
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - Silvia Cassiano Oler
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil
| | - João Renato Rebello Pinho
- Laboratório Clínico - Hospital Israelita Albert Einstein, Av. Albert Einstein, 627/701, Sao Paulo, SP, 05651-901, Brazil.
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Gonçalves J, Melro M, Alenquer M, Araújo C, Castro-Neves J, Amaral-Silva D, Ferreira F, Ramalho JS, Charepe N, Serrano F, Pontinha C, Amorim MJ, Soares H. Balance between maternal antiviral response and placental transfer of protection in gestational SARS-CoV-2 infection. JCI Insight 2023; 8:e167140. [PMID: 37490342 PMCID: PMC10544212 DOI: 10.1172/jci.insight.167140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
The intricate interplay between maternal immune response to SARS-CoV-2 and the transfer of protective factors to the fetus remains unclear. By analyzing mother-neonate dyads from second and third trimester SARS-CoV-2 infections, our study shows that neutralizing antibodies (NAbs) are infrequently detected in cord blood. We uncovered that this is due to impaired IgG-NAb placental transfer in symptomatic infection and to the predominance of maternal SARS-CoV-2 NAbs of the IgA and IgM isotypes, which are prevented from crossing the placenta. Crucially, the balance between maternal antiviral response and transplacental transfer of IgG-NAbs appears to hinge on IL-6 and IL-10 produced in response to SARS-CoV-2 infection. In addition, asymptomatic maternal infection was associated with expansion of anti-SARS-CoV-2 IgM and NK cell frequency. Our findings identify a protective role for IgA/IgM-NAbs in gestational SARS-CoV-2 infection and open the possibility that the maternal immune response to SARS-CoV-2 infection might benefit the neonate in 2 ways, first by skewing maternal immune response toward immediate viral clearance, and second by endowing the neonate with protective mechanisms to curtail horizontal viral transmission in the critical postnatal period, via the priming of IgA/IgM-NAbs to be transferred by the breast milk and via NK cell expansion in the neonate.
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Affiliation(s)
- Juliana Gonçalves
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Magda Melro
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Marta Alenquer
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | - Catarina Araújo
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
| | - Júlia Castro-Neves
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Daniela Amaral-Silva
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | | | - Nádia Charepe
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
- CHRC, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Fátima Serrano
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
- CHRC, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
| | - Carlos Pontinha
- Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Gulbenkian Institute of Science, Oeiras, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Portuguese Catholic University, Lisbon, Portugal
| | - Helena Soares
- Human Immunobiology and Pathogenesis Laboratory, iNOVA4Health, Nova Medical School, Faculty of Medical Sciences, Nova University, Lisbon, Portugal
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Mandal N, Rath SL. Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling. Chem Phys 2023; 573:111995. [PMID: 37342284 PMCID: PMC10265933 DOI: 10.1016/j.chemphys.2023.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/12/2023] [Accepted: 06/11/2023] [Indexed: 06/22/2023]
Abstract
Among the variants of SARS-CoV-2, some are more infectious than the Wild-type. Interestingly, these mutations enable the virus to evade the therapeutic efforts. Hence, there is a need for candidate drug molecules that can potently bind with all the variants. We have adopted a strategy combining virtual screening, molecular docking followed by rigorous sampling by metadynamics simulations to find candidate molecules. From our results we found four highly potent drug candidates that can bind to the Spike-RBD of all the variants of the virus. Additionally, we also found that certain signature residues on the RBM region commonly bind to each of these inhibitors. Thus, our study not only gives information on the chemical compounds, but also residues on the proteins which could be targeted for future drug and vaccine development studies.
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Affiliation(s)
- Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal, Telangana, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal, Telangana, India
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Kong X, Gao P, Jiang Y, Lu L, Zhao M, Liu Y, Deng G, Zhu H, Cao Y, Ma L. Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis. Virol J 2023; 20:192. [PMID: 37626353 PMCID: PMC10463914 DOI: 10.1186/s12985-023-02137-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/22/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron strain has multiple immune-escape mutations in the spike protein receptor-binding domain (RBD). Rapid detection of these mutations to identify Omicron and its lineages is essential for guiding public health strategies and patient treatments. We developed a two-tube, four-color assay employing asymmetric polymerase chain reaction (PCR)-based melting curve analysis to detect Omicron mutations and discriminate the BA.1, BA.2, BA.4/5, and BA.2.75 lineages. METHODS The presented technique involves combinatory analysis of the detection of six fluorescent probes targeting the immune-escape mutations L452R, N460K, E484A, F486V, Q493R, Q498R, and Y505H within one amplicon in the spike RBD and probes targeting the ORF1ab and N genes. After protocol optimization, the analytical performance of the technique was evaluated using plasmid templates. Sensitivity was assessed based on the limit of detection (LOD), and reliability was assessed by calculating the intra- and inter-run precision of melting temperatures (Tms). Specificity was assessed using pseudotyped lentivirus of common human respiratory pathogens and human genomic DNA. The assay was used to analyze 40 SARS-CoV-2-positive clinical samples (including 36 BA.2 and 4 BA.4/5 samples) and pseudotyped lentiviruses of wild-type and BA.1 viral RNA control materials, as well as 20 SARS-CoV-2-negative clinical samples, and its accuracy was evaluated by comparing the results with those of sequencing. RESULTS All genotypes were sensitively identified using the developed method with a LOD of 39.1 copies per reaction. The intra- and inter-run coefficients of variation for the Tms were ≤ 0.69% and ≤ 0.84%, with standard deviations ≤ 0.38 °C and ≤ 0.41 °C, respectively. Validation of the assay using known SARS-CoV-2-positive samples demonstrated its ability to correctly identify the targeted mutations and preliminarily characterize the Omicron lineages. CONCLUSION The developed assay can provide accurate, reliable, rapid, simple and low-cost detection of the immune-escape mutations located in the spike RBD to detect the Omicron variant and discriminate its lineages, and its use can be easily generalized in clinical laboratories with a fluorescent PCR platform.
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Affiliation(s)
- Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Lixia Lu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Haoyan Zhu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, No. 2 Yinghua East Street, Chaoyang District, Beijing, 100029, People's Republic of China.
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Giovanetti M, Branda F, Cella E, Scarpa F, Bazzani L, Ciccozzi A, Slavov SN, Benvenuto D, Sanna D, Casu M, Santos LA, Lai A, Zehender G, Caccuri F, Ianni A, Caruso A, Maroutti A, Pascarella S, Borsetti A, Ciccozzi M. Epidemic history and evolution of an emerging threat of international concern, the severe acute respiratory syndrome coronavirus 2. J Med Virol 2023; 95:e29012. [PMID: 37548148 DOI: 10.1002/jmv.29012] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
This comprehensive review focuses on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact as the cause of the COVID-19 pandemic. Its objective is to provide a cohesive overview of the epidemic history and evolutionary aspects of the virus, with a particular emphasis on its emergence, global spread, and implications for public health. The review delves into the timelines and key milestones of SARS-CoV-2's epidemiological progression, shedding light on the challenges encountered during early containment efforts and subsequent waves of transmission. Understanding the evolutionary dynamics of the virus is crucial in monitoring its potential for adaptation and future outbreaks. Genetic characterization of SARS-CoV-2 is discussed, with a focus on the emergence of new variants and their implications for transmissibility, severity, and immune evasion. The review highlights the important role of genomic surveillance in tracking viral mutations linked to establishing public health interventions. By analyzing the origins, global spread, and genetic evolution of SARS-CoV-2, valuable insights can be gained for the development of effective control measures, improvement of pandemic preparedness, and addressing future emerging infectious diseases of international concern.
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Affiliation(s)
- Marta Giovanetti
- Instituto Rene Rachou Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Italy, Rome, Italy
| | - Francesco Branda
- Department of Computer Science, Modeling, Electronics and Systems Engineering (DIMES), University of Calabria, Rende, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Liliana Bazzani
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Italy, Rome, Italy
| | - Alessandra Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Svetoslav Nanev Slavov
- Butantan Institute, São Paulo, Brazil
- Blood Center of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Luciane Amorim Santos
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Bahia, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador, Bahia, Brazil
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - Giangluglielmo Zehender
- Department of Biomedical and Clinical Sciences, L. Sacco Hospital, University of Milan, Milan, Italy
| | - Francesca Caccuri
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Andrea Ianni
- M.G. Vannini Hospital IFSC Rome, Research Unit in Hygiene UCBM Rome, Rome, Italy
| | - Arnaldo Caruso
- Section of Microbiology Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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Abduljaleel Z, Melebari S, Athar M, Dehlawi S, Udhaya Kumar S, Aziz SA, Dannoun AI, Malik SM, Thasleem J, George Priya Doss C. SARS-CoV-2 vaccine breakthrough infections (VBI) by Omicron variant (B.1.1.529) and consequences in structural and functional impact. Cell Signal 2023:110798. [PMID: 37423342 DOI: 10.1016/j.cellsig.2023.110798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/18/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
This study investigated the efficacy of existing vaccines against hospitalization and infection due to the Omicron variant of COVID-19, particularly for those who received two doses of Moderna or Pfizer vaccines and one dose of Johnson & Johnson vaccine or who were vaccinated more than five months before. A total of 36 variants in Omicron's spike protein, targeted by all three vaccinations, have made antibodies less effective at neutralizing the virus. The genotyping of the SARS-CoV-2 viral sequence revealed clinically significant variants such as E484K in three genetic mutations (T95I, D614G, and del142-144). A woman showed two of these mutations, indicating a potential risk of infection after successful immunization, as recently reported by Hacisuleyman (2021). We examine the effects of mutations on domains (NID, RBM, and SD2) found at the interfaces of the spike domains Omicron B.1.1529, Delta/B.1.1529, Alpha/B.1.1.7, VUM B.1.526, B.1.575.2, and B.1.1214 (formerly VOI Iota). We tested the affinity of Omicron for ACE2 and found that the wild- and mutant-spike proteins were using atomistic molecular dynamics simulations. According to the binding free energies calculated during mutagenesis, the ACE2 bound Omicron spikes more strongly than the wild strain SARS-CoV-2. T95I, D614G, and E484K are three substitutions that significantly contribute to RBD, corresponding to ACE2 binding energies and a doubling of the electrostatic potential of Omicron spike proteins. The Omicron appears to bind to ACE2 with greater affinity, increasing its infectivity and transmissibility. The spike virus was designed to strengthen antibody immune evasion through binding while boosting receptor binding by enhancing IgG and IgM antibodies that stimulate human β-cell, as opposed to the wild strain, which has more vital stimulation of both antibodies.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia.
| | - Sami Melebari
- Department of Molecular Biology, The Regional Laboratory, Ministry of Health (MOH), Makkah, Saudi Arabia
| | - Mohammed Athar
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia; Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Saied Dehlawi
- Department of Molecular Biology, The Regional Laboratory, Ministry of Health (MOH), Makkah, Saudi Arabia
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Syed A Aziz
- Department of Pathology and Lab Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Anas Ibrahim Dannoun
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia
| | - Shaheer M Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jasheela Thasleem
- Jamal Mohamed College, Bharathidasan University, 7, Race Course Road, Kaja Nagar, Tiruchirappalli, Tamil Nadu 620020, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
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Payen SH, Gorzalski A, Siao DD, Pandori M, Verma SC, Rossetto CC. Analysis of SARS-CoV-2 variants from patient specimens in Nevada from October 2020 to August 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105434. [PMID: 37059256 PMCID: PMC10098042 DOI: 10.1016/j.meegid.2023.105434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
In early 2020, the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the human population quickly developed into a global pandemic. SARS-CoV-2 is the etiological agent of coronavirus disease 2019 (COVID-19) which has a broad range of respiratory illnesses. As the virus circulates, it acquires nucleotide changes. These mutations are potentially due to the inherent differences in the selection pressures within the human population compared to the original zoonotic reservoir of SARS-CoV-2 and formerly naïve humans. The acquired mutations will most likely be neutral, but some may have implications for viral transmission, disease severity, and resistance to therapies or vaccines. This is a follow-up study from our early report (Hartley et al. J Genet Genomics. 01202021;48(1):40-51) which detected a rare variant (nsp12, RdRp P323F) circulating within Nevada in mid 2020 at high frequency. The primary goals of the current study were to determine the phylogenetic relationship of the SARS-CoV-2 genomes within Nevada and to determine if there are any unusual variants within Nevada compared to the current database of SARS-CoV-2 sequences. Whole genome sequencing and analysis of SARS-CoV-2 from 425 positively identified nasopharyngeal/nasal swab specimens were performed from October 2020 to August 2021 to determine any variants that could result in potential escape from current therapeutics. Our analysis focused on nucleotide mutations that generated amino acid variations in the viral Spike (S) protein, Receptor binding domain (RBD), and the RNA-dependent RNA-polymerase (RdRp) complex. The data indicate that SARS-CoV-2 sequences from Nevada did not contain any unusual variants that had not been previously reported. Additionally, we did not detect the previously identified the RdRp P323F variant in any of the samples. This suggests that the rare variant we detected before was only able to circulate because of the stay-at-home orders and semi-isolation experience during the early months of the pandemic. IMPORTANCE: SARS-COV-2 continues to circulate in the human population. In this study, SARS-CoV-2 positive nasopharyngeal/nasal swab samples were used for whole genome sequencing to determine the phylogenetic relationship of SARS-CoV-2 sequences within Nevada from October 2020 to August 2021. The resulting data is being added to a continually growing database of SARS-CoV-2 sequences that will be important for understanding the transmission and evolution of the virus as it spreads around the globe.
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Affiliation(s)
- Shannon Harger Payen
- Department of Microbiology & Immunology, University of Nevada, Reno, 1664 North Virginia St. MS 320 Reno, NV 89557, USA; School of Medicine, University of Nevada, Reno, 1664 North Virginia St., Reno, NV 89557, USA
| | - Andrew Gorzalski
- Nevada State Public Health Laboratory, 1664 North Virginia St., Reno, NV 89557, USA
| | - Danielle Denise Siao
- Nevada State Public Health Laboratory, 1664 North Virginia St., Reno, NV 89557, USA
| | - Mark Pandori
- School of Medicine, University of Nevada, Reno, 1664 North Virginia St., Reno, NV 89557, USA; Nevada State Public Health Laboratory, 1664 North Virginia St., Reno, NV 89557, USA
| | - Subhash C Verma
- Department of Microbiology & Immunology, University of Nevada, Reno, 1664 North Virginia St. MS 320 Reno, NV 89557, USA; School of Medicine, University of Nevada, Reno, 1664 North Virginia St., Reno, NV 89557, USA
| | - Cyprian C Rossetto
- Department of Microbiology & Immunology, University of Nevada, Reno, 1664 North Virginia St. MS 320 Reno, NV 89557, USA; School of Medicine, University of Nevada, Reno, 1664 North Virginia St., Reno, NV 89557, USA.
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Magaret C, Li L, deCamp A, Rolland M, Juraska M, Williamson B, Ludwig J, Molitor C, Benkeser D, Luedtke A, Simpkins B, Carpp L, Bai H, Deariove B, Greninger A, Roychoudhury P, Sadoff J, Gray G, Roels S, Vandebosch A, Stieh D, Le Gars M, Vingerhoets J, Grinsztejn B, Goepfert P, Truyers C, Van Dromme I, Swann E, Marovich M, Follmann D, Neuzil K, Corey L, Hyrien O, Paiva de Sousa L, Casapia M, Losso M, Little S, Gaur A, Bekker LG, Garrett N, Heng F, Sun Y, Gilbert P. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. RESEARCH SQUARE 2023:rs.3.rs-2743022. [PMID: 37398105 PMCID: PMC10312950 DOI: 10.21203/rs.3.rs-2743022/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
It is of interest to pinpoint SARS-CoV-2 sequence features defining vaccine resistance. In the ENSEMBLE randomized, placebo-controlled phase 3 trial, estimated single-dose Ad26.COV2.S vaccine efficacy (VE) was 56% against moderate to severe-critical COVID-19. SARS-CoV-2 Spike sequences were measured from 484 vaccine and 1,067 placebo recipients who acquired COVID-19 during the trial. In Latin America, where Spike diversity was greatest, VE was significantly lower against Lambda than against Reference and against all non-Lambda variants [family-wise error rate (FWER) p < 0.05]. VE also differed by residue match vs. mismatch to the vaccine-strain residue at 16 amino acid positions (4 FWER p < 0.05; 12 q-value ≤ 0.20). VE significantly decreased with physicochemical-weighted Hamming distance to the vaccine-strain sequence for Spike, receptor-binding domain, N-terminal domain, and S1 (FWER p < 0.001); differed (FWER ≤ 0.05) by distance to the vaccine strain measured by 9 different antibody-epitope escape scores and by 4 NTD neutralization-impacting features; and decreased (p = 0.011) with neutralization resistance level to vaccine recipient sera. VE against severe-critical COVID-19 was stable across most sequence features but lower against viruses with greatest distances. These results help map antigenic specificity of in vivo vaccine protection.
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Affiliation(s)
| | - Li Li
- Fred Hutchinson Cancer Center
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Beatriz Grinsztejn
- Evandro Chagas National Institute of Infectious Diseases-Fundacao Oswaldo Cruz
| | - Paul Goepfert
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham
| | | | | | | | - Mary Marovich
- National Institute of Allergy and Infectious Diseases
| | | | | | | | | | | | | | | | - Susan Little
- Department of Medicine, University of California, San Diego, CA 92903
| | | | | | - Nigel Garrett
- Centre for the AIDS Program of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa 4041
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Abas AH, Tallei TE, Fatimawali F, Celik I, Alhumaydhi FA, Emran TB, Dhama K, Rabaan AA, Garout MA, Halwani MA, Al Mutair A, Alhumaid S, Harapan H. 4’-fluorouridine as a potential COVID-19 oral drug?: a review. F1000Res 2023; 11:410. [DOI: 10.12688/f1000research.109701.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
The available antiviral drugs against coronavirus disease 2019 (COVID-19) are limited. Oral drugs that can be prescribed to non-hospitalized patients are required. The 4′-fluoruridine, a nucleoside analog similar to remdesivir, is one of the promising candidates for COVID-19 oral therapy due to its ability to stall viral RdRp. Available data suggested that 4'-fluorouridine has antiviral activity against the respiratory syncytial virus, hepatitis C virus, lymphocytic choriomeningitis virus, and other RNA viruses, including SARS-CoV-2. In vivo study revealed that SARS-CoV-2 is highly susceptible to 4'-fluorouridine and was effective with a single daily dose versus molnupiravir administered twice daily. Although 4'-fluorouridine is considered as strong candidates, further studies are required to determine its efficacy in the patients and it’s genetic effects on humans. In this review, we the antiviral activity of 4′-fluorouridine is reviewed and compared it to other drugs currently in development. The current literature on 4′-fluorouridine's antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is compiled and discussed.
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Harne R, Williams B, Abdelaal HFM, Baldwin SL, Coler RN. SARS-CoV-2 infection and immune responses. AIMS Microbiol 2023; 9:245-276. [PMID: 37091818 PMCID: PMC10113164 DOI: 10.3934/microbiol.2023015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
The recent pandemic caused by the SARS-CoV-2 virus continues to be an enormous global challenge faced by the healthcare sector. Availability of new vaccines and drugs targeting SARS-CoV-2 and sequelae of COVID-19 has given the world hope in ending the pandemic. However, the emergence of mutations in the SARS-CoV-2 viral genome every couple of months in different parts of world is a persistent danger to public health. Currently there is no single treatment to eradicate the risk of COVID-19. The widespread transmission of SARS-CoV-2 due to the Omicron variant necessitates continued work on the development and implementation of effective vaccines. Moreover, there is evidence that mutations in the receptor domain of the SARS-CoV-2 spike glycoprotein led to the decrease in current vaccine efficacy by escaping antibody recognition. Therefore, it is essential to actively identify the mechanisms by which SARS-CoV-2 evades the host immune system, study the long-lasting effects of COVID-19 and develop therapeutics targeting SARS-CoV-2 infections in humans and preclinical models. In this review, we describe the pathogenic mechanisms of SARS-CoV-2 infection as well as the innate and adaptive host immune responses to infection. We address the ongoing need to develop effective vaccines that provide protection against different variants of SARS-CoV-2, as well as validated endpoint assays to evaluate the immunogenicity of vaccines in the pipeline, medications, anti-viral drug therapies and public health measures, that will be required to successfully end the COVID-19 pandemic.
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Affiliation(s)
- Rakhi Harne
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Brittany Williams
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Hazem F. M. Abdelaal
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Susan L. Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Rhea N. Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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Park AK, Kim IH, Lee CY, Kim JA, Lee H, Kim HM, Lee NJ, Woo S, Lee J, Rhee J, Yoo CK, Kim EJ. Rapid Emergence of the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Korea. Ann Lab Med 2023; 43:211-213. [PMID: 36281518 PMCID: PMC9618911 DOI: 10.3343/alm.2023.43.2.211] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/28/2022] [Accepted: 09/11/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ae Kyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Il-Hwan Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Chae Young Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Jeong-Ah Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Hyeokjin Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Heui Man Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Nam-Joo Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - SangHee Woo
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Jaehee Lee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - JeeEun Rhee
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Cheon-Kwon Yoo
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea
| | - Eun-Jin Kim
- Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Korea,Corresponding author: Eun-Jin Kim, Ph.D. Division of Emerging Infectious Diseases, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), 187 Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju 28159, Korea Tel: +82-43-719-8140, Fax: +82-43-719-8229, E-mail:
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran; Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA.
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Fiaz N, Zahoor I, Saima S, Basheer A. Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan. PLoS One 2022; 17:e0276171. [PMID: 36512569 PMCID: PMC9746927 DOI: 10.1371/journal.pone.0276171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675-3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.
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Affiliation(s)
- Nazia Fiaz
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Zahoor
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Saima Saima
- Department of Animal Nutrition, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Atia Basheer
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
- * E-mail:
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Novel bridge multi-species ELISA for detection of SARS-CoV-2 antibodies. J Immunol Methods 2022; 511:113365. [PMID: 36202252 PMCID: PMC9529351 DOI: 10.1016/j.jim.2022.113365] [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: 04/28/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Considering the course of the current SARS-CoV-2 pandemic, it is important to have serological tests for monitoring humoral immune response against SARS-CoV-2 infection and vaccination. Herein we describe a novel bridge enzyme-linked immunosorbent assay (b-ELISA) for SARS-CoV-2 antibodies detection in human and other species, employing recombinant Spike protein as a unique antigen, which is produced at high scale in insect larvae. METHODS Eighty two human control sera/plasmas and 169 COVID-19 patients' sera/plasmas, confirmed by rRT-PCR, were analyzed by the b-ELISA assay. In addition, a total of 27 animal sera (5 horses, 13 rats, 2 cats and 7 dogs) were employed in order to evaluate the b-ELISA in other animal species. RESULTS Out of the 169 patient samples, 129 were positive for IgG anti-SARS-CoV-2 and 40 were negative when they were tested by ELISA COVIDAR® IgG. When a cut-off value of 5.0 SDs was established, 124 out of the 129 COVID-19 positive samples were also positive by our developed b-ELISA (sensitivity: 96.12%). Moreover, the test was able to evaluate the humoral immune response in animal models and also detected as positive a naturally infected cat and two dogs with symptoms, whose owners had suffered the COVID-19 disease. CONCLUSION The obtained results demonstrate that the method developed herein is versatile, as it is able to detect antibodies against SARS-CoV-2 in different animal species without the need to perform and optimize a new assay for each species.
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Chen J, Qiu Y, Wang R, Wei GW. Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants. Comput Biol Med 2022; 151:106262. [PMID: 36379191 PMCID: PMC10754203 DOI: 10.1016/j.compbiomed.2022.106262] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/21/2022] [Accepted: 10/30/2022] [Indexed: 11/15/2022]
Abstract
Due to its high transmissibility, Omicron BA.1 ousted the Delta variant to become a dominating variant in late 2021 and was replaced by more transmissible Omicron BA.2 in March 2022. An important question is which new variants will dominate in the future. Topology-based deep learning models have had tremendous success in forecasting emerging variants in the past. However, topology is insensitive to homotopic shape evolution in virus-human protein-protein binding, which is crucial to viral evolution and transmission. This challenge is tackled with persistent Laplacian, which is able to capture both the topological change and homotopic shape evolution of data. Persistent Laplacian-based deep learning models are developed to systematically evaluate variant infectivity. Our comparative analysis of Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron BA.1, BA.1.1, BA.2, BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 unveils that Omicron BA.2.11, BA.2.12.1, BA.3, BA.4, and BA.5 are more contagious than BA.2. In particular, BA.4 and BA.5 are about 36% more infectious than BA.2 and are projected to become new dominant variants by natural selection. Moreover, the proposed models outperform the state-of-the-art methods on three major benchmark datasets for mutation-induced protein-protein binding free energy changes. Our key projection about BA4 and BA.5's dominance made on May 1, 2022 (see arXiv:2205.00532) became a reality in late June 2022.
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Affiliation(s)
- Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Yuchi Qiu
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Rui Wang
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI 48824, USA; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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Sarkar P, Banerjee S, Chakrabarti S, Chakrabarti P, Bandyopadhyay A, Mitra AG, Saha S, Roy A, Sarkar S. Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India. Indian J Med Microbiol 2022; 43:66-72. [PMID: 36400646 PMCID: PMC9664238 DOI: 10.1016/j.ijmmb.2022.10.006] [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] [Received: 06/09/2022] [Revised: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022]
Abstract
Purpose The emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research. Method Here, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping. Results The predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61–831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations ‘Q493R + Q498R + N501Y’, and ‘K417 N + E484A + N501Y’ remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development. Conclusion These findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.
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Affiliation(s)
- Poulomi Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Sarthak Banerjee
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Saikat Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | - Partha Chakrabarti
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India
| | - Arun Bandyopadhyay
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India
| | | | - Soumen Saha
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Aviral Roy
- MEDICA Super-specialty Hospital, Kolkata, India
| | - Siddik Sarkar
- CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India,IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India,Corresponding author. CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB-700032, India
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Bhowmick S, Jing T, Wang W, Zhang EY, Zhang F, Yang Y. In Silico Protein Folding Prediction of COVID-19 Mutations and Variants. Biomolecules 2022; 12:1665. [PMID: 36359015 PMCID: PMC9688002 DOI: 10.3390/biom12111665] [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: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 08/27/2023] Open
Abstract
With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics.
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Affiliation(s)
| | | | | | | | | | - Yanmin Yang
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, 1201 Welch Road, MSLS, P259, Stanford, CA 94305, USA
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Dual Monoclonal Antibodies on Sars-Cov-2 Alpha and Delta Variants: Clinical and Virological Efficacy. Microbiol Spectr 2022; 10:e0215222. [PMID: 36125289 PMCID: PMC9603708 DOI: 10.1128/spectrum.02152-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Monoclonal antibodies (MAbs) targeting the Spike glycoprotein of SARS-CoV-2 is a key strategy to prevent severe COVID-19. Here, the efficacy of two monoclonal antibody bitherapies against SARS-CoV-2 was assessed on 92 patients at high risk of severe COVID-19 between March and October 2021 (Bichat-Claude Bernard Hospital, Paris, France). Nine patients died despite appropriate management. From 14 days following treatment initiation, we observed a slower viral load decay for patients treated with the bitherapy Bamlanivimab/Etsevimab compared to the Casirivimab/Imdevimab association therapy (P = 0.045). The emergence of several mutations on the Spike protein known to diminish antiviral efficacy was observed from 1 to 3 weeks after infusion. The Q493R mutation was frequently selected, located in a region of joint structural overlap by Bamlanivimab/Etsevimab antibodies. Despite that this study was done on former SARS-CoV-2 variants (Alpha and Delta), the results provide new insights into resistance mechanisms in SARS-CoV-2 antibodies neutralization escape and should be considered for current and novel variants. IMPORTANCE Monoclonal antibody bitherapies (MAbs) are commonly prescribed to treat severe SARS-CoV-2-positive patients, and the rapid growth of resistance mutation emergence is alarming globally. To explore this issue, we conducted both clinical and genomic analyses of SARS-CoV-2 in a series of patients treated in 2021. We first noticed that the two dual therapies prescribed during the study had different kinetics of viral load decay. Rapidly after initiation of the treatments, resistance mutations emerged in the interface between the MAbs and the target Spike glycoprotein, demonstrating the importance to continuously screen the viral genome during treatment course. Taken together, the results highlight that viral mutations may emerge under selective pressure, conferring a putative competitive advantage, and could rapidly spread, as observed for the Omicron variant.
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [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: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
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SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022. Viruses 2022; 14:v14091918. [PMID: 36146724 PMCID: PMC9505681 DOI: 10.3390/v14091918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the disparity between developed and developing countries for infectious disease surveillance and the sequencing of pathogen genomes. The majority of SARS-CoV-2 sequences published are from Europe, North America, and Asia. Between April 2020 and January 2022, 795 SARS-CoV-2-positive nares swabs from individuals in the U.S. Navy installation Camp Lemonnier, Djibouti, were collected, sequenced, and analyzed. In this study, we described the results of genomic sequencing and analysis for 589 samples, the first published viral sequences for Djibouti, including 196 cases of vaccine breakthrough infections. This study contributes to the knowledge base of circulating SARS-CoV-2 lineages in the under-sampled country of Djibouti, where only 716 total genome sequences are available at time of publication. Our analysis resulted in the detection of circulating variants of concern, mutations of interest in lineages in which those mutations are not common, and emerging spike mutations.
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Gutiérrez LJ, Tosso RD, Zarycz MNC, Enriz RD, Baldoni HA. Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Rodrigo D. Tosso
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - M. Natalia C. Zarycz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
| | - Ricardo D. Enriz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
- Institute of Applied Mathematics of San Luis (IMASL. CONICET), San Luis, Argentina
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Li R, Mor M, Ma B, Clark AE, Alter J, Werbner M, Lee JC, Leibel SL, Carlin AF, Dessau M, Gal-Tanamy M, Croker BA, Xiang Y, Freund NT. Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies. Commun Biol 2022; 5:789. [PMID: 35931732 PMCID: PMC9355996 DOI: 10.1038/s42003-022-03739-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022] Open
Abstract
As new variants of SARS-CoV-2 continue to emerge, it is important to assess the cross-neutralizing capabilities of antibodies naturally elicited during wild type SARS-CoV-2 infection. In the present study, we evaluate the activity of nine anti-SARS-CoV-2 monoclonal antibodies (mAbs), previously isolated from convalescent donors infected with the Wuhan-Hu-1 strain, against the SARS-CoV-2 variants of concern (VOC) Alpha, Beta, Gamma, Delta and Omicron. By testing an array of mutated spike receptor binding domain (RBD) proteins, cell-expressed spike proteins from VOCs, and neutralization of SARS-CoV-2 VOCs as pseudoviruses, or as the authentic viruses in culture, we show that mAbs directed against the ACE2 binding site (ACE2bs) are more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which retain their potency against all VOCs tested. At the second part of our study, we reveal the neutralization mechanisms at high molecular resolution of two anti-SARS-CoV-2 neutralizing mAbs by structural characterization. We solve the structures of the Delta-neutralizing ACE2bs mAb TAU-2303 with the SARS-CoV-2 spike trimer and RBD at 4.5 Å and 2.42 Å resolutions, respectively, revealing a similar mode of binding to that between the RBD and ACE2. Furthermore, we provide five additional structures (at resolutions of 4.7 Å, 7.3 Å, 6.4 Å, 3.3 Å, and 6.1 Å) of a second antibody, TAU-2212, complexed with the SARS-CoV-2 spike trimer. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunits. Our study provides additional mechanistic understanding about how antibodies neutralize SARS-CoV-2 and its emerging variants and provides insights on the likelihood of reinfections. The neutralization of SARS-CoV-2 and variants of concern by nine monoclonal antibodies (mAb) isolated from convalescent donors infected with the Wuhan-Hu-1 strain alongside structural characterization of two of the mAbs in complex with the RBD and spike are presented.
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Affiliation(s)
- Ruofan Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Michael Mor
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bingting Ma
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joel Alter
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Michal Werbner
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Jamie Casey Lee
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Moshe Dessau
- The Laboratory of Structural Biology of Infectious Diseases, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar Ilan University, Tsafed, Israel
| | - Ben A Croker
- Department of Pediatrics, School of Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
| | - Natalia T Freund
- Department for Microbiology and Clinical Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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45
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Scovino AM, Dahab EC, Vieira GF, Freire-de-Lima L, Freire-de-Lima CG, Morrot A. SARS-CoV-2’s Variants of Concern: A Brief Characterization. Front Immunol 2022; 13:834098. [PMID: 35958548 PMCID: PMC9361785 DOI: 10.3389/fimmu.2022.834098] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/13/2022] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disclose the variants of concern (VOC) including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and Omicron (B.1.1.529). Its spike protein (S) present on the surface of the virus is recognized by the host cell receptor, the angiotensin-2 converting enzyme (ACE2) which promotes their entry into the cell. The mutations presented by VOCs are found in RBD and the N-terminal region of S protein. Therefore, mutations occurring in RBD can modify the biological and immunogenic characteristics of the virus, such as modifying the spike affinity for ACE2, increasing the virus transmissibility, or conferring the ability to escape the immune responses. The raise of a potential new SARS-CoV-2 variant capable of evading the host defenses at the same time maintaining its fitness justifies the importance of continued genetic monitoring of the pandemic coronavirus.
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Affiliation(s)
- Aline Miranda Scovino
- Instituto de Microbiologia Paulo de Goes, Universidade federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Elizabeth Chen Dahab
- Instituto de Microbiologia Paulo de Goes, Universidade federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Leonardo Freire-de-Lima
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Alexandre Morrot
- Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Alexandre Morrot,
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46
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Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms. Biomolecules 2022; 12:biom12070964. [PMID: 35883520 PMCID: PMC9313167 DOI: 10.3390/biom12070964] [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] [Received: 06/18/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
In this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control points of long-range interactions and communications. Conformational dynamics and distance fluctuation analysis revealed the antibody-specific signatures of protein stability and flexibility of the spike complexes that can affect the pattern of mutational escape. A network-based perturbation approach for mutational profiling of allosteric residue potentials revealed how antibody binding can modulate allosteric interactions and identified allosteric control points that can form vulnerable sites for mutational escape. The results show that the protein stability and binding energetics of the SARS-CoV-2 spike complexes with the panel of ultrapotent antibodies are tolerant to the effect of Omicron mutations, which may be related to their neutralization efficiency. By employing an integrated analysis of conformational dynamics, binding energetics, and allosteric interactions, we found that the antibodies that neutralize the Omicron spike variant mediate the dominant binding energy hotpots in the conserved stability centers and allosteric control points in which mutations may be restricted by the requirements of the protein folding stability and binding to the host receptor. This study suggested a mechanism in which the patterns of escape mutants for the ultrapotent antibodies may not be solely determined by the binding interaction changes but are associated with the balance and tradeoffs of multiple local and global factors, including protein stability, binding affinity, and long-range interactions.
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47
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Rathnasinghe R, Jangra S, Ye C, Cupic A, Singh G, Martínez-Romero C, Mulder LCF, Kehrer T, Yildiz S, Choi A, Yeung ST, Mena I, Gillespie V, De Vrieze J, Aslam S, Stadlbauer D, Meekins DA, McDowell CD, Balaraman V, Corley MJ, Richt JA, De Geest BG, Miorin L, PVI study group KleinerGiulio1112SaksenaMiti1112SrivastavaKomal1112GleasonCharles R.1112Bermúdez-GonzálezMaria C.1112BeachKatherine F.1112RussoKayla T.1112SominskyLevy A.1112FerreriEmily D.1112ChernetRachel L.1112EakerLily Q.1112SalimbangonAshley-Beathrese T.1112JurczyszakDenise1112AlshammaryHala1112MendezWanni A.1112AmoakoAngela A.1112FabreShelcie1112AwawdaMahmoud H.1112ShinAmber S.1112, Krammer F, Martinez-Sobrido L, Simon V, García-Sastre A, Schotsaert M. Characterization of SARS-CoV-2 Spike mutations important for infection of mice and escape from human immune sera. Nat Commun 2022; 13:3921. [PMID: 35798721 PMCID: PMC9261898 DOI: 10.1038/s41467-022-30763-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/13/2022] [Indexed: 12/25/2022] Open
Abstract
Due to differences in human and murine angiotensin converting enzyme 2 (ACE-2) receptor, initially available SARS-CoV-2 isolates could not infect mice. Here we show that serial passaging of USA-WA1/2020 strain in mouse lungs results in "mouse-adapted" SARS-CoV-2 (MA-SARS-CoV-2) with mutations in S, M, and N genes, and a twelve-nucleotide insertion in the S gene. MA-SARS-CoV-2 infection causes mild disease, with more pronounced morbidity depending on genetic background and in aged and obese mice. Two mutations in the S gene associated with mouse adaptation (N501Y, H655Y) are present in SARS-CoV-2 variants of concern (VoCs). N501Y in the receptor binding domain of viruses of the B.1.1.7, B.1.351, P.1 and B.1.1.529 lineages (Alpha, Beta, Gamma and Omicron variants) is associated with high transmissibility and allows VoCs to infect wild type mice. We further show that S protein mutations of MA-SARS-CoV-2 do not affect neutralization efficiency by human convalescent and post vaccination sera.
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Affiliation(s)
- Raveen Rathnasinghe
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.476726.6Present Address: Seqirus, Cambridge, MT USA
| | - Sonia Jangra
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Chengjin Ye
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Anastasija Cupic
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Gagandeep Singh
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Carles Martínez-Romero
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Lubbertus C. F. Mulder
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Thomas Kehrer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Soner Yildiz
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Angela Choi
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - Stephen T. Yeung
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Ignacio Mena
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Virginia Gillespie
- grid.59734.3c0000 0001 0670 2351Center for Comparative Medicine and Surgery, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Jana De Vrieze
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Sadaf Aslam
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Daniel Stadlbauer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - David A. Meekins
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Chester D. McDowell
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Velmurugan Balaraman
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Michael J. Corley
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Juergen A. Richt
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Bruno G. De Geest
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Lisa Miorin
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | | | - Florian Krammer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Luis Martinez-Sobrido
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Viviana Simon
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
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48
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Mandal N, Padhi AK, Rath SL. Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern. J Mol Graph Model 2022; 114:108194. [PMID: 35453047 PMCID: PMC9009157 DOI: 10.1016/j.jmgm.2022.108194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected the lives and livelihood of millions of individuals around the world. It has mutated several times after its first inception, with an estimated two mutations occurring every month. Although we have been successful in developing vaccines against the virus, the emergence of variants has enabled it to escape therapy. Few of the generated variants are also reported to be more infectious than the wild-type (WT). In this study, we analyze the attributes of all RBD/ACE2 complexes for the reported VOCs, namely, Alpha, Beta, Gamma, and Delta through computer simulations. Results indicate differences in orientation and binding energies of the VOCs from the WT. Overall, it was observed that electrostatic interactions play a major role in the binding of the complexes. Detailed residue level energetics revealed that the most prominent changes in interaction energies were seen particularly at the mutated residues which were present at RBD/ACE2 interface. We found that the Delta variant is one of the most tightly bound variants of SARS-CoV-2 with dynamics similar to WT. The high binding affinity of RBD towards ACE2 is indicative of an increase in viral transmission and infectivity. The details presented in our study provide additional information for the design and development of effective therapeutic strategies for the emerging variants of the virus in the future.
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Affiliation(s)
- Nabanita Mandal
- National Institute of Technology, Warangal, Telangana, 506004, India
| | - Aditya K Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Soumya Lipsa Rath
- National Institute of Technology, Warangal, Telangana, 506004, India.
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49
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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022; 13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.
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Affiliation(s)
- Nathan M. Markarian
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Gaël Galli
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France
- CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
| | - Mark Hemmings
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Priya Nagpal
- Department of Pharmacology, McGill University, Montréal, QC, Canada
| | | | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
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50
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Fears AC, Beddingfield BJ, Chirichella NR, Slisarenko N, Killeen SZ, Redmann RK, Goff K, Spencer S, Picou B, Golden N, Midkiff CC, Bush DJ, Branco LM, Boisen ML, Gao H, Montefiori DC, Blair RV, Doyle-Meyers LA, Russell-Lodrigue K, Maness NJ, Roy CJ. Exposure modality influences viral kinetics but not respiratory outcome of COVID-19 in multiple nonhuman primate species. PLoS Pathog 2022; 18:e1010618. [PMID: 35789343 PMCID: PMC9286241 DOI: 10.1371/journal.ppat.1010618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/15/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 emerged in late 2019, rapidly reached pandemic status, and has maintained global ubiquity through the emergence of variants of concern. Efforts to develop animal models have mostly fallen short of recapitulating severe disease, diminishing their utility for research focusing on severe disease pathogenesis and life-saving medical countermeasures. We tested whether route of experimental infection substantially changes COVID-19 disease characteristics in two species of nonhuman primates (Macaca mulatta; rhesus macaques; RM, Chlorocebus atheiops; African green monkeys; AGM). Species-specific cohorts were experimentally infected with SARS-CoV-2 by either direct mucosal (intratracheal + intranasal) instillation or small particle aerosol in route-discrete subcohorts. Both species demonstrated analogous viral loads in all compartments by either exposure route although the magnitude and duration of viral loading was marginally greater in AGMs than RMs. Clinical onset was nearly immediate (+1dpi) in the mucosal exposure cohort whereas clinical signs and cytokine responses in aerosol exposure animals began +7dpi. Pathologies conserved in both species and both exposure modalities include pulmonary myeloid cell influx, development of pleuritis, and extended lack of regenerative capacity in the pulmonary compartment. Demonstration of conserved pulmonary pathology regardless of species and exposure route expands our understanding of how SARS-CoV-2 infection may lead to ARDS and/or functional lung damage and demonstrates the near clinical response of the nonhuman primate model for anti-fibrotic therapeutic evaluation studies.
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Affiliation(s)
- Alyssa C. Fears
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Biomedical Science Training Program, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | | | - Nicole R. Chirichella
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Nadia Slisarenko
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Stephanie Z. Killeen
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Rachel K. Redmann
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Kelly Goff
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Skye Spencer
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Breanna Picou
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Nadia Golden
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Cecily C. Midkiff
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Duane J. Bush
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, Maryland, United States of America
| | | | - Hongmei Gao
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, North Carolina, United States of America
| | - Robert V. Blair
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Lara A. Doyle-Meyers
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Kasi Russell-Lodrigue
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Nicholas J. Maness
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Chad J. Roy
- Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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