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Moguem Soubgui AF, Ndeme Mboussi WS, Kojom Foko LP, Embolo Enyegue EL, Koanga Mogtomo ML. Serological surveillance reveals a high exposure to SARS-CoV-2 and altered immune response among COVID-19 unvaccinated Cameroonian individuals. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002380. [PMID: 38346064 PMCID: PMC10861046 DOI: 10.1371/journal.pgph.0002380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Surveillance of COVID-19/SARS-CoV-2 dynamics is crucial to understanding natural history and providing insights into the population's exposure risk and specific susceptibilities. This study investigated the seroprevalence of SARS-CoV-2 antibodies, its predictors, and immunological status among unvaccinated patients in Cameroon. A multicentre cross-sectional study was conducted between January and September 2022 in the town of Douala. Patients were consecutively recruited, and data of interest were collected using a questionnaire. Blood samples were collected to determine Immunoglobin titres (IgM and IgG), interferon gamma (IFN- γ) and interleukin-6 (IL-6) by ELISA, and CD4+ cells by flow cytometry. A total of 342 patients aged 41.5 ± 13.9 years were included. Most participants (75.8%) were asymptomatic. The overall crude prevalence of IgM and IgG was 49.1% and 88.9%, respectively. After adjustment, the seroprevalence values were 51% for IgM and 93% for IgM. Ageusia and anosmia have displayed the highest positive predictive values (90.9% and 82.4%) and specificity (98.9% and 98.3%). The predictors of IgM seropositivity were being diabetic (aOR = 0.23, p = 0.01), frequently seeking healthcare (aOR = 1.97, p = 0.03), and diagnosed with ageusia (aOR = 20.63, p = 0.005), whereas those of IgG seropositivity included health facility (aOR = 0.15, p = 0.01), age of 40-50 years (aOR = 8.78, p = 0.01), married (aOR = 0.21, p = 0.02), fever (aOR = 0.08, p = 0.01), and ageusia (aOR = 0.08, p = 0.01). CD4+, IFN-γ, and IL-6 were impaired in seropositive individuals, with a confounding role of socio-demographic factors or comorbidities. Although the WHO declared the end of COVID-19 as a public health emergency, the findings of this study indicate the need for continuous surveillance to adequately control the disease in Cameroon.
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Affiliation(s)
- Arlette Flore Moguem Soubgui
- Faculty of Science, Department of Biochemistry, The University of Douala, Douala, Cameroon
- Centre de Recherche et d’Expertise en Biologie, Douala, Cameroon
| | - Wilfred Steve Ndeme Mboussi
- Faculty of Science, Department of Biochemistry, The University of Douala, Douala, Cameroon
- Centre de Recherche et d’Expertise en Biologie, Douala, Cameroon
| | - Loick Pradel Kojom Foko
- Centre de Recherche et d’Expertise en Biologie, Douala, Cameroon
- Department of Animal Biology, Faculty of Science, The University of Douala, Douala, Cameroon
| | - Elisée Libert Embolo Enyegue
- Center for Research on Health and Priority Diseases, Ministry of Scientific Research and Innovation, Yaoundé, Centre Region, Cameroon
| | - Martin Luther Koanga Mogtomo
- Faculty of Science, Department of Biochemistry, The University of Douala, Douala, Cameroon
- Centre de Recherche et d’Expertise en Biologie, Douala, Cameroon
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Shafiq A, Khalid U, Abdur Rehman U, Abdullah Almuqri E, Muddassir M, Ahmad S, Khan MI, Khan A, Wei DQ. Structural basis for the mechanism of interaction of SARS-CoV-2 B.1.640.2 variant RBD with the host receptors hACE2 and GRP78. J Biomol Struct Dyn 2024; 42:2034-2042. [PMID: 37286365 DOI: 10.1080/07391102.2023.2220053] [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: 01/23/2023] [Accepted: 04/09/2023] [Indexed: 06/09/2023]
Abstract
The inflicted chaos instigated by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) globally continues with the emergence of novel variants. The current global outbreak is aggravated by the manifestation of novel variants, which affect the effectiveness of the vaccine, attachment with hACE2 (human Angiotensin-converting enzyme 2) and immune evasion. Recently, a new variant named University Hospital Institute (IHU) (B.1.640.2) was reported in France in November 2021 and is spreading globally affecting public healthcare. The B.1.640.2 SARS-CoV-2 strain revealed 14 mutations and 9 deletions in spike protein. Thus, it is important to understand how these variations in the spike protein impact the communication with the host. A protein coupling approach along with molecular simulation protocols was used to interpret the variation in the binding of the wild type (WT) and B.1.640.2 variant with hACE2 and Glucose-regulating protein 78 (GRP78) receptors. The initial docking scores revealed a stronger binding of the B.1.640.2-RBD with both the hACE2 and GRP78. To further understand the crucial dynamic changes, we looked at the structural and dynamic characteristics and also explored the variations in the bonding networks between the WT and B.1.640.2-RBD (receptor-binding domain) in association with hACE2 and GRP78, respectively. Our findings revealed that the variant complex demonstrated distinct dynamic properties in contrast to the wild type due to the acquired mutations. Finally, to provide conclusive evidence on the higher binding by the B.1.640.2 variant the TBE was computed for each complex. For the WT with hACE2 the TBE was quantified to be-61.38 ± 0.96 kcal/mol and for B.1.640.2 variant the TBE was estimated to be -70.47 ± 1.00 kcal/mol. For the WT-RBD-GRP78 the TBE -was computed to be 32.32 ± 0.56 kcal/mol and for the B.1.640.2-RBD a TBE of -50.39 ± 0.88 kcal/mol was reported. This show that these mutations are the basis for higher binding and infectivity produced by B.1.640.2 variant and can be targeted for drug designing against it.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Athar Shafiq
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Ujala Khalid
- Fatima Jinnah Medical University, Lahore, Punjab, Pakistan
| | - Umar Abdur Rehman
- Aziz Fatimah Medical and Dental College, Faisalabad, Punjab, Pakistan
| | - Eman Abdullah Almuqri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Maria Muddassir
- Institute of Molecular Biology & Biotechnology, The University of Lahore (UOL), Lahore, Punjab, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Idrees Khan
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
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3
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Bolland W, Michel V, Planas D, Hubert M, Staropoli I, Guivel-Benhassine F, Porrot F, N'Debi M, Rodriguez C, Fourati S, Prot M, Planchais C, Hocqueloux L, Simon-Lorière E, Mouquet H, Prazuck T, Pawlotsky JM, Bruel T, Schwartz O, Buchrieser J. High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1. J Virol 2024; 98:e0135123. [PMID: 38088562 PMCID: PMC10805008 DOI: 10.1128/jvi.01351-23] [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: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
SARS-CoV-2 variants with undetermined properties have emerged intermittently throughout the COVID-19 pandemic. Some variants possess unique phenotypes and mutations which allow further characterization of viral evolution and Spike functions. Around 1,100 cases of the B.1.640.1 variant were reported in Africa and Europe between 2021 and 2022, before the expansion of Omicron. Here, we analyzed the biological properties of a B.1.640.1 isolate and its Spike. Compared to the ancestral Spike, B.1.640.1 carried 14 amino acid substitutions and deletions. B.1.640.1 escaped binding by some anti-N-terminal domain and anti-receptor-binding domain monoclonal antibodies, and neutralization by sera from convalescent and vaccinated individuals. In cell lines, infection generated large syncytia and a high cytopathic effect. In primary airway cells, B.1.640.1 replicated less than Omicron BA.1 and triggered more syncytia and cell death than other variants. The B.1.640.1 Spike was highly fusogenic when expressed alone. This was mediated by two poorly characterized and infrequent mutations located in the Spike S2 domain, T859N and D936H. Altogether, our results highlight the cytopathy of a hyper-fusogenic SARS-CoV-2 variant, supplanted upon the emergence of Omicron BA.1. (This study has been registered at ClinicalTrials.gov under registration no. NCT04750720.)IMPORTANCEOur results highlight the plasticity of SARS-CoV-2 Spike to generate highly fusogenic and cytopathic strains with the causative mutations being uncharacterized in previous variants. We describe mechanisms regulating the formation of syncytia and the subsequent consequences in a primary culture model, which are poorly understood.
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Affiliation(s)
- William Bolland
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Université Paris Cité, Paris, France
| | - Vincent Michel
- Pathogenesis of Vascular Infections Unit, Institut Pasteur, INSERM, Paris, France
| | - Delphine Planas
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | | | - Françoise Porrot
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
| | - Mélissa N'Debi
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Slim Fourati
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Matthieu Prot
- Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | | | - Etienne Simon-Lorière
- Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, Paris, France
| | | | - Jean-Michel Pawlotsky
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France
- Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Timothée Bruel
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
- Vaccine Research Institute, Créteil, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS UMR3569, Paris, France
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Vickos U, Camasta M, Grandi N, Scognamiglio S, Schindler T, Belizaire MRD, Lango-Yaya E, Koyaweda GW, Senzongo O, Pounguinza S, Estimé KKJF, N’yetobouko S, Gadia CLB, Feiganazoui DA, Le Faou A, Orsini M, Perno CF, Zinzula L, Rafaï CD. COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome. Viruses 2023; 15:2309. [PMID: 38140550 PMCID: PMC10748234 DOI: 10.3390/v15122309] [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: 10/05/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.
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Affiliation(s)
- Ulrich Vickos
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
- Department of Medicine, Infectious and Tropical Diseases, Sino-Central African Amitié Hospital, Bangui 94045, Central African Republic
| | - Marianna Camasta
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Sante Scognamiglio
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Monserrato, Italy; (M.C.); (S.S.)
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland;
- Department of Medical Parasitology and Infection Biology, University of Basel, 4051 Basel, Switzerland
| | | | - Ernest Lango-Yaya
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Giscard Wilfried Koyaweda
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Oscar Senzongo
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Simon Pounguinza
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Kaleb Kandou Jephté Francis Estimé
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Stephanie N’yetobouko
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Christelle Luce Bobossi Gadia
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Dominos-Alfred Feiganazoui
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
| | - Alain Le Faou
- EA 3452 CITHEFOR, Campus Brabois Santé, 54500 Vandœuvre-lès-Nancy, France;
- Faculty of Medicine, Maieutic and Health Sciences, University of Lorraine, Pole Brabois Santé, 54500 Nancy, France
| | - Massimiliano Orsini
- General and Experimental Microbiology, Laboratory of Microbial Ecology and Genomics of Microorganisms, Experimental Zooprophylactic Institute of the Venezie (IZSVe), 35020 Legnaro, Italy;
| | - Carlo Federico Perno
- Department of Diagnostic and Laboratory Medicine, UOC Microbiology and Immunology Diagnostics, Children’s Hospital Bambino Gesù, IRCCS, 00118 Rome, Italy;
| | - Luca Zinzula
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Clotaire Donatien Rafaï
- Clinical Biology and Public Health National Laboratory, Bangui 94045, Central African Republic; (E.L.-Y.); (G.W.K.); (O.S.); (S.P.); (K.K.J.F.E.); (S.N.); (C.L.B.G.); (D.-A.F.); (C.D.R.)
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Ciarmiello A, Tutino F, Giovannini E, Milano A, Barattini M, Yosifov N, Calvi D, Setti M, Sivori M, Sani C, Bastreri A, Staffiere R, Stefanini T, Artioli S, Giovacchini G. Multivariable Risk Modelling and Survival Analysis with Machine Learning in SARS-CoV-2 Infection. J Clin Med 2023; 12:7164. [PMID: 38002776 PMCID: PMC10672177 DOI: 10.3390/jcm12227164] [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: 10/10/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
AIM To evaluate the performance of a machine learning model based on demographic variables, blood tests, pre-existing comorbidities, and computed tomography(CT)-based radiomic features to predict critical outcome in patients with acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS We retrospectively enrolled 694 SARS-CoV-2-positive patients. Clinical and demographic data were extracted from clinical records. Radiomic data were extracted from CT. Patients were randomized to the training (80%, n = 556) or test (20%, n = 138) dataset. The training set was used to define the association between severity of disease and comorbidities, laboratory tests, demographic, and CT-based radiomic variables, and to implement a risk-prediction model. The model was evaluated using the C statistic and Brier scores. The test set was used to assess model prediction performance. RESULTS Patients who died (n = 157) were predominantly male (66%) over the age of 50 with median (range) C-reactive protein (CRP) = 5 [1, 37] mg/dL, lactate dehydrogenase (LDH) = 494 [141, 3631] U/I, and D-dimer = 6.006 [168, 152.015] ng/mL. Surviving patients (n = 537) had median (range) CRP = 3 [0, 27] mg/dL, LDH = 484 [78, 3.745] U/I, and D-dimer = 1.133 [96, 55.660] ng/mL. The strongest risk factors were D-dimer, age, and cardiovascular disease. The model implemented using the variables identified using the LASSO Cox regression analysis classified 90% of non-survivors as high-risk individuals in the testing dataset. In this sample, the estimated median survival in the high-risk group was 9 days (95% CI; 9-37), while the low-risk group did not reach the median survival of 50% (p < 0.001). CONCLUSIONS A machine learning model based on combined data available on the first days of hospitalization (demographics, CT-radiomics, comorbidities, and blood biomarkers), can identify SARS-CoV-2 patients at risk of serious illness and death.
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Affiliation(s)
- Andrea Ciarmiello
- Nuclear Medicine Unit, Ospedale Civile Sant’Andrea, Via Vittorio Veneto 170, 19124 La Spezia, Italy; (F.T.); (E.G.); (N.Y.); (G.G.)
| | - Francesca Tutino
- Nuclear Medicine Unit, Ospedale Civile Sant’Andrea, Via Vittorio Veneto 170, 19124 La Spezia, Italy; (F.T.); (E.G.); (N.Y.); (G.G.)
| | - Elisabetta Giovannini
- Nuclear Medicine Unit, Ospedale Civile Sant’Andrea, Via Vittorio Veneto 170, 19124 La Spezia, Italy; (F.T.); (E.G.); (N.Y.); (G.G.)
| | - Amalia Milano
- Oncology Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy;
| | - Matteo Barattini
- Radiology Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy; (M.B.); (T.S.)
| | - Nikola Yosifov
- Nuclear Medicine Unit, Ospedale Civile Sant’Andrea, Via Vittorio Veneto 170, 19124 La Spezia, Italy; (F.T.); (E.G.); (N.Y.); (G.G.)
| | - Debora Calvi
- Infectius Diseases Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy; (D.C.); (S.A.)
| | - Maurizo Setti
- Internal Medicine Unit, Ospedale San Bartolomeo, 19138 Sarzana, Italy;
| | | | - Cinzia Sani
- Intensive Care Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy;
| | - Andrea Bastreri
- Emergency Department, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy;
| | | | - Teseo Stefanini
- Radiology Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy; (M.B.); (T.S.)
| | - Stefania Artioli
- Infectius Diseases Unit, Ospedale Civile Sant’Andrea, 19124 La Spezia, Italy; (D.C.); (S.A.)
| | - Giampiero Giovacchini
- Nuclear Medicine Unit, Ospedale Civile Sant’Andrea, Via Vittorio Veneto 170, 19124 La Spezia, Italy; (F.T.); (E.G.); (N.Y.); (G.G.)
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6
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Bhardwaj P, Mishra SK, Behera SP, Zaman K, Kant R, Singh R. Genomic evolution of the SARS-CoV-2 Variants of Concern: COVID-19 pandemic waves in India. EXCLI JOURNAL 2023; 22:451-465. [PMID: 37534220 PMCID: PMC10390896 DOI: 10.17179/excli2023-6098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023]
Abstract
SARS-CoV-2 has mutated rapidly since its first case report in Wuhan, China, leading to the emergence of an indefinite number of variants. India has witnessed three waves of the COVID-19 pandemic. The country saw its first wave of SARS-CoV-2 illness from late January 2020 to February 2021. With a peak surge of cases in mid-September 2020, India recorded more than 11 million cases and a death toll of more than 0.165 million at this time. India faced a brutal second wave driven by the emergence of highly infectious SARS-CoV-2 variants B.1.617.2 (Delta variant) and the third wave with the leading cause of BA.2 (Omicron variant), which has led to an unprecedented rise in COVID-19 cases in the country. On September 14, 2022, India recorded a cumulative 44.51 million cases of COVID-19 with more than 0.528 million deaths. The discovery of common circulating mutants is facilitated by genome sequencing. The changes in the Spike surface glycoprotein recombinant binding domains served as the critical alterations, resulting in enhanced infectivity and transmissibility, with severe clinical effects. Further, the predominant mutation in the SARS-CoV-2 spike protein; the D614G strains served as a model for vaccine development. The mutation of the Wuhan strain to the Variant of Concern led to a significant increase in SARS-CoV-2 infections. In addition, there was a shift in the age group affected by SARS-CoV-2 variant infection. The current review summarized the COVID-19 pandemic's Variant of Concern and the advent of SARS-CoV-2 in India.
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Affiliation(s)
- Pooja Bhardwaj
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR) - Regional Medical Research Center Gorakhpur, BRD Medical College Campus, Gorakhpur-273013, U.P., India
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8
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Yu X, Juraszek J, Rutten L, Bakkers MJG, Blokland S, Melchers JM, van den Broek NJF, Verwilligen AYW, Abeywickrema P, Vingerhoets J, Neefs JM, Bakhash SAM, Roychoudhury P, Greninger A, Sharma S, Langedijk JPM. Convergence of immune escape strategies highlights plasticity of SARS-CoV-2 spike. PLoS Pathog 2023; 19:e1011308. [PMID: 37126534 PMCID: PMC10174534 DOI: 10.1371/journal.ppat.1011308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/11/2023] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
The global spread of the SARS-CoV-2 virus has resulted in emergence of lineages which impact the effectiveness of immunotherapies and vaccines that are based on the early Wuhan isolate. All currently approved vaccines employ the spike protein S, as it is the target for neutralizing antibodies. Here we describe two SARS-CoV-2 isolates with unusually large deletions in the N-terminal domain (NTD) of the spike. Cryo-EM structural analysis shows that the deletions result in complete reshaping of the NTD supersite, an antigenically important region of the NTD. For both spike variants the remodeling of the NTD negatively affects binding of all tested NTD-specific antibodies in and outside of the NTD supersite. For one of the variants, we observed a P9L mediated shift of the signal peptide cleavage site resulting in the loss of a disulfide-bridge; a unique escape mechanism with high antigenic impact. Although the observed deletions and disulfide mutations are rare, similar modifications have become independently established in several other lineages, indicating a possibility to become more dominant in the future. The observed plasticity of the NTD foreshadows its broad potential for immune escape with the continued spread of SARS-CoV-2.
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Affiliation(s)
- Xiaodi Yu
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Jarek Juraszek
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | - Lucy Rutten
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | - Sven Blokland
- Janssen Vaccines & Prevention BV, Leiden, the Netherlands
| | | | | | | | - Pravien Abeywickrema
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
| | - Johan Vingerhoets
- Janssen Pharmaceutica N.V., Clinical Microbiology and Immunology, Beerse, Belgium
| | - Jean-Marc Neefs
- Janssen Pharmaceutica N.V., Discovery Sciences, Beerse, Belgium
| | - Shah A Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Alex Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington, Seattle, Washington, United States of America
| | - Sujata Sharma
- Structural & Protein Sciences, Janssen Research and Development, Spring House, Pennsylvania, United States of America
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9
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Banerjee A, Mazumder A, Roy J, Das J, Majumdar A, Chatterjee A, Biswas NK, Chawla Sarkar M, Das S, Dutta S, Maitra A. Emergence of a unique SARS-CoV-2 Delta sub-cluster harboring a constellation of co-appearing non-Spike mutations. J Med Virol 2023; 95:e28413. [PMID: 36541745 PMCID: PMC9878222 DOI: 10.1002/jmv.28413] [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: 08/26/2022] [Revised: 11/21/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Accumulation of diverse mutations across the structural and nonstructural genes is leading to rapid evolution of SARS-CoV-2, altering its pathogenicity. We performed whole genome sequencing of 239 SARS-CoV-2 RNA samples collected from both adult and pediatric patients across eastern India (West Bengal), during the second pandemic wave in India (April-May 2021). In addition to several common spike mutations within the Delta variant, a unique constellation of eight co-appearing non-Spike mutations was identified, which revealed a high degree of positive mutual correlation. Our results also demonstrated the dynamics of SARS-CoV-2 variants among unvaccinated pediatric patients. 41.4% of our studied Delta strains harbored this signature set of eight co-appearing non-Spike mutations and phylogenetically out-clustered other Delta sub-lineages like 21J, 21A, or 21I. This is the first report from eastern India that portrayed a landscape of co-appearing mutations in the non-Spike proteins, which might have led to the evolution of a distinct Delta subcluster. Accumulation of such mutations in SARS-CoV-2 may lead to the emergence of "vaccine-evading variants." Hence, monitoring of such non-Spike mutations will be significant in the formulation of any future vaccines against those SARS-CoV-2 variants that might evade the current vaccine-induced immunity, among both the pediatric and adult populations.
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Affiliation(s)
| | - Anup Mazumder
- National Institute of Biomedical GenomicsKalyaniIndia
| | - Jayita Roy
- National Institute of Biomedical GenomicsKalyaniIndia
| | | | - Agniva Majumdar
- ICMR‐National Institute of Cholera and Enteric DiseasesKolkataIndia
| | | | | | | | - Saumitra Das
- National Institute of Biomedical GenomicsKalyaniIndia,Department of Microbiology and Cell BiologyIndian Institute of ScienceBengaluruIndia
| | - Shanta Dutta
- ICMR‐National Institute of Cholera and Enteric DiseasesKolkataIndia
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10
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Sazed SA, Kibria MG, Zamil MF, Hossain MS, Khan JZ, Juthi RT, Hossain ME, Ahmed D, Noor Z, Haque R, Alam MS. Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis. Microbiol Spectr 2022; 10:e0199822. [PMID: 36453913 PMCID: PMC9769842 DOI: 10.1128/spectrum.01998-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
Accurate and early diagnoses are prerequisites for prompt treatment. For coronavirus disease 2019 (COVID-19), it is even more crucial. Currently, choice of methods include rapid diagnostic tests and reverse transcription polymerase chain reaction (RT-PCR) using samples mostly of respiratory origin and sometimes saliva. We evaluated two rapid diagnostic tests with three specimen types using viral transport medium (VTM) containing naso-oropharyngeal (NOP) swabs, direct nasal and direct nasopharyngeal (NP) samples from 428 prospective patients. We also performed RT-PCR for 428 NOP VTM and 316 saliva samples to compare results. The sensitivity of the SD Biosensor Standard Q COVID-19 antigen (Ag) test kit drastically raised from an average of 65.55% (NOP VTM) to 85.25% (direct nasal samples), while RT-PCR was the gold standard. For the CareStart kit, the sensitivity was almost similar for direct NP swabs; the average was 84.57%. The specificities were ≥95% for both SD Biosensor Standard Q and CareStart COVID-19 Ag tests in all platforms. The kits were also able to detect patients with different variants as well. Alternatively, RT-PCR results from saliva and NOP VTM samples showed high sensitivities of 96.45% and 95.48% with respect to each other as standard. The overall results demonstrated high performance of the rapid tests, indicating the suitability for regular surveillance at clinical facilities when using direct nasal or direct NP samples rather than NOP VTM. Additionally, the analysis also signifies not showed that RT-PCR of saliva can be used as an choice of method to RT-PCR of NOP VTM, providing an easier, non-invasive sample collection method. IMPORTANCE There are several methods for the diagnosis of coronavirus disease 2019 (COVID-19), and the choice of methods depends mostly on the resources and level of sensitivity required by the user and health care providers. Still, reverse transcription polymerase chain reaction (RT-PCR) has been chosen as the best method using direct naso-oropharyngeal swabs. There are also other methods of fast detection, such as rapid diagnostic tests (RDTs), which offer result within 15 to 20 min and have become quite popular for self-testing and in the clinical setting. The major drawback of the currently used RT-PCR method is compliance, as it may cause irritation, and patients often refuse to test in such a way. RDTs, although inexpensive, suffer from low sensitivity due to technical issues. In this article, we propose saliva as a noninvasive source for RT-PCR samples and evaluate various specimen types at different times after infection for the best possible output from COVID-19 rapid tests.
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Affiliation(s)
- Saiful Arefeen Sazed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Golam Kibria
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Md Fahad Zamil
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Sharif Hossain
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Jeba Zaman Khan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Rifat Tasnim Juthi
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Enayet Hossain
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Shafiul Alam
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
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11
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D3AI-Spike: A deep learning platform for predicting binding affinity between SARS-CoV-2 spike receptor binding domain with multiple amino acid mutations and human angiotensin-converting enzyme 2. Comput Biol Med 2022; 151:106212. [PMID: 36327885 PMCID: PMC9597563 DOI: 10.1016/j.compbiomed.2022.106212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 12/27/2022]
Abstract
The number of SARS-CoV-2 spike Receptor Binding Domain (RBD) with multiple amino acid mutations is huge due to random mutations and combinatorial explosions, making it almost impossible to experimentally determine their binding affinities to human angiotensin-converting enzyme 2 (hACE2). Although computational prediction is an alternative way, there is still no online platform to predict the mutation effect of RBD on the hACE2 binding affinity until now. In this study, we developed a free online platform based on deep learning models, namely D3AI-Spike, for quickly predicting binding affinity between spike RBD mutants and hACE2. The models based on CNN and CNN-RNN methods have the concordance index of around 0.8. Overall, the test results of the models are in agreement with the experimental data. To further evaluate the prediction power of D3AI-Spike, we predicted and experimentally determined the binding affinity of a VUM (variants under monitoring) variant IHU (B.1.640.2), which has fourteen amino acid substitutions, including N501Y and E484K, and 9 deletions located in the spike protein. The predicted average affinity score for wild-type RBD and IHU to hACE2 are 0.483 and 0.438, while the determined Kaff values are 5.39 ± 0.38 × 107 L/mol and 1.02 ± 0.47 × 107 L/mol, respectively, demonstrating the strong predictive power of D3AI-Spike. We think D3AI-Spike will be helpful to the viral transmission prediction for the new emerging SARS-CoV-2 variants. D3AI-Spike is now available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3AI-Spike/index.php.
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12
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Savinkina A, Bilinski A, Fitzpatrick M, Paltiel AD, Rizvi Z, Salomon J, Thornhill T, Gonsalves G. Estimating deaths averted and cost per life saved by scaling up mRNA COVID-19 vaccination in low-income and lower-middle-income countries in the COVID-19 Omicron variant era: a modelling study. BMJ Open 2022; 12:e061752. [PMID: 36100306 PMCID: PMC9471205 DOI: 10.1136/bmjopen-2022-061752] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/21/2022] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES While almost 60% of the world has received at least one dose of COVID-19 vaccine, the global distribution of vaccination has not been equitable. Only 4% of the population of low-income countries (LICs) has received a full primary vaccine series, compared with over 70% of the population of high-income nations. DESIGN We used economic and epidemiological models, parameterised with public data on global vaccination and COVID-19 deaths, to estimate the potential benefits of scaling up vaccination programmes in LICs and lower-middle-income countries (LMICs) in 2022 in the context of global spread of the Omicron variant of SARS-CoV2. SETTING Low-income and lower-middle-income nations. MAIN OUTCOME MEASURES Outcomes were expressed as number of avertable deaths through vaccination, costs of scale-up and cost per death averted. We conducted sensitivity analyses over a wide range of parameter estimates to account for uncertainty around key inputs. FINDINGS Globally, universal vaccination in LIC/LMIC with three doses of an mRNA vaccine would result in an estimated 1.5 million COVID-19 deaths averted with a total estimated cost of US$61 billion and an estimated cost-per-COVID-19 death averted of US$40 800 (sensitivity analysis range: US$7400-US$81 500). Lower estimated infection fatality ratios, higher cost-per-dose and lower vaccine effectiveness or uptake lead to higher cost-per-death averted estimates in the analysis. CONCLUSIONS Scaling up COVID-19 global vaccination would avert millions of COVID-19 deaths and represents a reasonable investment in the context of the value of a statistical life. Given the magnitude of expected mortality facing LIC/LMIC without vaccination, this effort should be an urgent priority.
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Affiliation(s)
- Alexandra Savinkina
- Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut, USA
- Public Health Modeling Unit, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Alyssa Bilinski
- Departments of Health Services, Policy, and Practice and Biostatistics, Brown University, Providence, Rhode Island, USA
| | - Meagan Fitzpatrick
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - A David Paltiel
- Public Health Modeling Unit, Yale University School of Public Health, New Haven, Connecticut, USA
- Department of Health Policy and Management, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Zain Rizvi
- Public Citizen, Washington, District of Columbia, USA
| | - Joshua Salomon
- Center for Health Policy/Primary Care and Outcomes Research, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Thornhill
- Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, Connecticut, USA
- Public Health Modeling Unit, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Gregg Gonsalves
- Public Health Modeling Unit, Yale University School of Public Health, New Haven, Connecticut, USA
- Epidemiology of Microbial Diseases, Yale University Yale School of Public Health, New Haven, Connecticut, USA
- Yale University Yale Law School, New Haven, Connecticut, USA
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13
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Barroso da Silva FL, Giron CC, Laaksonen A. Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule. J Phys Chem B 2022; 126:6835-6852. [PMID: 36066414 DOI: 10.1021/acs.jpcb.2c04225] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
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Affiliation(s)
- Fernando L Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Av. Getúlio Guaritá, 38025-440 Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, 210009, P. R. China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden.,Department of Chemical and Geological Sciences, Campus Monserrato, University of Cagliari, SS 554 bivio per Sestu, 09042 Monserrato, Italy
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14
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Kamble P, Daulatabad V, Patil R, John NA, John J. Omicron variant in COVID-19 current pandemic: a reason for apprehension. Horm Mol Biol Clin Investig 2022; 44:89-96. [PMID: 36064193 DOI: 10.1515/hmbci-2022-0010] [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: 01/19/2022] [Accepted: 07/22/2022] [Indexed: 11/15/2022]
Abstract
COVID-19 emerged in Wuhan, China, but was caused by the original coronavirus, severe acute respiratory syndrome associated coronavirus-2 (SARS-CoV2). In early 2020, there was a widespread breakout of cases well over world, resulting in an epidemic that rapidly escalated to become a pandemic. This abruptly shook the global healthcare system. The emergence of the alpha, beta, and delta SARS-CoV-2 were associated with new waves of infections, sometimes across the entire world but until this month i.e., between Nov-Dec, 2021, Delta variant reigned supreme until the emergence of a newer variant i.e., Omicron (B.1.1.529) of SARS-CoV-2. Delta had 13 mutations. Of these, nine are in the spike protein, the protrusion on the surface of the virus that helps it latch onto human cells. Specifically, two are in a molecular hook, called the "receptor-binding domain". Omicron, a creation caused by monstrous mutations. At least 32 mutations are in the spike protein and 10 in the receptor-binding domain. was designated a COVID-19 variant of concern (VoC) by the World Health Organization (WHO) on 26th November 2021. Structurally, the omicron variant has shown too mutated at antibody binding sites which would leverage them for escaping the possible immune response by the body. We don't yet know much about the other alterations and how they might affect the virus's behavior. Omicron COVID-19 strain after identifying individuals with symptoms that were not the same as those seen in the Delta form. People with night sweats have also been reported. The new omicron variant has more mutations than the prevailing rampant delta virus. This makes the newer variant more transmissible, better able to evade itself from various vaccines readily available in the current scenario. These overall increases in the percentage changes in a single day cases of COVID-19 reported cases can be attributed to the beginning of third wave or can be speculated as newer surge of omicron variant cases. Yet another new variant has been detected in France with 46 mutations and 37 deletions in its genetic code, many affecting the spike protein. 'B.1.640.2' is the current nomenclature for this variation.
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Affiliation(s)
- Prafull Kamble
- Department of Physiology, All India Institute of Medical Sciences, Bibinagar, Telangana, India
| | - Vandana Daulatabad
- RVM Institute of Medical Sciences, Siddipet, Hyderabad, Telangana, India
| | - Ramesh Patil
- Ashwini Rural Medical College, Hospital and Research Centre, Solapur, India
| | - Nitin Ashok John
- Department of Physiology, All India Institute of Medical Sciences, Bibinagar, Telangana, India
| | - Jyoti John
- Department of Biochemistry, All India Institute of Medical Sciences, Nagpur, Maharashtra, India
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15
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Khalid Z, Huan M, Sohail Raza M, Abbas M, Naz Z, Kombe Kombe AJ, Zeng W, He H, Jin T. Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics. Front Microbiol 2022; 13:901848. [PMID: 35983322 PMCID: PMC9378778 DOI: 10.3389/fmicb.2022.901848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/10/2022] [Indexed: 12/15/2022] Open
Abstract
Due to fast transmission and various circulating SARS-CoV-2 variants, a significant increase of coronavirus 2019 infection cases with acute respiratory symptoms has prompted worries about the efficiency of current vaccines. The possible evasion from vaccine immunity urged scientists to identify novel therapeutic targets for developing improved vaccines to manage worldwide COVID-19 infections. Our study sequenced pooled peripheral blood mononuclear cells transcriptomes of SARS-CoV-2 patients with moderate and critical clinical outcomes to identify novel potential host receptors and biomarkers that can assist in developing new translational nanomedicines and vaccine therapies. The dysregulated signatures were associated with humoral immune responses in moderate and critical patients, including B-cell activation, cell cycle perturbations, plasmablast antibody processing, adaptive immune responses, cytokinesis, and interleukin signaling pathway. The comparative and longitudinal analysis of moderate and critically infected groups elucidated diversity in regulatory pathways and biological processes. Several immunoglobin genes (IGLV9-49, IGHV7-4, IGHV3-64, IGHV1-24, IGKV1D-12, and IGKV2-29), ribosomal proteins (RPL29, RPL4P2, RPL5, and RPL14), inflammatory response related cytokines including Tumor Necrosis Factor (TNF, TNFRSF17, and TNFRSF13B), C-C motif chemokine ligands (CCL3, CCL25, CCL4L2, CCL22, and CCL4), C-X-C motif chemokine ligands (CXCL2, CXCL10, and CXCL11) and genes related to cell cycle process and DNA proliferation (MYBL2, CDC20, KIFC1, and UHCL1) were significantly upregulated among SARS-CoV-2 infected patients. 60S Ribosomal protein L29 (RPL29) was a highly expressed gene among all COVID-19 infected groups. Our study suggested that identifying differentially expressed genes (DEGs) based on disease severity and onset can be a powerful approach for identifying potential therapeutic targets to develop effective drug delivery systems against SARS-CoV-2 infections. As a result, potential therapeutic targets, such as the RPL29 protein, can be tested in vivo and in vitro to develop future mRNA-based translational nanomedicines and therapies to combat SARS-CoV-2 infections.
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Affiliation(s)
- Zunera Khalid
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ma Huan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Misbah Abbas
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zara Naz
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Arnaud John Kombe Kombe
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Weihong Zeng
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hongliang He
- Department of Infectious Diseases, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, China
- *Correspondence: Tengchuan Jin,
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16
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Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication. Comput Struct Biotechnol J 2022; 20:4098-4109. [PMID: 35874091 PMCID: PMC9296228 DOI: 10.1016/j.csbj.2022.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
We aimed at investigating host-virus co-metabolism during SARS-CoV-2 infection. Therefore, we extended comprehensive sex-specific, whole-body organ resolved models of human metabolism with the necessary reactions to replicate SARS-CoV-2 in the lung as well as selected peripheral organs. Using this comprehensive host-virus model, we obtained the following key results: 1. The predicted maximal possible virus shedding rate was limited by isoleucine availability. 2. The supported initial viral load depended on the increase in CD4+ T-cells, consistent with the literature. 3. During viral infection, the whole-body metabolism changed including the blood metabolome, which agreed well with metabolomic studies from COVID-19 patients and healthy controls. 4. The virus shedding rate could be reduced by either inhibition of the guanylate kinase 1 or availability of amino acids, e.g., in the diet. 5. The virus variants differed in their maximal possible virus shedding rates, which could be inversely linked to isoleucine occurrences in the sequences. Taken together, this study presents the metabolic crosstalk between host and virus and emphasises the role of amino acid metabolism during SARS-CoV-2 infection, in particular of isoleucine. As such, it provides an example of how computational modelling can complement more canonical approaches to gain insight into host-virus crosstalk and to identify potential therapeutic strategies.
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17
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Pascarella S, Bianchi M, Giovanetti M, Benvenuto D, Borsetti A, Cauda R, Cassone A, Ciccozzi M. The Biological Properties of the SARS-CoV-2 Cameroon Variant Spike: An Intermediate between the Alpha and Delta Variants. Pathogens 2022; 11:pathogens11070814. [PMID: 35890058 PMCID: PMC9315702 DOI: 10.3390/pathogens11070814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
An analysis of the structural effect of the mutations of the B.1.640.2 (IHU) Spike Receptor Binding Domain (RBD) and N-terminal Domain (NTD) is reported along with a comparison with the sister lineage B.1.640.1. and a selection of variants of concern. The effect of the mutations on the RBD–ACE2 interaction was also assessed. The structural analysis applied computational methods that are able to carry out in silico mutagenesis to calculate energy minimization and the folding energy variation consequent to residue mutations. Tools for electrostatic calculation were applied to quantify and display the protein surface electrostatic potential. Interactions at the RBD–ACE2 interface were scrutinized using computational tools that identify the interactions and predict the contribution of each interface residue to the stability of the complex. The comparison among the RBDs shows that the most evident differences between the variants is in the distribution of the surface electrostatic potential: that of B.1.640.1 is as that of the Alpha RBD, while B.1.640.2 appears to have an intermediate surface potential pattern with characteristics between those of the Alpha and Delta variants. Moreover, the B.1.640.2 Spike includes the mutation E484K that in other variants has been suggested to be involved in immune evasion. These properties may hint at the possibility that B.1.640.2 emerged with a potentially increased infectivity with respect to the sister B.1.640.1 variant, but significantly lower than that of the Delta and Omicron variants. However, the analysis of their NTD domains highlights deletions, destabilizing mutations and charge alterations that can limit the ability of the B.1.640.1 and B.1.640.2 variants to interact with cellular components, such as cell surface receptors.
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Affiliation(s)
- Stefano Pascarella
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Martina Bianchi
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma La Sapienza, 00185 Roma, Italy; (S.P.); (M.B.)
| | - Marta Giovanetti
- Laboratory of Flavivirus, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil;
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00185 Rome, Italy
| | - Domenico Benvenuto
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
| | | | - Roberto Cauda
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Roma, Italy;
| | - Antonio Cassone
- Universita degli Studi di Siena—Sede di Arezzo, 52100 Arezzo, Italy;
| | - Massimo Ciccozzi
- Faculty of Medicine, University of Campus Bio-Medico di Roma, 00185 Rome, Italy;
- Correspondence: ; Tel.: +39-06-225411
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18
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Balloux F, Tan C, Swadling L, Richard D, Jenner C, Maini M, van Dorp L. The past, current and future epidemiological dynamic of SARS-CoV-2. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac003. [PMID: 35872966 PMCID: PMC9278178 DOI: 10.1093/oxfimm/iqac003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.
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Affiliation(s)
- François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Cedric Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 138672 Singapore, Singapore
| | - Leo Swadling
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Damien Richard
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Charlotte Jenner
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Mala Maini
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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19
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Arora P, Kempf A, Nehlmeier I, Graichen L, Schulz S, Cossmann A, Dopfer-Jablonka A, Winkler MS, Jäck HM, Behrens GMN, Pöhlmann S, Hoffmann M. Efficient antibody evasion but reduced ACE2 binding by the emerging SARS-CoV-2 variant B.1.640.2. Cell Mol Immunol 2022; 19:1067-1069. [PMID: 35581351 PMCID: PMC9110932 DOI: 10.1038/s41423-022-00870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
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20
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Rajpal VR, Sharma S, Sehgal D, Singh A, Kumar A, Vaishnavi S, Tiwari M, Bhalla H, Goel S, Raina SN. A comprehensive account of SARS-CoV-2 genome structure, incurred mutations, lineages and COVID-19 vaccination program. Future Virol 2022. [PMID: 35747328 PMCID: PMC9203033 DOI: 10.2217/fvl-2021-0277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
This review collates information on the onset of COVID-19, SARS-CoV-2 genome architecture, emergence of novel viral lineages that drove multiple waves of infection around the world and standard and fast track development of vaccines. With the passage of time, the continuously evolving SARS-CoV-2 has acquired an expanded mutational landscape. The functional characterization of spike protein mutations, the primary target of diagnostics, therapeutics and vaccines has revealed increased transmission, pathogenesis and immune escape potential in the variant lineages of the virus. The incurred mutations have also resulted in substantial viral neutralization escape to vaccines, monoclonal, polyclonal and convalescent antibodies presently in use. The present situation suggests the need for development of precise next-generation vaccines and therapeutics by targeting the more conservative genomic viral regions for providing adequate protection.
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Affiliation(s)
| | - Shashi Sharma
- Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - Deepmala Sehgal
- International Maize & Wheat Improvement Center (CIMMYT) Carretera México-Veracruz Km. 45, El Batán, Texcoco, 56237, México
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, India
| | - Avinash Kumar
- Department of Botany, Vinoba Bhave University, Hazaribag, Jharkhand, 825319, India
| | - Samantha Vaishnavi
- Department of Botany, Central University of Jammu, Rahya Suchani (Bagla), Distt. Samba, Jammu and Kashmir, 181143, India
| | - Mugdha Tiwari
- ICMR-National Institute of Occupational Health (ICMR-NIOH), Meghaninagar, Ahmedabad, 380016, India
| | - Hemal Bhalla
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, Uttar Pradesh, India
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21
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Maimaitiyiming Y, Yang T, Wang QQ, Feng Y, Chen Z, Björklund M, Wang F, Hu C, Hsu CH, Naranmandura H. Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Research (Wash D C) 2022; 2022:9802969. [PMID: 35321260 PMCID: PMC8918953 DOI: 10.34133/2022/9802969] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 01/18/2023] Open
Abstract
Despite extensive efforts, COVID-19 pandemic caused by the SARS-CoV-2 virus is still at large. Vaccination is an effective approach to curb virus spread, but several variants (e.g., delta, delta plus, omicron, and IHU) appear to weaken or possibly escape immune protection. Thus, novel and quickly scalable approaches to restrain SARS-CoV-2 are urgently needed. Multiple evidences showed thermal sensitivity of SARS-CoV-2 and negative correlation between environmental temperature and COVID-19 transmission with unknown mechanism. Here, we reveal a potential mechanism by which mild heat treatment destabilizes the wild-type RNA-dependent RNA polymerase (also known as nonstructural protein 12 (NSP12)) of SARS-CoV-2 as well as the P323L mutant commonly found in SARS-CoV-2 variants, including omicron and IHU. Mechanistically, heat treatment promotes E3 ubiquitin ligase ZNF598-dependent NSP12 ubiquitination leading to proteasomal degradation and significantly decreases SARS-CoV-2 RNA copy number and viral titer. A mild daily heat treatment maintains low levels of both wild-type and P323L mutant of NSP12, suggesting clinical potential. Collectively, this novel mechanism, heat-induced NSP12 degradation, suggests a prospective heat-based intervention against SARS-CoV-2.
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Affiliation(s)
- Yasen Maimaitiyiming
- Department of Public Health and Department of Hematology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University Cancer Center, Hangzhou 310058, China.,Department of Neurobiology and Department of Neurology of the First Affiliated Hospital, Zhejiang University School of Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou 310058, China
| | - Tao Yang
- Department of Public Health and Department of Hematology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Qian Qian Wang
- Department of Public Health and Department of Hematology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Yan Feng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Zhi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mikael Björklund
- Zhejiang University-University of Edinburgh (ZJU-UoE) Institute, Haining 314499, Zhejiang, China
| | - Fudi Wang
- The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, Zhejiang University School of Medicine, Hangzhou 310058, China.,Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Chonggao Hu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Chih-Hung Hsu
- Women's Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Hua Naranmandura
- Department of Public Health and Department of Hematology of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Zhejiang University Cancer Center, Hangzhou 310058, China
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22
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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23
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Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042392. [PMID: 35206580 PMCID: PMC8877900 DOI: 10.3390/ijerph19042392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Several coronaviruses (CoVs) have been identified as human pathogens, including the α-CoVs strains HCoV-229E and HCoV-NL63 and the β-CoVs strains HCoV-HKU1 and HCoV-OC43. SARS-CoV, MERS-CoV, and SARS-CoV-2 are also classified as β-coronavirus. New SARS-CoV-2 spike genomic variants are responsible for human-to-human and interspecies transmissibility, consequences of adaptations of strains from animals to humans. The receptor-binding domain (RBD) of SARS-CoV-2 binds to receptor ACE2 in humans and animal species with high affinity, suggesting there have been adaptive genomic variants. New genomic variants including the incorporation, replacement, or deletion of the amino acids at a variety of positions in the S protein have been documented and are associated with the emergence of new strains adapted to different hosts. Interactions between mutated residues and RBD have been demonstrated by structural modelling of variants including D614G, B.1.1.7, B1.351, P.1, P2; other genomic variants allow escape from antibodies generated by vaccines. Epidemiological and molecular tools are being used for real-time tracking of pathogen evolution and particularly new SARS-CoV-2 variants. COVID-19 vaccines obtained from classical and next-generation vaccine production platforms have entered clinicals trials. Biotechnology strategies of the first generation (attenuated and inactivated virus–CoronaVac, CoVaxin; BBIBP-CorV), second generation (replicating-incompetent vector vaccines–ChAdOx-1; Ad5-nCoV; Sputnik V; JNJ-78436735 vaccine-replicating-competent vector, protein subunits, virus-like particles–NVX-CoV2373 vaccine), and third generation (nucleic-acid vaccines–INO-4800 (DNA); mRNA-1273 and BNT 162b (RNA vaccines) have been used. Additionally, dendritic cells (LV-SMENP-DC) and artificial antigen-presenting (aAPC) cells modified with lentiviral vector have also been developed to inhibit viral activity. Recombinant vaccines against COVID-19 are continuously being applied, and new clinical trials have been tested by interchangeability studies of viral vaccines developed by classical and next-generation platforms.
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